PubAnnotation

Id	Subject	Object	Predicate	Lexical cue
T15	0-2	Sentence	denotes	1.
T16	3-15	Sentence	denotes	Introduction
T17	16-118	Sentence	denotes	Influenza viruses are the members of Orthomyxoviridae family and have a wide host range [1,2,3,4,5,6].
T18	119-212	Sentence	denotes	Due to unique physiology, swine are considered the “mixing vessel” for influenza viruses [7].
T19	213-382	Sentence	denotes	Four types of influenza viruses have been reported in swine i.e., influenza A virus (IAV), influenza B virus (IBV), influenza C virus (ICV), and influenza D virus (IDV).
T20	383-535	Sentence	denotes	The genomes of IAV and IBV have eight gene segments of single-stranded negative sense RNA while the genomes of ICV and IDV have seven gene segments [8].
T21	536-741	Sentence	denotes	Among the eight gene segments of IAV and IBV, the hemagglutinin (HA) and neuraminidase (NA) are most significant and crucial for the pathogenicity of these viruses which determine the antigenic properties.
T22	742-891	Sentence	denotes	The HA gene regulates the attachment of virus particles to the host receptor while NA gene regulates the release of progeny virus into the host cell.
T23	892-1064	Sentence	denotes	Co-infection of swine with two or more IAV strains may trigger the reassortment [9] which in turn, could facilitate the emergence of new influenza virus strains [10,11,12].
T24	1065-1277	Sentence	denotes	Point mutations which occur due to an error-prone RNA polymerase that lacks the ability of proof-reading and corrections during replication may also complement the genetic diversity of the influenza viruses [13].
T25	1278-1501	Sentence	denotes	The mechanisms of reassortment and point mutations may give rise to “antigenic shift” and “antigenic drift” within HA and NA genes, respectively, facilitating the emergence of new subtypes and lineages of influenza viruses.
T26	1502-1669	Sentence	denotes	As a result, total 18 HA and 11 NA subtypes of IAV [14,15,16] and two lineages (Victoria/B and Yamagata/B) of IBV have been reported so far in different hosts [17,18].
T27	1670-1760	Sentence	denotes	The host range of IAV and IBV is determined by their specificity to sialic acid receptors.
T28	1761-1894	Sentence	denotes	The HA proteins of IAV can bind to α-2,3 and α-2,6 sialic acid receptors present in avian and human trachea, respectively [19,20,21].
T29	1895-2074	Sentence	denotes	Interestingly, swine trachea has both, α-2,3 as well as α-2,6 sialic acid receptors, due to which swine can become infected with avian and human strains of influenza viruses [22].
T30	2075-2252	Sentence	denotes	The genomes of ICV and IDV have a gene segment termed as “hemagglutinin–esterase-fusion” (HEF) which carries out the functions similar to that of HA and NA genes of IAV and IBV.
T31	2253-2364	Sentence	denotes	The HEF is responsible for attachment and release of ICV and IDV virus particles into the host cell [23,24,25].
T32	2365-2473	Sentence	denotes	The particles of both virus types ICV and IDV bind to 9-O-acetylated sialic acid receptors of the host [25].
T33	2474-2672	Sentence	denotes	Several studies have shown that human and avian origin influenza viruses can be transmitted to swine in natural settings and thus may evolve into new strains of reassorted influenza viruses [26,27].
T34	2673-2819	Sentence	denotes	Historically, the first flu pandemic (Spanish flu) hit the human population in 1918 [28] and killed approximately 50 million people globally [29].
T35	2820-3062	Sentence	denotes	The 1918 influenza pandemic emerged as a result of reassortment in which human H1 virus acquired avian (poultry) N1 neuraminidase along with internal protein genes and evolved into what is now termed as “classical H1N1” virus [30] (Figure 1).
T36	3063-3200	Sentence	denotes	The second flu pandemic occurred in 1957 (Asian flu) and was traced to the H2N2 virus which killed approximately two million people [31].
T37	3201-3347	Sentence	denotes	The third flu pandemic hit the human population in 1968 (Hong Kong flu) with an H3N2 outbreak and killed approximately two million people [31,32].
T38	3348-3501	Sentence	denotes	The most recent flu pandemic (Swine flu) originated in swine in Mexico during March–May 2009 [33] and killed approximately 575,000 people worldwide [31].
T39	3502-3602	Sentence	denotes	The swine flu occurred due to a pandemic reassortant H1N1 virus termed as “A(H1N1)pdm09” virus [33].
T40	3603-3729	Sentence	denotes	Among four types of the influenza viruses, IAV is the most prevalent type and has been reported in swine in several countries.
T41	3730-3838	Sentence	denotes	The IAV was first isolated from the nasal discharge of a swine in 1931 [34] and from the human in 1933 [35].
T42	3839-3943	Sentence	denotes	Strains of IAV have been reported to cause mild to severe upper respiratory tract illness in swine [36].
T43	3944-4124	Sentence	denotes	Strains of Victoria/B and Yamagata/B lineages of IBV were first reported in swine in the United States in 2010 [37] while the ICV in swine was first isolated in China in 1983 [38].
T44	4125-4201	Sentence	denotes	Both, the IBV and ICV cause mild respiratory illness in swine [39,40,41,42].
T45	4202-4392	Sentence	denotes	The IDV in swine was first detected in Oklahoma based swine in the United States in 2011 [5,43] which in later years has been detected in swine in China [44], Italy [45] and Luxembourg [46].
T46	4393-4569	Sentence	denotes	Interestingly, influenza viruses can be detected in the swine throughout the year unlike humans where seasonality affects the occurrence and progression of the disease [47,48].
T47	4570-4852	Sentence	denotes	An active surveillance of influenza viruses in swine is necessary for two basic reasons; to track the influenza virus evolution for improvements of the currently available diagnostic tests as well as for generating more effective vaccines for prevention and control of disease [49].
T48	4853-5009	Sentence	denotes	The currently available scientific data on swine influenza viruses would serve as a key to understand their evolutionary dynamics and transmission patterns.
T49	5010-5147	Sentence	denotes	Therefore, this systematic review, for the first time, summarizes all four types of influenza viruses in the swine populations worldwide.
T50	5149-5151	Sentence	denotes	2.
T51	5152-5159	Sentence	denotes	Methods
T52	5161-5165	Sentence	denotes	2.1.
T53	5166-5212	Sentence	denotes	Systematic Review Protocol and Search Strategy
T54	5213-5397	Sentence	denotes	The guidelines and the procedures as detailed by the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) [50] were followed for drafting this systematic review.
T55	5398-5583	Sentence	denotes	Original research articles reporting influenza virus types IAV, IBV, ICV, and IDV in swine populations until February 21, 2020 were searched through PubMed and Google Scholar databases.
T56	5584-5819	Sentence	denotes	The influenza virus sequence information was also verified using “Influenza Virus Resource” of NCBI (https://www.ncbi.nlm.nih.gov/genomes/FLU/) and “Influenza Research Database” (https://www.fludb.org/brc/home.spg?decorator=influenza).
T57	5820-5956	Sentence	denotes	The sequence information helped in the identification of additional relevant articles reported from Indonesia, Kazakhstan and Sri Lanka.
T58	5957-6356	Sentence	denotes	The search terms including “Influenza outbreak in swine” OR “Influenza A virus in swine” OR “Influenza B virus in swine” OR “Influenza C virus in swine” OR “Influenza D virus in swine” OR “Influenza virus in pigs” were entered one by one in PubMed and Google Scholar databases to identify all full-text research publications or case reports which reported influenza virus types or subtypes in swine.
T59	6357-6653	Sentence	denotes	The outcome suggesting research publications reporting influenza virus types and subtypes in swine along with the transmission of influenza viruses between human and swine, birds and swine, poultry and swine, cattle and swine as well as horse and swine were thoroughly investigated for inclusion.
T60	6654-6801	Sentence	denotes	The search results suggesting influenza virus prevalence and/or transmission in or between species other than swine were omitted from the analysis.
T61	6802-6927	Sentence	denotes	Occasionally, the full-text articles were also requested from the authors, if the full-text article was not available online.
T62	6928-7004	Sentence	denotes	Two publications which could not be accessed were omitted from the analysis.
T63	7005-7102	Sentence	denotes	Search results yielding articles in a language other than English were omitted from the analysis.
T64	7103-7336	Sentence	denotes	The articles were first screened through their abstracts to find out their relevance for inclusion, and, if required, the introduction and/or results and discussion sections were also screened to assess their relevance for inclusion.
T65	7337-7481	Sentence	denotes	The relevant articles were downloaded and stored on the computer drive for further screening and refinement according to PRISMA guidelines [50].
T66	7482-7669	Sentence	denotes	The references of downloaded publications were also screened to identify relevant articles reporting the influenza viruses in swine, which were also downloaded to include in the analysis.
T67	7670-7748	Sentence	denotes	An overview of the methodology can be observed in the PRISMA chart (Figure 2).
T68	7750-7754	Sentence	denotes	2.2.
T69	7755-7787	Sentence	denotes	Inclusion and Exclusion Criteria
T70	7788-7863	Sentence	denotes	The following criteria were applied for screening of the eligible articles:
T71	7864-8027	Sentence	denotes	The original research articles and case reports which documented the influenza viruses in swine in natural settings across the world were included in the analysis.
T72	8028-8124	Sentence	denotes	The experimental studies which did not report the natural cases were excluded from the analysis.
T73	8125-8263	Sentence	denotes	The reviews, letters, editorials, conference proceedings, and articles in a language other than English were not included in the analysis.
T74	8264-8320	Sentence	denotes	Duplicate articles were also excluded from the analysis.
T75	8321-8424	Sentence	denotes	The eligible articles (n = 281) thus selected were included in the analysis for this systematic review.
T76	8426-8430	Sentence	denotes	2.3.
T77	8431-8448	Sentence	denotes	Ethical Approvals
T78	8449-8548	Sentence	denotes	This systematic review did not involve animal sampling or experimental protocols in the laboratory.
T79	8549-8647	Sentence	denotes	The data used for writing this article were obtained from the PubMed and Google Scholar databases.
T80	8648-8890	Sentence	denotes	This systematic review is part of a research project which has already obtained the relevant ethical approvals from the Animal Research Ethics Committee (AREC), University of KwaZulu-Natal, Durban, South Africa; AREC Reference: AREC/041/019D.
T81	8891-9025	Sentence	denotes	Additionally, the authors have the required permission to do research in terms of Section 20 of the Animal Diseases Act, 1984 (Act No.
T82	9026-9164	Sentence	denotes	35 of 1984) from the Department of Agriculture, Forestry and Fisheries (DAFF), Government of the Republic of South Africa; DAFF Reference:
T83	9165-9184	Sentence	denotes	12/11/1/5/4 (1425).
T84	9186-9188	Sentence	denotes	3.
T85	9189-9196	Sentence	denotes	Results
T86	9197-9451	Sentence	denotes	The original research articles and case reports on the serological and virological prevalence of all the four genera of influenza viruses i.e., IAV, IBV, ICV and IDV were downloaded, analyzed and summarized in the region-specific manner across the world.
T87	9452-9577	Sentence	denotes	Influenza viruses have been reported from 53 countries located across six continents (Figure 3; Table 1) until February 2020.
T88	9579-9583	Sentence	denotes	3.1.
T89	9584-9620	Sentence	denotes	Influenza Viruses in Swine in Africa
T90	9622-9628	Sentence	denotes	3.1.1.
T91	9629-9637	Sentence	denotes	Cameroon
T92	9638-9748	Sentence	denotes	The first report of IAV in Cameroonian swine appeared when A(H1N1)pdm09 virus was documented during 2009–2010.
T93	9749-9870	Sentence	denotes	The youngest infected swine was four-month old which suggested that A(H1N1)pdm09 virus can infect the young piglets [51].
T94	9871-9986	Sentence	denotes	Nine more swine herds in Cameroon were found infected with A(H1N1)pdm09 and H1N1 viruses during May–June 2011 [52].
T95	9987-10204	Sentence	denotes	A multiple-site study including free-roaming and penned swine along with domestic poultry and Columbiformes birds between December 2009 and August 2012 identified one IAV positive swine at each of the two study sites.
T96	10205-10305	Sentence	denotes	The inter-species transmission of IAV was ruled out as all the birds were negative for the IAV [53].
T97	10307-10313	Sentence	denotes	3.1.2.
T98	10314-10321	Sentence	denotes	Nigeria
T99	10322-10503	Sentence	denotes	The first evidence of the past IAV infection in Nigerian swine appeared in 2008 when H1N1 and H3N2 virus antibodies were detected in swine sampled at three different locations [54].
T100	10504-10669	Sentence	denotes	Shortly after that, in 2009, the first report of A(H1N1)pdm09 virus appeared in the Nigerian swine when one swine herd was found seropositive for A(H1N1)pdm09 virus.
T101	10670-10809	Sentence	denotes	Interestingly, eight other swine herds were found seropositive for the H1N1 and four herds were found positive for human-like H3N2 viruses.
T102	10810-10983	Sentence	denotes	The seroprevalence of IAV further increased as 66 swine herds were detected positive for A(H1N1)pdm09 virus and 53 herds were found seropositive for H1N1 virus in 2012 [52].
T103	10984-11183	Sentence	denotes	The active infection (viral RNA) of A(H1N1)pdm09 virus was first reported in the Nigerian swine between July 2010–June 2012 when 18 A(H1N1)pdm09 virus isolates were retrieved from the swine in Lagos.
T104	11184-11346	Sentence	denotes	The zoonotic transmission of A(H1N1)pdm09 virus to the exposed human workers was ruled out as all the human samples were negative for the A(H1N1)pdm09 virus [55].
T105	11347-11469	Sentence	denotes	Nineteen more A(H1N1)pdm09 and five human-origin H3N2 viruses were identified in the Nigerian swine during 2013-2015 [56].
T106	11470-11578	Sentence	denotes	Later one more report of the human strain of H3N2 virus appeared in swine during January–February 2014 [57].
T107	11579-11654	Sentence	denotes	A high seroprevalence of IAV in a commercial piggery was reported in Lagos.
T108	11655-11919	Sentence	denotes	Total 197 human and 281 swine sera samples were screened which determined that 87% human and 67% swine sera had antibodies for IAV depicting the past exposure [58] but the active infection was absent given that all nasal swabs were negative for IAV infection [58].
T109	11920-12214	Sentence	denotes	Lately, highly pathogenic avian influenza virus (HPAIV) strain H5N1 was detected in 22 swine samples between December 2015 and February 2016 during an ongoing H5N1 disease outbreak in Nigerian poultry [59] which indicated the inter-species transmission of H5N1 virus from poultry to swine [59].
T110	12216-12222	Sentence	denotes	3.1.3.
T111	12223-12228	Sentence	denotes	Egypt
T112	12229-12547	Sentence	denotes	A molecular study reported the negative prevalence of avian-like H5N1 and H5N2 viruses in Egyptian swine in May 2008 [60] but the serological investigation identified H5N1 virus antibodies in seven and H5N2 virus antibodies in four swine sera samples [60] which suggested a past exposure of these swine to the viruses.
T113	12548-12850	Sentence	denotes	The active H5N1 infection in Egyptian swine was again ruled out in October 2013 as the viral RNA could not be detected in 36 swine samples but interestingly, the antibodies against avian-like H5N1, H9N2, and A(H1N1)pdm09 viruses were detected in swine sera samples which suggested a past exposure [61].
T114	12851-12995	Sentence	denotes	Interestingly, 122 of the 157 swine nasal swab samples collected during 2014 and 2015 were found positive for IAV active infection using RT-PCR.
T115	12996-13099	Sentence	denotes	As a result, HA subtyping identified 46 avian-origin H5N1, seven H9N2 and 69 A(H1N1)pdm09 viruses [61].
T116	13101-13107	Sentence	denotes	3.1.4.
T117	13108-13113	Sentence	denotes	Kenya
T118	13114-13316	Sentence	denotes	The first report of IAV in swine in Kenya appeared in May 2010 when A(H1N1)pdm09 virus were detected in eight swine samples collected from the Asembo and Kibera counties and at a Nairobi based abattoir.
T119	13317-13439	Sentence	denotes	The extended serological study further identified H1N1 and H3N2 viruses in swine during August 2011 to December 2012 [62].
T120	13440-13647	Sentence	denotes	The active IAV infection was reported in four household members having acute respiratory illness while the backyard swine were negative for the IAV and IBV in Kiambu county during September 2013–August 2014.
T121	13648-13773	Sentence	denotes	On the contrary, the serology identified the IAV antibodies in 230 swine sera samples suggesting a past exposure of IAV [63].
T122	13774-13916	Sentence	denotes	The A(H1N1)pdm09 virus was again reported in five swine samples collected from a slaughterhouse in Kenya during September 2013–September 2014.
T123	13917-14128	Sentence	denotes	Interestingly, all the 288 human subjects including the slaughterhouse workers or the traders and farmers who had visited the slaughterhouse were negative for IAV, hence ruled out the zoonotic transmission [64].
T124	14130-14136	Sentence	denotes	3.1.5.
T125	14137-14160	Sentence	denotes	Other African Countries
T126	14161-14383	Sentence	denotes	Swine in Benin and Cote d’Ivoire reported no prevalence of IAV during 2009–2010 [65] while A(H1N1)pdm09 virus was detected in swine in Reunion Island during 2009–2011 [66] and in Togo during October 2012–January 2014 [67].
T127	14384-14480	Sentence	denotes	The human strain of H3N2 virus was detected in swine in Ghana during January–February 2014 [57].
T128	14481-14561	Sentence	denotes	One more report documented IAV in swine in two districts of Uganda in 2015 [68].
T129	14562-14741	Sentence	denotes	Overall, influenza viruses have been reported in swine from eight African countries including Cameroon, Nigeria, Egypt, Kenya, Reunion island, Togo, Ghana, and Uganda (Figure 4A).
T130	14742-14858	Sentence	denotes	The A(H1N1)pdm09 virus, which originated in Mexican swine in 2009, has been reported in all except Ghana and Uganda.
T131	14859-15088	Sentence	denotes	Interestingly, the HPAIV strain of H5N1 has been reported in swine in Nigeria and Egypt while HPAIV strain H5N2 and low pathogenic avian influenza virus (LPAIV) strain H9N2 have also been reported in the Egyptian swine (Table 1).
T132	15090-15094	Sentence	denotes	3.2.
T133	15095-15129	Sentence	denotes	Influenza Viruses in Swine in Asia
T134	15131-15137	Sentence	denotes	3.2.1.
T135	15138-15143	Sentence	denotes	China
T136	15144-15204	Sentence	denotes	China is considered the epicenter of influenza viruses [69].
T137	15205-15436	Sentence	denotes	The first seroprevalence of IAV in Chinese swine was documented during 1977-1982 when antibodies for 38 H1N1, 22 H3N2, 12 H4N6, 12 H5N3, and seven H9N2 viruses was detected in swine sera obtained from apparently healthy swine [70].
T138	15437-15605	Sentence	denotes	The first ever report of ICV in swine was documented from the apparently healthy swine in Beijing when 15 ICV isolates were retrieved during January–December 1981 [38].
T139	15606-15777	Sentence	denotes	Three isolates of reassortant H1N2 virus were identified after an influenza-like illness triggered abortions and mortalities in sows on a swine farm in November 2004 [71].
T140	15778-15936	Sentence	denotes	The same year, LPAIV strain H9N2 was isolated from the sick or dead swine in China which was the first ever isolate of H9N2 virus retrieved from a swine [72].
T141	15937-16057	Sentence	denotes	First human-origin H1N1 and four human-origin H3N2 virus isolates in Chinese swine were retrieved during 2005–2006 [73].
T142	16058-16315	Sentence	denotes	Further, two isolates of swine H3N2 viruses, four isolates of avian-origin HPAIV strain H5N1 and two isolates of H1N1 viruses were detected in swine nasal swab and lung tissue samples collected from swine in central provinces of China during 2004–2006 [74].
T143	16316-16445	Sentence	denotes	Surprisingly, two isolates of equine influenza virus H3N8 were also detected in swine during December 2005 and January 2006 [74].
T144	16446-16640	Sentence	denotes	Another report of avian-origin H9N2 virus in Chinese swine was documented during 2006–2007 when four H9N2 virus isolates with closely related nucleotide sequences were retrieved from swine [75].
T145	16641-16890	Sentence	denotes	Each of the two different investigations reported 19 H1N1, one H1N2 and nine H3N2 virus isolates from Chinese swine during 2006–2009 [76,77]; the H1N2 virus and all nine isolates of H3N2 viruses were either double or triple-reassortant viruses [76].
T146	16891-17061	Sentence	denotes	The first report of HPAIV strain H5N1 in swine was documented during October 2008–May 2009 when two H5N1 virus isolates were retrieved from apparently healthy swine [78].
T147	17062-17311	Sentence	denotes	The third report of avian-origin H9N2 virus in Chinese swine appeared when 144 apparently healthy swine across four provinces viz., Yunnan, Guangdong, Fujian and Zhejiang were found H9N2 positive over a four-year period during March 2008–March 2012.
T148	17312-17459	Sentence	denotes	The frequent interactions of birds to the swine at the study sites was reported which was suspected to be the most likely source of infection [79].
T149	17460-17558	Sentence	denotes	Further, a novel strain of avian-origin H4N1 virus was isolated from a Chinese swine in 2009 [80].
T150	17559-17773	Sentence	denotes	Several classical and avian-like H1N1, Eurasian avian-like H1N1, triple-reassortant H1N1, H1N2, H3N2 and A(H1N1)pdm09 viruses were reported in Chinese swine between 2009 and 2016 [81,82,83,84,85,86,87,88,89,90,91].
T151	17774-17983	Sentence	denotes	A triple-reassortant H1N1 virus having the internal genes of avian, human, and swine lineages of influenza viruses was reported from a two-month old piglet on a Guangdong based swine farm in January 2010 [92].
T152	17984-18130	Sentence	denotes	Three reassortant H3N2 virus isolates having internal genes of A(H1N1)pdm09 virus were reported in swine between November 2010 and June 2011 [93].
T153	18131-18357	Sentence	denotes	A three-year old boy was diagnosed with European origin avian-like H1N1 virus on a family swine farm in a rural area of the Jiangsu province in December 2010 which speculated a zoonotic transmission from swine to the boy [94].
T154	18358-18636	Sentence	denotes	The first report of H10N5 avian-origin influenza virus in a domestic swine in Hubei province further extended the diversity of swine influenza viruses and provided another evidence of interspecies transmission of avian influenza virus to the swine under natural conditions [95].
T155	18637-18794	Sentence	denotes	Several other avian-origin H3N2, H4N8, H6N6, H7N9, H5N1, and H9N2 virus antibodies were detected in swine in China during April 2010–June 2014 [86,96,97,98].
T156	18795-19039	Sentence	denotes	Another interspecies transmission of avian-like H1N1 virus in southern China was observed when 219 swine and 61 swine farm workers were identified to be infected with avian-like H1N1 swine influenza virus between March 2011 and March 2013 [99].
T157	19040-19234	Sentence	denotes	Further a zoonotic transmission of H9N2 virus was identified at a Shandong based swine farm during May 2013–April 2014 when H9N2 virus antibodies were detected in 84 swine and four farm workers.
T158	19235-19358	Sentence	denotes	The wild birds visiting swine feeding sites at the swine farm were speculated to serve as the carrier for H9N2 virus [100].
T159	19359-19550	Sentence	denotes	Zoonotic transmission of H1N1 virus was reported on a swine farm in Shandong province between March 2015 and February 2016 among the swine exposed human workers having influenza-like illness.
T160	19551-19706	Sentence	denotes	As a result, five of the 32 (15.6%) nasal swab samples were found IAV positive; a married couple exposed to swine were found infected with H1N1 virus [88].
T161	19707-19832	Sentence	denotes	The IAV infection was also documented in 44 wild boars in Jilin province of China between April 2015 and February 2016 [101].
T162	19833-19961	Sentence	denotes	The first report of the IDV prevalence in Chinese swine documented 21 IDV positive swine in the Guangdong province in 2016 [44].
T163	19962-20164	Sentence	denotes	The swine IDV sequences shared high similarity (99–100%) with IDV sequences reported earlier from the bovine species in China [102] which indicated the transmission of IDV from bovine to swine in China.
T164	20166-20172	Sentence	denotes	3.2.2.
T165	20173-20192	Sentence	denotes	Hong Kong and Tibet
T166	20193-20337	Sentence	denotes	Hong Kong is a special administrative region while Tibet is an autonomous administrative region under the control of People’s Republic of China.
T167	20338-20475	Sentence	denotes	The H1N1 and H3N2 virus isolates were successfully retrieved from apparently healthy swine in Hong Kong during July 1993–June 1994 [103].
T168	20476-20734	Sentence	denotes	Further, classical swine H1N1, H3N2 and avian-like H9N2 viruses were identified in Hong Kong based swine between March 1998–June 2000; two independent introductions of the avian-like H9N2 viruses were ascertained from avian species to the swine [27,104,105].
T169	20735-20933	Sentence	denotes	The first information of IAV seroprevalence in Tibetan swine appeared during April–December 2010 when antibodies against H1N1 and H3N2 viruses were detected in swine sera collected from Tibet [106].
T170	20935-20941	Sentence	denotes	3.2.3.
T171	20942-20948	Sentence	denotes	Bhutan
T172	20949-21128	Sentence	denotes	The first report of H1N1 seroprevalence in swine in Bhutan appeared when H1N1 virus was detected in backyard as well as breeding swine during October 2011 and February 2012 [107].
T173	21130-21136	Sentence	denotes	3.2.4.
T174	21137-21145	Sentence	denotes	Cambodia
T175	21146-21300	Sentence	denotes	The H1N1 virus was reported in swine over a five year-period between 2006–2010 while the A(H1N1)pdm09 and H3N2 viruses were identified only in 2010 [108].
T176	21301-21432	Sentence	denotes	Later three triple-assortant H3N2 viruses were isolated and sequenced from the backyard swine between May 2011 and July 2012 [109].
T177	21434-21440	Sentence	denotes	3.2.5.
T178	21441-21446	Sentence	denotes	Japan
T179	21447-21584	Sentence	denotes	The antibodies against A/Hong Kong(H3N2) virus termed as “A/Swine/Wadayama/5/69” were first detected in Japanese swine in 1969 [110,111].
T180	21585-21764	Sentence	denotes	The H3N2 virus seroprevalence in Japanese swine was further documented in Sendai City during 1977 to 1980 [112]; the transmission between human and swine was also suggested [112].
T181	21765-21927	Sentence	denotes	The first active IAV infection was reported when two reassortant H1N2 virus isolates were retrieved from the Japanese swine having influenza-like disease in 1978.
T182	21928-22016	Sentence	denotes	The isolated H1N2 virus was believed to be a recombinant of H1N1 and H3N2 viruses [113].
T183	22017-22110	Sentence	denotes	Further 340 swine were diagnosed with H1N1 antibodies in Toyama Prefecture between 1978–1982.
T184	22111-22250	Sentence	denotes	A lower seroprevalence was observed during the summer months while the seroprevalence was relatively higher during the winter season [114].
T185	22251-22367	Sentence	denotes	Again, one more H1N2 virus was isolated and characterized from the sows in Ehime Prefecture in September 1980 [115].
T186	22368-22553	Sentence	denotes	Intriguingly, 18 H1N1, H1N2 and H3N2 viruses were detected in swine imported from the United States, however, all the imported swine from the Europe were negative for the IAV infection.
T187	22554-22629	Sentence	denotes	This was the first report of the IAV infection in the imported swine [116].
T188	22630-22944	Sentence	denotes	The ICV seroprevalence (19%) in Japanese swine was first reported in the Hyogo Prefecture during July 1981–June 1982 [117] but swine in Yamagata Prefecture were found seronegative for the ICV between August 1979 and March 1986 which suggested a localized transmission of ICV in swine within Hyogo Prefecture [118].
T189	22945-23040	Sentence	denotes	Several other reassortant H1N2 virus isolates were reported in Japanese swine after 1991 [119].
T190	23041-23298	Sentence	denotes	One novel reassortant H1N2 virus appeared to have emerged from the A(H1N1)pdm09 virus was reported in swine in Gunma Prefecture while two other H1N2 viruses appeared to have emerged from the Japanese H1N2 viruses with internal genes from A(H1N1)pdm09 virus.
T191	23299-23400	Sentence	denotes	One more H1N2 virus was detected in swine which was closely related to the Japanese H1N2 virus [120].
T192	23401-23519	Sentence	denotes	The immunohistochemistry identified lesions in the lungs of the sick swine infected with reassortant H1N2 virus [121].
T193	23520-23638	Sentence	denotes	Additionally, several H1N1 and H3N2 viruses have also been reported in Japanese swine between 1990 and 2017 [122,123].
T194	23639-23866	Sentence	denotes	Interestingly, six H1N1 virus isolates were identified with reassorted genes from A(H1N1)pdm09 virus while one H1N1 isolate appeared to have H1 gene from Japanese swine influenza virus with internal genes of A(H1N1)pdm09 virus.
T195	23867-23987	Sentence	denotes	Further, one H3N2 virus isolate was determined to have genes of Japanese swine influenza and A(H1N1)pdm09 viruses [124].
T196	23988-24112	Sentence	denotes	These results reflected the occurrence of the reassortment events between Japanese swine influenza and A(H1N1)pdm09 viruses.
T197	24113-24205	Sentence	denotes	IAV seroprevalence has lately been reported in wild boars (Sus scrofa leucomystax) in Japan.
T198	24206-24385	Sentence	denotes	Three wild boars in the Yamaguchi Prefecture were found seropositive for A(H1N1)pdm09 virus while nine wild boars in Tochigi Prefecture were seropositive for the swine H1N1 virus.
T199	24386-24526	Sentence	denotes	But, the active IAV infection could not be identified in these wild boars as all the nasal swab samples were negative for IAV and IBV [125].
T200	24527-24782	Sentence	denotes	In a more recent investigation, fifteen wild boars were found seropositive for A(H1N1)pdm09 virus in Kagoshima Prefecture between November 2014–December 2017 while two of these fifteen wild boars had antibodies against H1N2 and H3N2 viruses as well [126].
T201	24783-24860	Sentence	denotes	This reflected a past exposure of the Japanese wild boars to the IAV strains.
T202	24862-24868	Sentence	denotes	3.2.6.
T203	24869-24880	Sentence	denotes	South Korea
T204	24881-25082	Sentence	denotes	The first active IAV infection in the Korean swine was identified in December 1998 when three H3N2 virus isolates were recovered from the swine experiencing an acute influenza-like respiratory disease.
T205	25083-25257	Sentence	denotes	The close relatedness of these Korean swine H3N2 isolates with human-origin H3N2 viruses reported from Korea between 1987–1999 suggested the events of reverse zoonosis [127].
T206	25258-25477	Sentence	denotes	One unique H7N2 virus isolate was detected in swine which had seven gene segments originated from Hong Kong avian-origin H7N2 virus isolated in 1978 and the NS gene originated from Hong Kong H5N3 virus isolated in 1977.
T207	25478-25565	Sentence	denotes	Additionally, four typical swine influenza H1N1 viruses were identified in swine [128].
T208	25566-25688	Sentence	denotes	Several H1N1, H1N2, and H3N2 viruses were detected in symptomatic South Korean swine after 2000 [129,130,131,132,133,134].
T209	25689-25780	Sentence	denotes	The IAV localization in the swine lung tissues was confirmed by immunohistochemistry [130].
T210	25781-25977	Sentence	denotes	Total 35 avian-origin H5N2 viruses of Eurasian lineage were identified in swine in different South Korean provinces during 2004–2008 which suggested cross-species transmission of H5N2 virus [135].
T211	25978-26106	Sentence	denotes	Three H1N1 virus isolates closely related to US isolates of H1N1 were obtained from 45-day-old piglets in Korea in January 2005.
T212	26107-26204	Sentence	denotes	The other swine farms in the proximity of this index farm were negative for the H1N1 virus [136].
T213	26205-26539	Sentence	denotes	Further, one H1N1, two H1N2, and one H3N2 subtypes of IAV identical to the American strains based on their HA and NA gene sequences were obtained from swine nasal swab, lung, and thoracic fluid samples during 2005–2006 which suggested that there was no probability of arising of these IAV strains in Korea through recombination [137].
T214	26540-26757	Sentence	denotes	Two novel isolates of swine H3N1 virus with high genomic similarity to each other were retrieved from two different swine farms in Korea during March–April 2006 which would be due to a common origin of these isolates.
T215	26758-26874	Sentence	denotes	These viruses had human-like H3 gene while other gene segments originated from swine influenza viruses within Korea.
T216	26875-27046	Sentence	denotes	High reactivity of the 52 swine sera samples to H3N1 virus antibodies suggested a previous exposure and probability of the swine to swine transmission of H3N1 virus [138].
T217	27047-27217	Sentence	denotes	The human to swine transmission of A(H1N1)pdm09 virus was reported in Chungbuk province where 42 A(H1N1)pdm09 virus isolates were recovered from swine lung tissues [139].
T218	27218-27338	Sentence	denotes	The reassortment between A(H1N1)pdm09 and swine H1N2 viruses emerged into a novel reassortant H1N2 virus in swine [140].
T219	27339-27501	Sentence	denotes	A triple-reassortant H3N2 virus was identified in swine during December 2011–May 2012 which indicated the IAV reassortment was taking place in Korean swine [141].
T220	27502-27683	Sentence	denotes	A swine fever eradication campaign identified nine A(H1N1)pdm09, two classical H1N1 and one H1N2 viruses in wild boars which were hunted and killed in South Korea during 2012 [142].
T221	27684-27798	Sentence	denotes	More recently, a complete genome sequence of H1N1 virus was reported from a domestic swine in Korea in 2016 [143].
T222	27800-27806	Sentence	denotes	3.2.7.
T223	27807-27815	Sentence	denotes	Thailand
T224	27816-27901	Sentence	denotes	The occurrence of IAV in Thai swine was first reported during November–December 1978.
T225	27902-28002	Sentence	denotes	Active H3N2 infection was detected in one swine while several other swine had H3N2 antibodies [144].
T226	28003-28086	Sentence	denotes	Two H1N1 virus isolates from Thai swine were first recovered in January 1988 [145].
T227	28087-28225	Sentence	denotes	Several studies reported H1N1, A(H1N1)pdm09, H1N2, and H3N2 viruses in swine exhibiting respiratory disease symptoms between 2000 to 2014.
T228	28226-28377	Sentence	denotes	Intriguingly, one swine sample was found co-infected with four IAV subtypes including H1N1, H1N2, H3N1, and H3N2 viruses [146,147,148,149,150,151,152].
T229	28378-28523	Sentence	denotes	The first evidence of H5N1 seroprevalence in Thai swine was documented in 2004 when eight H5N1 positive swine sera samples were identified [153].
T230	28524-28645	Sentence	denotes	Later ten H1N1 and two H3N2 virus isolates were retrieved from piglets aged between 4 to 12 weeks during 2008–2009 [154].
T231	28646-28912	Sentence	denotes	Interestingly, most of the virus isolates retrieved in this study were obtained from 4 to 8 week-old piglets which was in agreement of a previous report stating that swine influenza viruses can be successfully retrieved from piglets less than ten weeks of age [155].
T232	28913-29048	Sentence	denotes	A zoonotic transmission of IAV was reported at a Thai swine farm where all the swine were found positive for either H1N1 or H1N2 virus.
T233	29049-29200	Sentence	denotes	Interestingly, two farm owners, 46 swine handlers, four veterinarians, five farm cleaners and two farm office workers also reported IAV seroprevalence.
T234	29201-29370	Sentence	denotes	This study claimed that there was transmission of swine influenza viruses from swine to human however the possibility of human to swine transmission was ruled out [156].
T235	29371-29523	Sentence	denotes	After a respiratory disease outbreak in nursery piglets, 15 nasal swabs were found positive for A(H1N1)pdm09 virus between December 2009 and March 2010.
T236	29524-29717	Sentence	denotes	Fifteen sera samples of the farm workers along with three sera from dogs and one serum obtained from a cat were negative for IAV, hence the interspecies transmission of IAV was ruled out [157].
T237	29718-29999	Sentence	denotes	The first report of active infection with reassortant H1N1 virus in Thai swine appeared in February 2010 but the follow up screenings conducted after two and three months, respectively confirmed the cessation of the active infection as the viral RNA was not detected anymore [158].
T238	30000-30100	Sentence	denotes	The reshuffling and reassortment of IAV internal genes were reported in Thai swine in February 2012.
T239	30101-30255	Sentence	denotes	The HA and NA genes of H1N1 virus isolates clustered with the Eurasian swine-like IAV lineage while the H3N2 viruses diverged and formed a separate group.
T240	30256-30410	Sentence	denotes	All the internal genes of H1N1 and H3N2 virus isolates appeared to be derived from A(H1N1)pdm09 viruses which confirmed the events of reassortments [159].
T241	30412-30418	Sentence	denotes	3.2.8.
T242	30419-30426	Sentence	denotes	Vietnam
T243	30427-30587	Sentence	denotes	The events of reverse zoonoses were suggested after the detection of A(H1N1)pdm09 virus seroprevalence in Vietnamese swine during October 2009–March 2010 [160].
T244	30588-30803	Sentence	denotes	One more evidence of reverse zoonosis was identified during February–March 2010 after six triple-reassortant H3N2 viruses having a novel cluster of the Triple Reassortant Internal Gene (TRIG) cassette were isolated.
T245	30804-31022	Sentence	denotes	The HA and NA genes of these reassortant H3N2 isolates originated from human H3N2 viruses reported between 2004–2006 while the other six internal genes had a high similarity with the Korean and American isolates [161].
T246	31023-31213	Sentence	denotes	Two more studies reported the H1N1, A(H1N1)pdm09, HIN2, and H3N2 virus isolates during February 2010–December 2013 from clinically healthy swine with no influenza disease symptoms [162,163].
T247	31214-31364	Sentence	denotes	Additionally, the antibodies for A(H1N1)pdm09 and H3N2 viruses were detected in swine which suggested a past exposure of swine to these viruses [163].
T248	31366-31372	Sentence	denotes	3.2.9.
T249	31373-31378	Sentence	denotes	India
T250	31379-31511	Sentence	denotes	A high seroprevalence of H1N1, H2N2 and H3N2 viruses was detected in human and swine sera in Calcutta, India during 1982–1990 [164].
T251	31512-31669	Sentence	denotes	The first active infection of IAV in Indian swine appeared in 2009 when A(H1N1)pdm09 virus isolates were reported from a swine farm located in Uttar Pradesh.
T252	31670-31857	Sentence	denotes	Interestingly, the retrieved A(H1N1)pdm09 virus sequences were similar to the North American and Korean viruses which might be either because of trade or long-distance transmission [165].
T253	31859-31866	Sentence	denotes	3.2.10.
T254	31867-31874	Sentence	denotes	Lebanon
T255	31875-31999	Sentence	denotes	After an influenza outbreak on Lebanese poultry farms in 2005 the farmers fed the carcasses of the dead flocks to the swine.
T256	32000-32210	Sentence	denotes	Intriguingly, a following investigation found that three swine were seropositive for the H9N2 virus while approximately one-third of the poultry farm workers were seropositive either for H1 or H9 viruses [166].
T257	32211-32309	Sentence	denotes	These results revealed the interspecies transmission of IAV among poultry, farm workers and swine.
T258	32311-32318	Sentence	denotes	3.2.11.
T259	32319-32327	Sentence	denotes	Malaysia
T260	32328-32467	Sentence	denotes	The seroprevalence of H1N1 and H3N2 viruses in four to six-month-old Malaysian swine at 41 swine farms was reported during May–August 2005.
T261	32468-32539	Sentence	denotes	Co-infections of H1N1 and H3N2 were detected in 29 swine samples [167].
T262	32541-32548	Sentence	denotes	3.2.12.
T263	32549-32553	Sentence	denotes	Laos
T264	32554-32698	Sentence	denotes	The seroprevalence of H3N2 virus in swine samples obtained from the slaughterhouses in Laos was reported between May 2008 to January 2009 [168].
T265	32700-32707	Sentence	denotes	3.2.13.
T266	32708-32714	Sentence	denotes	Russia
T267	32715-32815	Sentence	denotes	A full-length genome sequence of a reassortant H1N1 virus was reported from a Russian swine in 2016.
T268	32816-32961	Sentence	denotes	The HA and NA genes of this virus isolate shared 90% identity with the H1N1 viruses that were reported from humans in the USA in the 1980s [169].
T269	32963-32970	Sentence	denotes	3.2.14.
T270	32971-32977	Sentence	denotes	Taiwan
T271	32978-33116	Sentence	denotes	The human to swine transmission of IAV was speculated after IAV antibodies were detected in 147 Taiwanese swine during June 1969–May 1970.
T272	33117-33211	Sentence	denotes	The results were further confirmed with virus isolation which retrieved 13 IAV isolates [170].
T273	33212-33369	Sentence	denotes	More recently, IBV of Victoria/B lineage was detected in swine nasal swab samples collected from apparently healthy swine at three swine farms in 2014 [171].
T274	33371-33378	Sentence	denotes	3.2.15.
T275	33379-33388	Sentence	denotes	Indonesia
T276	33389-33492	Sentence	denotes	An active IAV infection in 52 swine within four provinces in Indonesia was identified during 2005–2009.
T277	33493-33579	Sentence	denotes	Interestingly, 39 H5N1 virus isolates were successfully retrieved and sequenced [172].
T278	33581-33588	Sentence	denotes	3.2.16.
T279	33589-33598	Sentence	denotes	Sri Lanka
T280	33599-33728	Sentence	denotes	The first report of influenza in Sri Lankan swine was documented during 2004–2005 after one human-like H3N2 virus was identified.
T281	33729-33806	Sentence	denotes	Later, A(H1N1)pdm09 virus isolates were identified in swine during 2009–2012.
T282	33807-33877	Sentence	denotes	A spillover of these viruses from human to swine was speculated [173].
T283	33879-33886	Sentence	denotes	3.2.17.
T284	33887-33897	Sentence	denotes	Kazakhstan
T285	33898-34071	Sentence	denotes	One recent investigation in Kazakhstan during 2017–2018 identified nine H1N1 and eight H3N2 viruses in human while seven H1N1 and four H3N2 viruses were identified in swine.
T286	34072-34200	Sentence	denotes	Interestingly, 10 of the human samples were also positive for IBV infection while the swine samples were negative for IBV [174].
T287	34201-34457	Sentence	denotes	In summary, the influenza viruses have been reported in swine in 16 Asian countries including China, Japan, Thailand, South Korea, Viet Nam, Cambodia, Taiwan, India, Bhutan, Russia, Laos, Malaysia, Lebanon, Indonesia, Kazakhstan, and Sri Lanka (Figure 4B).
T288	34458-34677	Sentence	denotes	Apart from the most common IAV strains of H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses, several avian-origin H5N1, H5N3, H4N1, H4N6, H4N8, H6N6, H7N9, H9N2, and H10N5 influenza viruses were also reported in Chinese swine.
T289	34678-34759	Sentence	denotes	Horse to swine transmission of equine influenza virus H3N8 was reported in China.
T290	34760-34888	Sentence	denotes	Additionally, avian-origin H7N2, H5N2 viruses were identified in South Korean swine while H5N1 was reported in Indonesian swine.
T291	34889-35014	Sentence	denotes	Interestingly, after the swine were fed upon dead poultry carcasses in Lebanon the H9N2 virus was detected in Lebanese swine.
T292	35015-35188	Sentence	denotes	The IBV was reported in Asian swine only in Taiwan while strains of ICV were reported in swine in China and Japan while IDV was recently reported in Chinese swine (Table 1).
T293	35190-35194	Sentence	denotes	3.3.
T294	35195-35234	Sentence	denotes	Influenza Viruses in Swine in Australia
T295	35235-35367	Sentence	denotes	Swine influenza was first reported in Australian swine only in 2009 after a swine farm owner reported coughing symptoms among swine.
T296	35368-35509	Sentence	denotes	Simultaneously, some of the human workers on the farm also developed influenza like symptoms and hence stayed out of the farm until recovery.
T297	35510-35641	Sentence	denotes	Later, the farm owner also developed similar symptoms following which he was tested for A(H1N1)pdm09 virus which resulted positive.
T298	35642-35852	Sentence	denotes	As a result, a representative number of swine showing coughing symptoms and loss in appetite were sampled for molecular diagnostics and serology which confirmed that 12 swine were positive for H1N1 virus [175].
T299	35853-36029	Sentence	denotes	Second report of IAV in Australian swine appeared on a Queensland farm in August 2009 when a veterinarian observed elevated temperature, coughing and loss of appetite in swine.
T300	36030-36181	Sentence	denotes	Simultaneously, two of the staff members on the farm exhibited influenza-like symptoms and hence were sampled for diagnostic testing using nasal swabs.
T301	36182-36289	Sentence	denotes	Interestingly, both the staff members and four of the swine were found positive for the A(H1N1)pdm09 virus.
T302	36290-36514	Sentence	denotes	Sequencing identified that the HA gene of A(H1N1)pdm09 virus retrieved from a staff member was identical to the virus retrieved from the swine which suggested transmission of A(H1N1)pdm09 virus between swine and human [176].
T303	36515-36718	Sentence	denotes	Third report of IAV in Australian swine appeared when a respiratory disease outbreak in swine and the farm workers occurred in Perth, Western Australia during 2012 which identified 43 IAV positive swine.
T304	36719-36857	Sentence	denotes	Sanger sequencing of HA and NA genes identified six novel HIN2, three novel H3N2, one A(H1N1)pdm09 and two seasonal H3N2 viruses in swine.
T305	36858-36955	Sentence	denotes	On the contrary, only one out of eight human workers were found positive for seasonal H3N2 virus.
T306	36956-37078	Sentence	denotes	This study could not conclude the event of zoonotic transmission of IAV between swine and human workers at the farm [177].
T307	37079-37278	Sentence	denotes	The fourth report of IAV was documented when 14 IAV positive swine were identified at a commercial swine farm in Western Australia during July–September 2012 and later during September–November 2016.
T308	37279-37360	Sentence	denotes	Additionally, 17 swine were determined to be IAV positive in southern Queensland.
T309	37361-37549	Sentence	denotes	The complete genomes of 10 IAV isolates retrieved in Western Australia and Queensland were successfully sequenced which identified seven H1N2, two human-like H3N2 and one H1N1 virus [178].
T310	37550-37678	Sentence	denotes	Overall, four reports of IAV outbreaks in swine in New South Wales, Queensland and Western Australia were available (Figure 4C).
T311	37679-37798	Sentence	denotes	The H1N1, H1N2, H3N2 and A(H1N1)pdm09 subtypes have been reported from Australian swine with relatively low prevalence.
T312	37800-37804	Sentence	denotes	3.4.
T313	37805-37841	Sentence	denotes	Influenza Viruses in Swine in Europe
T314	37843-37849	Sentence	denotes	3.4.1.
T315	37850-37857	Sentence	denotes	Belgium
T316	37858-38024	Sentence	denotes	The H1N1 virus was identified in swine lung tissues or trachea of two of the deceased sows after an influenza-like disease erupted at two swine farms in January 1979.
T317	38025-38130	Sentence	denotes	Interestingly, it was also reported that the identical virus was detected in wild ducks in Germany [179].
T318	38131-38354	Sentence	denotes	Since it was already established that H1N1 from wild ducks can successfully infect swine if inoculated via intranasal route [179] hence this observation suggested the transmission of H1N1 from wild ducks to the swine [180].
T319	38355-38508	Sentence	denotes	A second investigation isolated three avian-like H1N1, two H1N2 and twelve human-like H3N2 viruses from eight commercial swine farms in March 1999 [181].
T320	38510-38516	Sentence	denotes	3.4.2.
T321	38517-38524	Sentence	denotes	Denmark
T322	38525-38619	Sentence	denotes	Denmark has been running a passive surveillance program for IAV detection in swine since 2011.
T323	38620-38792	Sentence	denotes	The H1N2 virus having the H1 gene which evolved from H1N1 avian-like viruses and N2 gene which evolved from human H3N2 viruses was reported in swine during 2011–2013 [182].
T324	38793-38893	Sentence	denotes	This was an example of how IAV can evolve through reassortment and may emerge into a new IAV strain.
T325	38894-39096	Sentence	denotes	The other investigation included swine sampling at different time intervals to assess the persistence of IAV shedding in Danish swine which detected one avian-like H1N1 and 107 reassortant H1N2 viruses.
T326	39097-39198	Sentence	denotes	This study observed that most of the swine were shedding IAV right before achieving six weeks of age.
T327	39199-39284	Sentence	denotes	Surprisingly, a piglet as young as just three days was found infected with IAV [183].
T328	39285-39588	Sentence	denotes	Two H3N2 isolates having H3 genes from seasonal human influenza along with internal genes that originated from A(H1N1)pdm09 virus and NA genes from contemporary N2 swine influenza viruses that have been in circulation in Denmark were retrieved from young piglets at two locations during 2011–2014 [184].
T329	39589-39737	Sentence	denotes	H3N2 virus was also detected from piglets having respiratory illness and from sows with reproductive problems in commercial piggeries in 2014 [184].
T330	39739-39745	Sentence	denotes	3.4.3.
T331	39746-39760	Sentence	denotes	United Kingdom
T332	39761-39894	Sentence	denotes	The H3N2 virus antibodies were first detected in English swine in 1973 which revealed the past exposure of swine to H3N2 virus [185].
T333	39895-40020	Sentence	denotes	Later, the antibodies for H1N1 and H3N2 viruses were detected in swine at a slaughterhouse in England during 1991–1992 [186].
T334	40021-40144	Sentence	denotes	Interestingly, this serological investigation also reported the antibodies for IBV in eight and for ICV in 198 swine [186].
T335	40145-40487	Sentence	denotes	A molecular investigation identified a novel H1N7 virus in swine in England which had six of its RNA segments closely related to those of human viruses while two RNA segments were identical to those of equine viruses which concluded that the H1N7 strain may have evolved due to reassortment between human H1 and equine H7N7 viruses [187,188].
T336	40488-40744	Sentence	denotes	The first report of A(H1N1)pdm09 virus in English swine appeared in September 2009 when histology and immunofluorescence assays followed by molecular diagnostics and sequencing confirmed four A(H1N1)pdm09 virus infected swine in the Northern Ireland [189].
T337	40745-40972	Sentence	denotes	After this, 17 more A(H1N1)pdm09 virus isolates were reported in swine in England during September 2009–October 2010 which revealed that A(H1N1)pdm09 virus was in circulation in English swine during the 2009 flu pandemic [190].
T338	40973-41202	Sentence	denotes	The same year, four H1N2 virus isolates were reported in English swine which had six internal genes of A(H1N1)pdm09 virus along with HA and NA genes of H1N2 virus hence were identified as the novel reassortant H1N2 strains [191].
T339	41203-41307	Sentence	denotes	In a more recent study, two more IAV positive swine were identified in the United Kingdom in 2016 [192].
T340	41309-41315	Sentence	denotes	3.4.4.
T341	41316-41323	Sentence	denotes	Finland
T342	41324-41711	Sentence	denotes	However the first report of seroprevalence of H1N1 virus in Finnish swine appeared in 2008 during an investigation which detected H1N1 virus antibodies in swine at seven swine farms which further increased to 24 swine farms in 2009 [193] but the first isolate of avian-like swine H1N1 virus (indicative of active infection) was detected from the lung tissues of a swine in February 2009.
T343	41712-41801	Sentence	denotes	Later, the first A(H1N1)pdm09 virus in Finnish swine was detected in November 2009 [193].
T344	41802-41930	Sentence	denotes	Three more swine were identified with IAV antibodies during May 2011–January 2014 which was due to a past exposure to IAV [194].
T345	41932-41938	Sentence	denotes	3.4.5.
T346	41939-41945	Sentence	denotes	France
T347	41946-42171	Sentence	denotes	The H1N1 viruses in turkey and swine were identified after the swine influenza outbreak hit the turkey population in Brittany, France in February 1983 which suggested that IAV transmission happened from swine to turkey [195].
T348	42172-42302	Sentence	denotes	Later two strains of H1N2 virus were isolated from six swine exhibiting influenza-like illness in Brittany during 1987–1988 [196].
T349	42303-42436	Sentence	denotes	Another investigation reported H1N1, H1N2, and H3N2 viruses in swine herds experiencing respiratory disease in Brittany region [197].
T350	42437-42686	Sentence	denotes	A negative prevalence of IAV was reported in wild boars in Camargue during September 2009–November 2010 given that all the 315 nasal swabs obtained from either hunted or trapped wild boars along with all the sera samples were negative for IAV [198].
T351	42687-42811	Sentence	denotes	A more recent investigation reported the zoonotic transmission of A(H1N1)pdm09 virus from swine to a farmer in January 2018.
T352	42812-43060	Sentence	denotes	This farmer along with a veterinarian collected nasal swab samples from three pregnant sows exhibiting influenza-like illness on the swine farm and submitted to a local diagnostic laboratory for analysis which, as a result, were found IAV positive.
T353	43061-43152	Sentence	denotes	Few days later, the farmer and the veterinarian both developed the influenza-like symptoms.
T354	43153-43214	Sentence	denotes	The farmer was later diagnosed with A(H1N1)pdm09 virus [199].
T355	43216-43222	Sentence	denotes	3.4.6.
T356	43223-43230	Sentence	denotes	Germany
T357	43231-43325	Sentence	denotes	Sixty-five IAV positive wild boars were identified across five German states during 1997–2006.
T358	43326-43408	Sentence	denotes	Cloning and sequencing identified H1N1 and H3N2 viruses in these wild boars [200].
T359	43409-43522	Sentence	denotes	Later thirteen H1N1, three reassorted A(H1N1)pdm09 and four H1N2 viruses were detected in swine during 2009–2010.
T360	43523-43742	Sentence	denotes	Interestingly, the A(H1N1)pdm09 virus isolates had high similarity with the A(H1N1)pdm09 viruses reported earlier in humans within Germany which suggested a reverse zoonotic transmission of the A(H1N1)pdm09 virus [201].
T361	43743-44052	Sentence	denotes	A nationwide sero-surveillance identified 12,585 swine with H1N1, 9,566 swine with human-like H1N2, 12,220 swine with human-like H3N2 and 11,086 swine with A(H1N1)pdm09 virus antibodies during June 2009–December 2012 which reflected a high seroprevalence of influenza viruses in German swine population [202].
T362	44053-44165	Sentence	denotes	Later 273 IAV positive swine exhibiting influenza-like illness were detected between January 2010–December 2013.
T363	44166-44269	Sentence	denotes	Subtyping successfully distinguished 198 of 273 samples into H1N1, H1N2, H3N2 and A(H1N1)pdm09 viruses.
T364	44270-44388	Sentence	denotes	The H1N1 virus was the most widely occurring in German swine while A(H1N1)pdm09 virus had the lowest prevalence [203].
T365	44390-44396	Sentence	denotes	3.4.7.
T366	44397-44403	Sentence	denotes	Greece
T367	44404-44609	Sentence	denotes	The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were detected in swine sera samples collected from apparently healthy swine at 42 swine farms during 2002–2004 and from 46 swine farms during 2010–2012 [204].
T368	44611-44617	Sentence	denotes	3.4.8.
T369	44618-44623	Sentence	denotes	Italy
T370	44624-44783	Sentence	denotes	The seropositivity of Italian swine to H3N2 virus was first reported during December 1976–November 1977 when 24 swine were detected with H3N2 antibodies [205].
T371	44784-44949	Sentence	denotes	The first report of H1N1 active infection in Italian swine appeared during an influenza disease outbreak between 1977 to 1986 which identified 63 H1N1 viruses [206].
T372	44950-45085	Sentence	denotes	Further, four H3N2 viruses were detected in swine nasal swabs originated from three swine farms and an abattoir during 1981–1982 [207].
T373	45086-45160	Sentence	denotes	Later 47 H1N1 and 37 H3N2 viruses were detected in swine during 1992–1995.
T374	45161-45343	Sentence	denotes	Interestingly, four human sera samples were also positive for H1N1 and 77 samples were positive for H3N2 viruses which might be due to the transmission between human and swine [208].
T375	45344-45462	Sentence	denotes	Further IAV seroprevalence was detected in the age group of three-month to four-year old swine during 2002–2004 [209].
T376	45463-45633	Sentence	denotes	The first report of A(H1N1)pdm09 virus in Italian swine appeared after a respiratory disease outbreak in piggeries in Lombardia region of Northern Italy in November 2009.
T377	45634-45743	Sentence	denotes	Piglets experienced diarrhea and weight loss while the sows experienced reduction in reproduction rate [210].
T378	45744-45963	Sentence	denotes	Two more A(H1N1)pdm09 virus isolates were reported in female swine in Sicily in December 2009 [211] while five isolates of A(H1N1)pdm09 virus were identified in swine at three different locations during 2011–2012 [212].
T379	45964-46174	Sentence	denotes	A novel strain of reassorted H1N2 virus having 99–100% identity through six gene segments with A(H1N1)pdm09 virus along with HA and NA genes similar to H1N2 virus was reported in swine in Mantua Province [213].
T380	46175-46256	Sentence	denotes	Reassorted H1N2 viruses were again detected in 34 piglets during 2013–2014 [214].
T381	46257-46392	Sentence	denotes	Seroprevalence of Italian wild boars with one H1N1, ten H1N2, and one H3N2 viruses at two different locations was reported during 2012.
T382	46393-46512	Sentence	denotes	On the contrary, active infection was found only in three wild boars whose nasal swabs were positive for the IAV [215].
T383	46513-46657	Sentence	denotes	One more investigation reported active infection of IAV in 12 wild boars while 78 wild boars had IAV antibodies during July–December 2012 [216].
T384	46658-46768	Sentence	denotes	Further molecular and serological investigations detected avian-like H1N1 viruses in Italian wild boars [216].
T385	46769-46977	Sentence	denotes	The first complete genome sequence of IDV in Italian swine was retrieved from a symptomatic sow in 2015 which was identified to be closely related to the IDV sequence reported in Oklahoma swine in 2011 [217].
T386	46978-47188	Sentence	denotes	Further IDV prevalence in Italian swine was reported when 14, three and four swine were found positive for IDV antibodies in Veneto, Emilia Romagna and Lombardia regions, respectively during June 2015–May 2016.
T387	47189-47332	Sentence	denotes	As a result, swine clinical samples collected during 2013–2014 were investigated retrospectively for IDV prevalence but were reported negative.
T388	47333-47443	Sentence	denotes	An extended serological investigation detected IDV antibodies in 364 swine sera samples collected during 2015.
T389	47444-47546	Sentence	denotes	These findings suggested that IDV was in circulation in Italian swine population only after 2014 [45].
T390	47548-47554	Sentence	denotes	3.4.9.
T391	47555-47560	Sentence	denotes	Spain
T392	47561-47811	Sentence	denotes	Isolation and characterization of 12 H3N2, nine H1N1 and one H1N2 viruses reported the prevalence of influenza viruses for the first time in Spanish swine herds experiencing the respiratory illness and pneumonia during November 2001–April 2004 [218].
T393	47812-47947	Sentence	denotes	More strains of H1N1, H1N2 and H3N2 viruses were isolated, sequenced and characterized in Spanish swine during 2006–2011 [219,220,221].
T394	47948-48212	Sentence	denotes	Interestingly, five H1N1, three H1N2, and four H3N2 virus isolates retrieved between January 2010 and August 2011 had significant similarities with other European isolates which was an evidence of continent-wide transmission of these swine influenza viruses [220].
T395	48214-48221	Sentence	denotes	3.4.10.
T396	48222-48232	Sentence	denotes	Luxembourg
T397	48233-48406	Sentence	denotes	A molecular investigation reported a negative prevalence of IDV in swine in Luxembourg during 2009 but later successfully detected three IDV positive swine during 2014–2015.
T398	48407-48607	Sentence	denotes	Further, the serological investigation confirmed that swine in Luxembourg were free from IDV during 2012 but interestingly, IDV antibodies were detected in 17 swine samples collected during 2014–2015.
T399	48608-48859	Sentence	denotes	These observations suggested that IDV was not in circulation in swine in Luxembourg during 2009–2012 but became prevalent at a low frequency later during 2014–2015 [46] which was almost the same time IDV was reported in Italian swine populations [45].
T400	48861-48868	Sentence	denotes	3.4.11.
T401	48869-48884	Sentence	denotes	The Netherlands
T402	48885-49117	Sentence	denotes	A serological investigation of swine in the Netherlands identified 601 H1N1, 584 H1N2, and 229 H3N2 virus antibodies in 29 swine herds during January–May 1999 [222] with no further evidence of IAV in swine in the country after that.
T403	49119-49126	Sentence	denotes	3.4.12.
T404	49127-49133	Sentence	denotes	Norway
T405	49134-49426	Sentence	denotes	After the 18 swine which were experiencing influenza-like illness were found infected with A(H1N1)pdm09 virus on a Norwegian swine farm in October 2009 the surveillance was expanded to the 39 nearby swine farms which determined that 23 of these farms were positive for the A(H1N1)pdm09 virus.
T406	49427-49556	Sentence	denotes	Intriguingly, one human subject at the index farm who had influenza-like symptoms was also found positive for A(H1N1)pdm09 virus.
T407	49557-49701	Sentence	denotes	This study suggested that the symptoms first appeared in the human subject at the index farm and later the disease got transmitted to the swine.
T408	49702-49813	Sentence	denotes	Hence the findings of this study suggested the reverse zoonosis of the influenza virus from human to pig [223].
T409	49814-49962	Sentence	denotes	Further molecular and serological investigations identified 48 more swine herds that were positive for IAV during September 2009–October 2010 [224].
T410	49963-50149	Sentence	denotes	A more comprehensive nation-wide surveillance in Norwegian swine identified 16 A(H1N1)pdm09 virus positive swine herds during 2009 which later increased to 190 swine herds in 2010 [225].
T411	50150-50338	Sentence	denotes	Later 194 more swine were found infected with A(H1N1)pdm09 virus in Norway between April and July 2011 and reported that the IAV infected swine took longer to weigh 100 kg body mass [226].
T412	50340-50347	Sentence	denotes	3.4.13.
T413	50348-50354	Sentence	denotes	Poland
T414	50355-50505	Sentence	denotes	The first active IAV infection in swine in Poland was reported in 2010 when 21 oral fluid samples collected from three swine farms detected IAV [227].
T415	50506-50612	Sentence	denotes	Soon after, five avian-like H1N1 viruses were reported from the swine lung tissues during 2011–2013 [228].
T416	50613-50774	Sentence	denotes	Later a serological surveillance identified 1212 H1N1, 851 H1N2, 1012 H3N2, and 572 A(H1N1)pdm09 virus antibodies in swine during March 2011–February 2015 [229].
T417	50775-50941	Sentence	denotes	Surprisingly, 34 of these swine had antibodies against all four IAV subtypes i.e., H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses [229] suggesting the past co-infections.
T418	50943-50950	Sentence	denotes	3.4.14.
T419	50951-50965	Sentence	denotes	Czechoslovakia
T420	50966-51132	Sentence	denotes	The human-like H3N2 virus was isolated from a swine in Czechoslovakia during 1969–1972 [230]; however, no other reports ever appeared from the country in later years.
T421	51134-51141	Sentence	denotes	3.4.15.
T422	51142-51149	Sentence	denotes	Hungary
T423	51150-51269	Sentence	denotes	Complete genome of an H1N1 virus was reported from a Hungarian swine having fever and conjunctivitis in May 2011 [231].
T424	51270-51333	Sentence	denotes	This was the only report of H1N1 virus in the swine in Hungary.
T425	51335-51342	Sentence	denotes	3.4.16.
T426	51343-51393	Sentence	denotes	Multi-National Surveillances in European Countries
T427	51394-51704	Sentence	denotes	A large-scale investigation across seven European countries reported a high seroprevalence (˃62%) of IAV antibodies in swine populations of Belgium, Germany, Spain, Italy while a relatively lower (˂21.25%) seroprevalence was observed in swine populations of Czech Republic, Poland and Ireland during 2002–2003.
T428	51705-51894	Sentence	denotes	Antibodies against H1N1, H1N2, and H3N2 viruses were reported in swine from the European countries under surveillance except Poland where swine had antibodies against only H1N1 virus [232].
T429	51895-52061	Sentence	denotes	A virological surveillance across five European countries including Belgium, United Kingdom, Italy, France and Spain reported 169 IAV positive swine during 2006–2008.
T430	52062-52251	Sentence	denotes	The H1N1, H1N2, and H3N2 viruses were detected in swine from Belgium, Italy, and Spain while the samples from United Kingdom and France were found infected with H1N1 and H1N2 viruses [233].
T431	52252-52692	Sentence	denotes	Briefly, the virological and/or serological prevalence of influenza viruses in European countries (Figure 4D) identified the strains of H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses in swine populations of the United Kingdom, Ireland, Italy, Germany, France, Norway, Finland, Denmark, Belgium, Spain, Poland, Greece, Hungary, Netherlands, Czech Republic, and Czechoslovakia while the swine in Luxembourg and Italy were found infected with IDV.
T432	52694-52698	Sentence	denotes	3.5.
T433	52699-52742	Sentence	denotes	Influenza Viruses in Swine in North America
T434	52744-52750	Sentence	denotes	3.5.1.
T435	52751-52757	Sentence	denotes	Canada
T436	52758-52878	Sentence	denotes	Shortly after a respiratory disease outbreak in swine in Manitoba, an autopsy was done on a dead swine on March 1, 1967.
T437	52879-53042	Sentence	denotes	The histopathology confirmed the bronchitis in the deceased swine and a strain of IAV designated as “S/Manitoba/647/67” was characterized using IAV antisera [234].
T438	53043-53186	Sentence	denotes	The first report of H1N1 virus in Canadian swine appeared in Quebec during 1980s–1990s when five genotypes of H1N1 virus were identified [235].
T439	53187-53308	Sentence	denotes	Since then several studies have reported H1N1, H1N2 and H3N2 viruses in Canadian swine [236,237,238,239,240,241,242,243].
T440	53309-53491	Sentence	denotes	Another study reported nine isolates of swine influenza viruses with an antigenic variant from the sick swine having proliferative pneumonia in Quebec, Canada during 1990–1991 [244].
T441	53492-53653	Sentence	denotes	In a retrospective diagnosis, only one formalin-fixed paraffin embedded swine lung tissue collected during 1991 was found IAV positive with immunohistochemistry.
T442	53654-53785	Sentence	denotes	This investigation suggested that immunohistochemistry can be useful in retrospective diagnosis of the swine influenza virus [245].
T443	53786-53966	Sentence	denotes	The broncho-intestinal pneumonia in lung tissues of dead swine was reported on a swine farm which exhibited disease symptoms including coughing, weight loss, and labored breathing.
T444	53967-54172	Sentence	denotes	Interestingly, before the onset of the disease symptoms, this farm conducted a routine serological surveillance of influenza virus which identified H1N1 virus in only one of the twelve swine samples [246].
T445	54173-54295	Sentence	denotes	Following this surveillance, a three-month old swine from the same farm was found positive for avian influenza virus H4N6.
T446	54296-54356	Sentence	denotes	The complete genome of this H4N6 virus was reported in 1999.
T447	54357-54427	Sentence	denotes	This was the first ever report of an avian-origin H4N6 virus in swine.
T448	54428-54671	Sentence	denotes	The proximity of the swine farm to a natural lake where several wild bird species including waterfowls which were reported to visit frequently might be the reason behind the introduction of this avian influenza virus strain to the swine [246].
T449	54672-54828	Sentence	denotes	Later three avian-origin H3N3 influenza virus isolates were recovered from swine in eastern Ontario exhibiting weight loss and coughing during October 2001.
T450	54829-54937	Sentence	denotes	On a nearby farm located approximately 30 kms away, another H3N3 virus isolate was recovered from the swine.
T451	54938-55006	Sentence	denotes	There was no recorded movement of the swine between these two farms.
T452	55007-55110	Sentence	denotes	Since these were avian-origin H3N3 viruses hence the role of birds in transmission cannot be ruled out.
T453	55111-55260	Sentence	denotes	Later, on a third farm, where an influenza like disease had been affecting mainly the nursery piglets, an H1N1 virus was recovered in May 2002 [247].
T454	55261-55475	Sentence	denotes	Reassortant H1N1 and H1N2 viruses were detected in swine nasal swab or lung tissue samples obtained from three-week old piglets and sows exhibiting typical influenza-like symptoms in Ontario during 2003–2004 [248].
T455	55476-55646	Sentence	denotes	First triple-reassortant (avian/classical swine/human triple-reassortant) H3N2 viruses from four swine and one human nasal samples were identified in Ontario during 2005.
T456	55647-55850	Sentence	denotes	The phylogenetic analysis determined that all the virus sequences were 100% identical to each other which apparently emerged from triple-reassortant H3N2 viruses reported in US based swine in 1988 [249].
T457	55851-56010	Sentence	denotes	One more report of triple-reassortant H3N2 (trH3N2) viruses appeared on the swine farms located in Saint-Hyacinthe, Assomption and Saint-Foy during early 2009.
T458	56011-56158	Sentence	denotes	The trH3N2 viruses identified in this study were determined to be closely related to North American/Canadian trH3N2 viruses reported earlier [250].
T459	56159-56362	Sentence	denotes	Later A(H1N1)pdm09 and H1N1 viruses having internal genes of triple reassortant H3N2 virus were reported in swine in four provinces including Manitoba, Alberta, Saskatchewan and Quebec during 2009 [251].
T460	56363-56512	Sentence	denotes	The first evidence of A(H1N1)pdm09 virus in Canadian swine appeared in 2009 after the human workers at a swine farm developed influenza-like illness.
T461	56513-56625	Sentence	denotes	The investigation identified that two farm workers along with 56 swine were positive for the A(H1N1)pdm09 virus.
T462	56626-56701	Sentence	denotes	Transmission of A(H1N1)pdm09 virus from human to swine was suggested [252].
T463	56702-56839	Sentence	denotes	The same year 17 more swine were detected with A(H1N1)pdm09 virus after a respiratory disease outbreak hit the Alberta swine farms [253].
T464	56840-57001	Sentence	denotes	A reverse zoonotic transmission of A(H1N1)pdm09 virus to swine from a human subject who visited Mexico and returned to the swine farm was reported in April 2009.
T465	57002-57165	Sentence	denotes	As a result, ten swine having severe disease were sacrificed for necropsy which identified lesions in the bronchioles corresponding to the influenza virus disease.
T466	57166-57231	Sentence	denotes	Virus isolation and sequencing identified the A(H1N1)pdm09 virus.
T467	57232-57404	Sentence	denotes	Additionally, A(H1N1)pdm09 virus was identified in two more human subjects who were exposed to the swine hence indicated the occurrence of zoonoses on the swine farm [254].
T468	57405-57509	Sentence	denotes	Later during summer 2009, ten more A(H1N1)pdm09 viruses from five swine herds in Manitoba were reported.
T469	57510-57628	Sentence	denotes	Virus shedding was observed up to 20 days post-infection after the appearance of the clinical symptoms in swine [255].
T470	57629-57860	Sentence	denotes	This observation was in agreement of a previous report which documented the experimental infection of swine in the laboratory and determined that virus shedding occurs until 11th day after appearance of the clinical symptoms [256].
T471	57861-58025	Sentence	denotes	Another investigation reported nine A(H1N1)pdm09 and four H3N2 viruses after an influenza-like disease outbreak on a Quebec based swine farm in December 2010 [257].
T472	58026-58321	Sentence	denotes	The effect of microclimatic conditions on the transmission dynamics of swine IAV in the barns was studied which observed that high relative humidity in the environment during summer months suppresses the aerosol transmission of the droplets which in turn decreases the transmission of IAV [240].
T473	58322-58594	Sentence	denotes	The high relative humidity in the environment would facilitate the generation of larger droplets which do not tend to shrink easily and hence are less likely to be aerosol transmitted to a longer distance as they fall on the ground quickly after their formation [240,258].
T474	58595-58681	Sentence	denotes	As a result, a lower transmission of IAV is observed usually during the summer months.
T475	58682-58800	Sentence	denotes	On the contrary, the IAV transmission increases during winter months when relative humidity is relatively lower [258].
T476	58802-58808	Sentence	denotes	3.5.2.
T477	58809-58822	Sentence	denotes	United States
T478	58823-58952	Sentence	denotes	The IAV was first isolated from the nasal discharge of a swine in the United States in 1931 [34] and from the human in 1933 [35].
T479	58953-59230	Sentence	denotes	The first report of human-origin IAV in swine appeared in the United States on 24 May 1937 after an unexpected result was observed when the serum sample of a sick swine obtained from a State Prison Farm located in New Jersey neutralized the antibodies of human influenza virus.
T480	59231-59361	Sentence	denotes	A series of investigations made a strikingly new observation that swine had suffered from a human strain of influenza virus [259].
T481	59362-59517	Sentence	denotes	Serological investigations conducted during 1950s suggested that the weight loss and mortalities among swine were due to swine influenza viruses [260,261].
T482	59518-59642	Sentence	denotes	Swine influenza viruses were isolated from febrile swine at nine occasions during 1965–1968 in Wisconsin and Nebraska [262].
T483	59643-59756	Sentence	denotes	Additionally, swine influenza antibodies were also detected in swine sera samples collected from six farms [262].
T484	59757-60030	Sentence	denotes	A virological surveillance conducted in Memphis, Tennessee and Madison, Wisconsin during May 1976 to June 1977 successfully isolated 478 influenza viruses from swine nasal swabs collected at abattoirs; approximately 300 of which were characterized to be swine H1N1 viruses.
T485	60031-60163	Sentence	denotes	Additionally, the serological surveillance identified that 21% of the 9400 swine sera samples had swine H1N1 virus antibodies [263].
T486	60164-60312	Sentence	denotes	A small percentage (1.4%) of swine sera samples were found positive for the swine H3N2 viruses which was further confirmed by virus isolation [263].
T487	60313-60434	Sentence	denotes	Interestingly, this study identified inter-species transmission of swine influenza viruses between human and swine [263].
T488	60435-60578	Sentence	denotes	A novel swine-origin H1N1 virus termed as “A/New Jersey/76 (Hsw1N1)” was detected at Fort Dix Army training camp in New Jersey in January 1976.
T489	60579-60639	Sentence	denotes	The outbreak was localized and was limited to Fort Dix only.
T490	60640-60804	Sentence	denotes	As a result, 230 soldiers were found infected with this novel virus; 13 of which had severe respiratory disease with one death due to viral pneumonia [264,265,266].
T491	60805-60964	Sentence	denotes	Since this novel swine-origin H1N1 virus quickly disappeared from Fort Dix hence the epidemiology and the origin of the disease could not be ascertained [264].
T492	60965-61083	Sentence	denotes	The H1N1 and H3N2 virus antibodies were detected in swine sera collected from an abattoir in North-West United States.
T493	61084-61180	Sentence	denotes	Interestingly, a higher IAV seroprevalence was observed during the Fall and early winter months.
T494	61181-61314	Sentence	denotes	Virus isolation and sequencing identified that the H1N1 viruses were closely related to the classical H1 swine influenza virus [267].
T495	61315-61471	Sentence	denotes	Classical swine-like H1N1 and triple-reassortant H3N2 viruses were identified in swine samples collected across 23 states in the USA during 1998–1999 [268].
T496	61472-61648	Sentence	denotes	The Minnesota Veterinary Diagnostic Laboratory (MVDL) detected large number of H1N1, H1N2 and H3N2 subtypes of IAV in swine samples during 1998–2001 and again during 2007–2009.
T497	61649-61742	Sentence	denotes	Interestingly, some of the samples were co-infected with H1N1 and H3N2 viruses [269,270,271].
T498	61743-61968	Sentence	denotes	A second-generation reassortant H1N2 virus having genes from a reassortant H3N2 and classical H1 swine influenza viruses was obtained from the lung tissue samples of a dead sow at an Indiana swine farm in November 1999 [272].
T499	61969-62152	Sentence	denotes	A novel subtype of H3N1 virus termed as “A/Swine/Minnesota/00395/2004 (H3N1)” was identified during a severe respiratory disease outbreak on a swine farm in Minnesota in October 2004.
T500	62153-62444	Sentence	denotes	Sequencing observed that the HA gene of this strain was closely related to swine influenza H3N2 virus while the NA gene was related to classical H1N1 virus which suggested that the novel H3N1 virus emerged due to reassortment between H1N1 and H3N2 viruses in the Midwest United States [273].
T501	62445-62674	Sentence	denotes	Further an H2N3 subtype of IAV which may have emerged as a result of a reassortment between avian and swine influenza viruses was identified on a commercial swine farm in Minnesota in April 2006 and again in September 2006 [274].
T502	62675-62926	Sentence	denotes	The first evidence of A(H1N1)pdm09 virus infection in US swine appeared when four A(H1N1)pdm09 and one triple-reassortant H1N2 viruses were identified and characterized in the exhibition swine in the states of Minnesota and South Dakota in 2009 [275].
T503	62927-63144	Sentence	denotes	During last ten years, a large number of H1N1, H1N2, H3N2, A(H1N1)pdm09 along with reassortant IAV subtypes have been reported in the US swine populations [243,276,277,278,279,280,281,282,283,284,285,286,287,288,289].
T504	63145-63261	Sentence	denotes	The United States has a large feral swine population which is considered a reservoir of H1N1 and H3N2 viruses [290].
T505	63262-63527	Sentence	denotes	The swine-like H1N1, avian-like H1N1, swine-like H1N2, swine-like H3N2, human-like H3N2, A(H1N1)pdm09 along with avian-like H6N2 and H7N2 viruses were identified in feral swine samples collected across 35 states in the USA between October 2009–September 2013 [291].
T506	63528-63824	Sentence	denotes	Histological examination of the lung tissues obtained from two backyard piglets suffering from pneumonia and weight loss in Colorado in November 2010 suggested that the piglets were infected with swine influenza virus which were later confirmed to be infected with IAV subtype A(H1N1)pdm09 virus.
T507	63825-64060	Sentence	denotes	Since the piglets were raised at the house of a pharmacist hence a possible human to swine transmission was speculated given the possibility of an occupational exposure of the pharmacist to the A(H1N1)pdm09 virus at the pharmacy [292].
T508	64061-64225	Sentence	denotes	The first report of IBV infection in swine appeared when swine in the Midwest United States were found infected with IBV lineages of Yagamata/B and Victoria/B [37].
T509	64226-64359	Sentence	denotes	This was a new finding because initially IBV was thought to have a host range limited to human, pheasants, horses and seal [1,2,3,4].
T510	64360-64480	Sentence	denotes	A novel strain of swine influenza virus was detected in Oklahoma swine exhibiting influenza-like symptoms in April 2011.
T511	64481-64561	Sentence	denotes	The nasal swab samples taken from the swine were negative for the IAV infection.
T512	64562-64702	Sentence	denotes	Hence the virus isolation was attempted in swine testicle cells; the cells in culture showed influenza-like cytopathic effects by third day.
T513	64703-64851	Sentence	denotes	Electron microscopic observations revealed particles typical of a virus of Orthomyxoviridae family, but the RT-PCR was negative for the IBV and ICV.
T514	64852-64975	Sentence	denotes	After ultracentrifugation was used for virus isolation, the genome of the virus was sequenced using Ion Torrent sequencing.

T15

0-2

Sentence

denotes

1.

T16

3-15

Sentence

denotes

Introduction

T17

16-118

Sentence

denotes

Influenza viruses are the members of Orthomyxoviridae family and have a wide host range [1,2,3,4,5,6].

T18

119-212

Sentence

denotes

Due to unique physiology, swine are considered the “mixing vessel” for influenza viruses [7].

T19

213-382

Sentence

denotes

Four types of influenza viruses have been reported in swine i.e., influenza A virus (IAV), influenza B virus (IBV), influenza C virus (ICV), and influenza D virus (IDV).

T20

383-535

Sentence

denotes

The genomes of IAV and IBV have eight gene segments of single-stranded negative sense RNA while the genomes of ICV and IDV have seven gene segments [8].

T21

536-741

Sentence

denotes

Among the eight gene segments of IAV and IBV, the hemagglutinin (HA) and neuraminidase (NA) are most significant and crucial for the pathogenicity of these viruses which determine the antigenic properties.

T22

742-891

Sentence

denotes

The HA gene regulates the attachment of virus particles to the host receptor while NA gene regulates the release of progeny virus into the host cell.

T23

892-1064

Sentence

denotes

Co-infection of swine with two or more IAV strains may trigger the reassortment [9] which in turn, could facilitate the emergence of new influenza virus strains [10,11,12].

T24

1065-1277

Sentence

denotes

Point mutations which occur due to an error-prone RNA polymerase that lacks the ability of proof-reading and corrections during replication may also complement the genetic diversity of the influenza viruses [13].

T25

1278-1501

Sentence

denotes

The mechanisms of reassortment and point mutations may give rise to “antigenic shift” and “antigenic drift” within HA and NA genes, respectively, facilitating the emergence of new subtypes and lineages of influenza viruses.

T26

1502-1669

Sentence

denotes

As a result, total 18 HA and 11 NA subtypes of IAV [14,15,16] and two lineages (Victoria/B and Yamagata/B) of IBV have been reported so far in different hosts [17,18].

T27

1670-1760

Sentence

denotes

The host range of IAV and IBV is determined by their specificity to sialic acid receptors.

T28

1761-1894

Sentence

denotes

The HA proteins of IAV can bind to α-2,3 and α-2,6 sialic acid receptors present in avian and human trachea, respectively [19,20,21].

T29

1895-2074

Sentence

denotes

Interestingly, swine trachea has both, α-2,3 as well as α-2,6 sialic acid receptors, due to which swine can become infected with avian and human strains of influenza viruses [22].

T30

2075-2252

Sentence

denotes

The genomes of ICV and IDV have a gene segment termed as “hemagglutinin–esterase-fusion” (HEF) which carries out the functions similar to that of HA and NA genes of IAV and IBV.

T31

2253-2364

Sentence

denotes

The HEF is responsible for attachment and release of ICV and IDV virus particles into the host cell [23,24,25].

T32

2365-2473

Sentence

denotes

The particles of both virus types ICV and IDV bind to 9-O-acetylated sialic acid receptors of the host [25].

T33

2474-2672

Sentence

denotes

Several studies have shown that human and avian origin influenza viruses can be transmitted to swine in natural settings and thus may evolve into new strains of reassorted influenza viruses [26,27].

T34

2673-2819

Sentence

denotes

Historically, the first flu pandemic (Spanish flu) hit the human population in 1918 [28] and killed approximately 50 million people globally [29].

T35

2820-3062

Sentence

denotes

The 1918 influenza pandemic emerged as a result of reassortment in which human H1 virus acquired avian (poultry) N1 neuraminidase along with internal protein genes and evolved into what is now termed as “classical H1N1” virus [30] (Figure 1).

T36

3063-3200

Sentence

denotes

The second flu pandemic occurred in 1957 (Asian flu) and was traced to the H2N2 virus which killed approximately two million people [31].

T37

3201-3347

Sentence

denotes

The third flu pandemic hit the human population in 1968 (Hong Kong flu) with an H3N2 outbreak and killed approximately two million people [31,32].

T38

3348-3501

Sentence

denotes

The most recent flu pandemic (Swine flu) originated in swine in Mexico during March–May 2009 [33] and killed approximately 575,000 people worldwide [31].

T39

3502-3602

Sentence

denotes

The swine flu occurred due to a pandemic reassortant H1N1 virus termed as “A(H1N1)pdm09” virus [33].

T40

3603-3729

Sentence

denotes

Among four types of the influenza viruses, IAV is the most prevalent type and has been reported in swine in several countries.

T41

3730-3838

Sentence

denotes

The IAV was first isolated from the nasal discharge of a swine in 1931 [34] and from the human in 1933 [35].

T42

3839-3943

Sentence

denotes

Strains of IAV have been reported to cause mild to severe upper respiratory tract illness in swine [36].

T43

3944-4124

Sentence

denotes

Strains of Victoria/B and Yamagata/B lineages of IBV were first reported in swine in the United States in 2010 [37] while the ICV in swine was first isolated in China in 1983 [38].

T44

4125-4201

Sentence

denotes

Both, the IBV and ICV cause mild respiratory illness in swine [39,40,41,42].

T45

4202-4392

Sentence

denotes

The IDV in swine was first detected in Oklahoma based swine in the United States in 2011 [5,43] which in later years has been detected in swine in China [44], Italy [45] and Luxembourg [46].

T46

4393-4569

Sentence

denotes

Interestingly, influenza viruses can be detected in the swine throughout the year unlike humans where seasonality affects the occurrence and progression of the disease [47,48].

T47

4570-4852

Sentence

denotes

An active surveillance of influenza viruses in swine is necessary for two basic reasons; to track the influenza virus evolution for improvements of the currently available diagnostic tests as well as for generating more effective vaccines for prevention and control of disease [49].

T48

4853-5009

Sentence

denotes

The currently available scientific data on swine influenza viruses would serve as a key to understand their evolutionary dynamics and transmission patterns.

T49

5010-5147

Sentence

denotes

Therefore, this systematic review, for the first time, summarizes all four types of influenza viruses in the swine populations worldwide.

T50

5149-5151

Sentence

denotes

2.

T51

5152-5159

Sentence

denotes

Methods

T52

5161-5165

Sentence

denotes

2.1.

T53

5166-5212

Sentence

denotes

Systematic Review Protocol and Search Strategy

T54

5213-5397

Sentence

denotes

The guidelines and the procedures as detailed by the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) [50] were followed for drafting this systematic review.

T55

5398-5583

Sentence

denotes

Original research articles reporting influenza virus types IAV, IBV, ICV, and IDV in swine populations until February 21, 2020 were searched through PubMed and Google Scholar databases.

T56

5584-5819

Sentence

denotes

The influenza virus sequence information was also verified using “Influenza Virus Resource” of NCBI (https://www.ncbi.nlm.nih.gov/genomes/FLU/) and “Influenza Research Database” (https://www.fludb.org/brc/home.spg?decorator=influenza).

T57

5820-5956

Sentence

denotes

The sequence information helped in the identification of additional relevant articles reported from Indonesia, Kazakhstan and Sri Lanka.

T58

5957-6356

Sentence

denotes

The search terms including “Influenza outbreak in swine” OR “Influenza A virus in swine” OR “Influenza B virus in swine” OR “Influenza C virus in swine” OR “Influenza D virus in swine” OR “Influenza virus in pigs” were entered one by one in PubMed and Google Scholar databases to identify all full-text research publications or case reports which reported influenza virus types or subtypes in swine.

T59

6357-6653

Sentence

denotes

The outcome suggesting research publications reporting influenza virus types and subtypes in swine along with the transmission of influenza viruses between human and swine, birds and swine, poultry and swine, cattle and swine as well as horse and swine were thoroughly investigated for inclusion.

T60

6654-6801

Sentence

denotes

The search results suggesting influenza virus prevalence and/or transmission in or between species other than swine were omitted from the analysis.

T61

6802-6927

Sentence

denotes

Occasionally, the full-text articles were also requested from the authors, if the full-text article was not available online.

T62

6928-7004

Sentence

denotes

Two publications which could not be accessed were omitted from the analysis.

T63

7005-7102

Sentence

denotes

Search results yielding articles in a language other than English were omitted from the analysis.

T64

7103-7336

Sentence

denotes

The articles were first screened through their abstracts to find out their relevance for inclusion, and, if required, the introduction and/or results and discussion sections were also screened to assess their relevance for inclusion.

T65

7337-7481

Sentence

denotes

The relevant articles were downloaded and stored on the computer drive for further screening and refinement according to PRISMA guidelines [50].

T66

7482-7669

Sentence

denotes

The references of downloaded publications were also screened to identify relevant articles reporting the influenza viruses in swine, which were also downloaded to include in the analysis.

T67

7670-7748

Sentence

denotes

An overview of the methodology can be observed in the PRISMA chart (Figure 2).

T68

7750-7754

Sentence

denotes

2.2.

T69

7755-7787

Sentence

denotes

Inclusion and Exclusion Criteria

T70

7788-7863

Sentence

denotes

The following criteria were applied for screening of the eligible articles:

T71

7864-8027

Sentence

denotes

The original research articles and case reports which documented the influenza viruses in swine in natural settings across the world were included in the analysis.

T72

8028-8124

Sentence

denotes

The experimental studies which did not report the natural cases were excluded from the analysis.

T73

8125-8263

Sentence

denotes

The reviews, letters, editorials, conference proceedings, and articles in a language other than English were not included in the analysis.

T74

8264-8320

Sentence

denotes

Duplicate articles were also excluded from the analysis.

T75

8321-8424

Sentence

denotes

The eligible articles (n = 281) thus selected were included in the analysis for this systematic review.

T76

8426-8430

Sentence

denotes

2.3.

T77

8431-8448

Sentence

denotes

Ethical Approvals

T78

8449-8548

Sentence

denotes

This systematic review did not involve animal sampling or experimental protocols in the laboratory.

T79

8549-8647

Sentence

denotes

The data used for writing this article were obtained from the PubMed and Google Scholar databases.

T80

8648-8890

Sentence

denotes

This systematic review is part of a research project which has already obtained the relevant ethical approvals from the Animal Research Ethics Committee (AREC), University of KwaZulu-Natal, Durban, South Africa; AREC Reference: AREC/041/019D.

T81

8891-9025

Sentence

denotes

Additionally, the authors have the required permission to do research in terms of Section 20 of the Animal Diseases Act, 1984 (Act No.

T82

9026-9164

Sentence

denotes

35 of 1984) from the Department of Agriculture, Forestry and Fisheries (DAFF), Government of the Republic of South Africa; DAFF Reference:

T83

9165-9184

Sentence

denotes

12/11/1/5/4 (1425).

T84

9186-9188

Sentence

denotes

3.

T85

9189-9196

Sentence

denotes

Results

T86

9197-9451

Sentence

denotes

The original research articles and case reports on the serological and virological prevalence of all the four genera of influenza viruses i.e., IAV, IBV, ICV and IDV were downloaded, analyzed and summarized in the region-specific manner across the world.

T87

9452-9577

Sentence

denotes

Influenza viruses have been reported from 53 countries located across six continents (Figure 3; Table 1) until February 2020.

T88

9579-9583

Sentence

denotes

3.1.

T89

9584-9620

Sentence

denotes

Influenza Viruses in Swine in Africa

T90

9622-9628

Sentence

denotes

3.1.1.

T91

9629-9637

Sentence

denotes

Cameroon

T92

9638-9748

Sentence

denotes

The first report of IAV in Cameroonian swine appeared when A(H1N1)pdm09 virus was documented during 2009–2010.

T93

9749-9870

Sentence

denotes

The youngest infected swine was four-month old which suggested that A(H1N1)pdm09 virus can infect the young piglets [51].

T94

9871-9986

Sentence

denotes

Nine more swine herds in Cameroon were found infected with A(H1N1)pdm09 and H1N1 viruses during May–June 2011 [52].

T95

9987-10204

Sentence

denotes

A multiple-site study including free-roaming and penned swine along with domestic poultry and Columbiformes birds between December 2009 and August 2012 identified one IAV positive swine at each of the two study sites.

T96

10205-10305

Sentence

denotes

The inter-species transmission of IAV was ruled out as all the birds were negative for the IAV [53].

T97

10307-10313

Sentence

denotes

3.1.2.

T98

10314-10321

Sentence

denotes

Nigeria

T99

10322-10503

Sentence

denotes

The first evidence of the past IAV infection in Nigerian swine appeared in 2008 when H1N1 and H3N2 virus antibodies were detected in swine sampled at three different locations [54].

T100

10504-10669

Sentence

denotes

Shortly after that, in 2009, the first report of A(H1N1)pdm09 virus appeared in the Nigerian swine when one swine herd was found seropositive for A(H1N1)pdm09 virus.

T101

10670-10809

Sentence

denotes

Interestingly, eight other swine herds were found seropositive for the H1N1 and four herds were found positive for human-like H3N2 viruses.

T102

10810-10983

Sentence

denotes

The seroprevalence of IAV further increased as 66 swine herds were detected positive for A(H1N1)pdm09 virus and 53 herds were found seropositive for H1N1 virus in 2012 [52].

T103

10984-11183

Sentence

denotes

The active infection (viral RNA) of A(H1N1)pdm09 virus was first reported in the Nigerian swine between July 2010–June 2012 when 18 A(H1N1)pdm09 virus isolates were retrieved from the swine in Lagos.

T104

11184-11346

Sentence

denotes

The zoonotic transmission of A(H1N1)pdm09 virus to the exposed human workers was ruled out as all the human samples were negative for the A(H1N1)pdm09 virus [55].

T105

11347-11469

Sentence

denotes

Nineteen more A(H1N1)pdm09 and five human-origin H3N2 viruses were identified in the Nigerian swine during 2013-2015 [56].

T106

11470-11578

Sentence

denotes

Later one more report of the human strain of H3N2 virus appeared in swine during January–February 2014 [57].

T107

11579-11654

Sentence

denotes

A high seroprevalence of IAV in a commercial piggery was reported in Lagos.

T108

11655-11919

Sentence

denotes

Total 197 human and 281 swine sera samples were screened which determined that 87% human and 67% swine sera had antibodies for IAV depicting the past exposure [58] but the active infection was absent given that all nasal swabs were negative for IAV infection [58].

T109

11920-12214

Sentence

denotes

Lately, highly pathogenic avian influenza virus (HPAIV) strain H5N1 was detected in 22 swine samples between December 2015 and February 2016 during an ongoing H5N1 disease outbreak in Nigerian poultry [59] which indicated the inter-species transmission of H5N1 virus from poultry to swine [59].

T110

12216-12222

Sentence

denotes

3.1.3.

T111

12223-12228

Sentence

denotes

Egypt

T112

12229-12547

Sentence

denotes

A molecular study reported the negative prevalence of avian-like H5N1 and H5N2 viruses in Egyptian swine in May 2008 [60] but the serological investigation identified H5N1 virus antibodies in seven and H5N2 virus antibodies in four swine sera samples [60] which suggested a past exposure of these swine to the viruses.

T113

12548-12850

Sentence

denotes

The active H5N1 infection in Egyptian swine was again ruled out in October 2013 as the viral RNA could not be detected in 36 swine samples but interestingly, the antibodies against avian-like H5N1, H9N2, and A(H1N1)pdm09 viruses were detected in swine sera samples which suggested a past exposure [61].

T114

12851-12995

Sentence

denotes

Interestingly, 122 of the 157 swine nasal swab samples collected during 2014 and 2015 were found positive for IAV active infection using RT-PCR.

T115

12996-13099

Sentence

denotes

As a result, HA subtyping identified 46 avian-origin H5N1, seven H9N2 and 69 A(H1N1)pdm09 viruses [61].

T116

13101-13107

Sentence

denotes

3.1.4.

T117

13108-13113

Sentence

denotes

Kenya

T118

13114-13316

Sentence

denotes

The first report of IAV in swine in Kenya appeared in May 2010 when A(H1N1)pdm09 virus were detected in eight swine samples collected from the Asembo and Kibera counties and at a Nairobi based abattoir.

T119

13317-13439

Sentence

denotes

The extended serological study further identified H1N1 and H3N2 viruses in swine during August 2011 to December 2012 [62].

T120

13440-13647

Sentence

denotes

The active IAV infection was reported in four household members having acute respiratory illness while the backyard swine were negative for the IAV and IBV in Kiambu county during September 2013–August 2014.

T121

13648-13773

Sentence

denotes

On the contrary, the serology identified the IAV antibodies in 230 swine sera samples suggesting a past exposure of IAV [63].

T122

13774-13916

Sentence

denotes

The A(H1N1)pdm09 virus was again reported in five swine samples collected from a slaughterhouse in Kenya during September 2013–September 2014.

T123

13917-14128

Sentence

denotes

Interestingly, all the 288 human subjects including the slaughterhouse workers or the traders and farmers who had visited the slaughterhouse were negative for IAV, hence ruled out the zoonotic transmission [64].

T124

14130-14136

Sentence

denotes

3.1.5.

T125

14137-14160

Sentence

denotes

Other African Countries

T126

14161-14383

Sentence

denotes

Swine in Benin and Cote d’Ivoire reported no prevalence of IAV during 2009–2010 [65] while A(H1N1)pdm09 virus was detected in swine in Reunion Island during 2009–2011 [66] and in Togo during October 2012–January 2014 [67].

T127

14384-14480

Sentence

denotes

The human strain of H3N2 virus was detected in swine in Ghana during January–February 2014 [57].

T128

14481-14561

Sentence

denotes

One more report documented IAV in swine in two districts of Uganda in 2015 [68].

T129

14562-14741

Sentence

denotes

Overall, influenza viruses have been reported in swine from eight African countries including Cameroon, Nigeria, Egypt, Kenya, Reunion island, Togo, Ghana, and Uganda (Figure 4A).

T130

14742-14858

Sentence

denotes

The A(H1N1)pdm09 virus, which originated in Mexican swine in 2009, has been reported in all except Ghana and Uganda.

T131

14859-15088

Sentence

denotes

Interestingly, the HPAIV strain of H5N1 has been reported in swine in Nigeria and Egypt while HPAIV strain H5N2 and low pathogenic avian influenza virus (LPAIV) strain H9N2 have also been reported in the Egyptian swine (Table 1).

T132

15090-15094

Sentence

denotes

3.2.

T133

15095-15129

Sentence

denotes

Influenza Viruses in Swine in Asia

T134

15131-15137

Sentence

denotes

3.2.1.

T135

15138-15143

Sentence

denotes

China

T136

15144-15204

Sentence

denotes

China is considered the epicenter of influenza viruses [69].

T137

15205-15436

Sentence

denotes

The first seroprevalence of IAV in Chinese swine was documented during 1977-1982 when antibodies for 38 H1N1, 22 H3N2, 12 H4N6, 12 H5N3, and seven H9N2 viruses was detected in swine sera obtained from apparently healthy swine [70].

T138

15437-15605

Sentence

denotes

The first ever report of ICV in swine was documented from the apparently healthy swine in Beijing when 15 ICV isolates were retrieved during January–December 1981 [38].

T139

15606-15777

Sentence

denotes

Three isolates of reassortant H1N2 virus were identified after an influenza-like illness triggered abortions and mortalities in sows on a swine farm in November 2004 [71].

T140

15778-15936

Sentence

denotes

The same year, LPAIV strain H9N2 was isolated from the sick or dead swine in China which was the first ever isolate of H9N2 virus retrieved from a swine [72].

T141

15937-16057

Sentence

denotes

First human-origin H1N1 and four human-origin H3N2 virus isolates in Chinese swine were retrieved during 2005–2006 [73].

T142

16058-16315

Sentence

denotes

Further, two isolates of swine H3N2 viruses, four isolates of avian-origin HPAIV strain H5N1 and two isolates of H1N1 viruses were detected in swine nasal swab and lung tissue samples collected from swine in central provinces of China during 2004–2006 [74].

T143

16316-16445

Sentence

denotes

Surprisingly, two isolates of equine influenza virus H3N8 were also detected in swine during December 2005 and January 2006 [74].

T144

16446-16640

Sentence

denotes

Another report of avian-origin H9N2 virus in Chinese swine was documented during 2006–2007 when four H9N2 virus isolates with closely related nucleotide sequences were retrieved from swine [75].

T145

16641-16890

Sentence

denotes

Each of the two different investigations reported 19 H1N1, one H1N2 and nine H3N2 virus isolates from Chinese swine during 2006–2009 [76,77]; the H1N2 virus and all nine isolates of H3N2 viruses were either double or triple-reassortant viruses [76].

T146

16891-17061

Sentence

denotes

The first report of HPAIV strain H5N1 in swine was documented during October 2008–May 2009 when two H5N1 virus isolates were retrieved from apparently healthy swine [78].

T147

17062-17311

Sentence

denotes

The third report of avian-origin H9N2 virus in Chinese swine appeared when 144 apparently healthy swine across four provinces viz., Yunnan, Guangdong, Fujian and Zhejiang were found H9N2 positive over a four-year period during March 2008–March 2012.

T148

17312-17459

Sentence

denotes

The frequent interactions of birds to the swine at the study sites was reported which was suspected to be the most likely source of infection [79].

T149

17460-17558

Sentence

denotes

Further, a novel strain of avian-origin H4N1 virus was isolated from a Chinese swine in 2009 [80].

T150

17559-17773

Sentence

denotes

Several classical and avian-like H1N1, Eurasian avian-like H1N1, triple-reassortant H1N1, H1N2, H3N2 and A(H1N1)pdm09 viruses were reported in Chinese swine between 2009 and 2016 [81,82,83,84,85,86,87,88,89,90,91].

T151

17774-17983

Sentence

denotes

A triple-reassortant H1N1 virus having the internal genes of avian, human, and swine lineages of influenza viruses was reported from a two-month old piglet on a Guangdong based swine farm in January 2010 [92].

T152

17984-18130

Sentence

denotes

Three reassortant H3N2 virus isolates having internal genes of A(H1N1)pdm09 virus were reported in swine between November 2010 and June 2011 [93].

T153

18131-18357

Sentence

denotes

A three-year old boy was diagnosed with European origin avian-like H1N1 virus on a family swine farm in a rural area of the Jiangsu province in December 2010 which speculated a zoonotic transmission from swine to the boy [94].

T154

18358-18636

Sentence

denotes

The first report of H10N5 avian-origin influenza virus in a domestic swine in Hubei province further extended the diversity of swine influenza viruses and provided another evidence of interspecies transmission of avian influenza virus to the swine under natural conditions [95].

T155

18637-18794

Sentence

denotes

Several other avian-origin H3N2, H4N8, H6N6, H7N9, H5N1, and H9N2 virus antibodies were detected in swine in China during April 2010–June 2014 [86,96,97,98].

T156

18795-19039

Sentence

denotes

Another interspecies transmission of avian-like H1N1 virus in southern China was observed when 219 swine and 61 swine farm workers were identified to be infected with avian-like H1N1 swine influenza virus between March 2011 and March 2013 [99].

T157

19040-19234

Sentence

denotes

Further a zoonotic transmission of H9N2 virus was identified at a Shandong based swine farm during May 2013–April 2014 when H9N2 virus antibodies were detected in 84 swine and four farm workers.

T158

19235-19358

Sentence

denotes

The wild birds visiting swine feeding sites at the swine farm were speculated to serve as the carrier for H9N2 virus [100].

T159

19359-19550

Sentence

denotes

Zoonotic transmission of H1N1 virus was reported on a swine farm in Shandong province between March 2015 and February 2016 among the swine exposed human workers having influenza-like illness.

T160

19551-19706

Sentence

denotes

As a result, five of the 32 (15.6%) nasal swab samples were found IAV positive; a married couple exposed to swine were found infected with H1N1 virus [88].

T161

19707-19832

Sentence

denotes

The IAV infection was also documented in 44 wild boars in Jilin province of China between April 2015 and February 2016 [101].

T162

19833-19961

Sentence

denotes

The first report of the IDV prevalence in Chinese swine documented 21 IDV positive swine in the Guangdong province in 2016 [44].

T163

19962-20164

Sentence

denotes

The swine IDV sequences shared high similarity (99–100%) with IDV sequences reported earlier from the bovine species in China [102] which indicated the transmission of IDV from bovine to swine in China.

T164

20166-20172

Sentence

denotes

3.2.2.

T165

20173-20192

Sentence

denotes

Hong Kong and Tibet

T166

20193-20337

Sentence

denotes

Hong Kong is a special administrative region while Tibet is an autonomous administrative region under the control of People’s Republic of China.

T167

20338-20475

Sentence

denotes

The H1N1 and H3N2 virus isolates were successfully retrieved from apparently healthy swine in Hong Kong during July 1993–June 1994 [103].

T168

20476-20734

Sentence

denotes

Further, classical swine H1N1, H3N2 and avian-like H9N2 viruses were identified in Hong Kong based swine between March 1998–June 2000; two independent introductions of the avian-like H9N2 viruses were ascertained from avian species to the swine [27,104,105].

T169

20735-20933

Sentence

denotes

The first information of IAV seroprevalence in Tibetan swine appeared during April–December 2010 when antibodies against H1N1 and H3N2 viruses were detected in swine sera collected from Tibet [106].

T170

20935-20941

Sentence

denotes

3.2.3.

T171

20942-20948

Sentence

denotes

Bhutan

T172

20949-21128

Sentence

denotes

The first report of H1N1 seroprevalence in swine in Bhutan appeared when H1N1 virus was detected in backyard as well as breeding swine during October 2011 and February 2012 [107].

T173

21130-21136

Sentence

denotes

3.2.4.

T174

21137-21145

Sentence

denotes

Cambodia

T175

21146-21300

Sentence

denotes

The H1N1 virus was reported in swine over a five year-period between 2006–2010 while the A(H1N1)pdm09 and H3N2 viruses were identified only in 2010 [108].

T176

21301-21432

Sentence

denotes

Later three triple-assortant H3N2 viruses were isolated and sequenced from the backyard swine between May 2011 and July 2012 [109].

T177

21434-21440

Sentence

denotes

3.2.5.

T178

21441-21446

Sentence

denotes

Japan

T179

21447-21584

Sentence

denotes

The antibodies against A/Hong Kong(H3N2) virus termed as “A/Swine/Wadayama/5/69” were first detected in Japanese swine in 1969 [110,111].

T180

21585-21764

Sentence

denotes

The H3N2 virus seroprevalence in Japanese swine was further documented in Sendai City during 1977 to 1980 [112]; the transmission between human and swine was also suggested [112].

T181

21765-21927

Sentence

denotes

The first active IAV infection was reported when two reassortant H1N2 virus isolates were retrieved from the Japanese swine having influenza-like disease in 1978.

T182

21928-22016

Sentence

denotes

The isolated H1N2 virus was believed to be a recombinant of H1N1 and H3N2 viruses [113].

T183

22017-22110

Sentence

denotes

Further 340 swine were diagnosed with H1N1 antibodies in Toyama Prefecture between 1978–1982.

T184

22111-22250

Sentence

denotes

A lower seroprevalence was observed during the summer months while the seroprevalence was relatively higher during the winter season [114].

T185

22251-22367

Sentence

denotes

Again, one more H1N2 virus was isolated and characterized from the sows in Ehime Prefecture in September 1980 [115].

T186

22368-22553

Sentence

denotes

Intriguingly, 18 H1N1, H1N2 and H3N2 viruses were detected in swine imported from the United States, however, all the imported swine from the Europe were negative for the IAV infection.

T187

22554-22629

Sentence

denotes

This was the first report of the IAV infection in the imported swine [116].

T188

22630-22944

Sentence

denotes

The ICV seroprevalence (19%) in Japanese swine was first reported in the Hyogo Prefecture during July 1981–June 1982 [117] but swine in Yamagata Prefecture were found seronegative for the ICV between August 1979 and March 1986 which suggested a localized transmission of ICV in swine within Hyogo Prefecture [118].

T189

22945-23040

Sentence

denotes

Several other reassortant H1N2 virus isolates were reported in Japanese swine after 1991 [119].

T190

23041-23298

Sentence

denotes

One novel reassortant H1N2 virus appeared to have emerged from the A(H1N1)pdm09 virus was reported in swine in Gunma Prefecture while two other H1N2 viruses appeared to have emerged from the Japanese H1N2 viruses with internal genes from A(H1N1)pdm09 virus.

T191

23299-23400

Sentence

denotes

One more H1N2 virus was detected in swine which was closely related to the Japanese H1N2 virus [120].

T192

23401-23519

Sentence

denotes

The immunohistochemistry identified lesions in the lungs of the sick swine infected with reassortant H1N2 virus [121].

T193

23520-23638

Sentence

denotes

Additionally, several H1N1 and H3N2 viruses have also been reported in Japanese swine between 1990 and 2017 [122,123].

T194

23639-23866

Sentence

denotes

Interestingly, six H1N1 virus isolates were identified with reassorted genes from A(H1N1)pdm09 virus while one H1N1 isolate appeared to have H1 gene from Japanese swine influenza virus with internal genes of A(H1N1)pdm09 virus.

T195

23867-23987

Sentence

denotes

Further, one H3N2 virus isolate was determined to have genes of Japanese swine influenza and A(H1N1)pdm09 viruses [124].

T196

23988-24112

Sentence

denotes

These results reflected the occurrence of the reassortment events between Japanese swine influenza and A(H1N1)pdm09 viruses.

T197

24113-24205

Sentence

denotes

IAV seroprevalence has lately been reported in wild boars (Sus scrofa leucomystax) in Japan.

T198

24206-24385

Sentence

denotes

Three wild boars in the Yamaguchi Prefecture were found seropositive for A(H1N1)pdm09 virus while nine wild boars in Tochigi Prefecture were seropositive for the swine H1N1 virus.

T199

24386-24526

Sentence

denotes

But, the active IAV infection could not be identified in these wild boars as all the nasal swab samples were negative for IAV and IBV [125].

T200

24527-24782

Sentence

denotes

In a more recent investigation, fifteen wild boars were found seropositive for A(H1N1)pdm09 virus in Kagoshima Prefecture between November 2014–December 2017 while two of these fifteen wild boars had antibodies against H1N2 and H3N2 viruses as well [126].

T201

24783-24860

Sentence

denotes

This reflected a past exposure of the Japanese wild boars to the IAV strains.

T202

24862-24868

Sentence

denotes

3.2.6.

T203

24869-24880

Sentence

denotes

South Korea

T204

24881-25082

Sentence

denotes

The first active IAV infection in the Korean swine was identified in December 1998 when three H3N2 virus isolates were recovered from the swine experiencing an acute influenza-like respiratory disease.

T205

25083-25257

Sentence

denotes

The close relatedness of these Korean swine H3N2 isolates with human-origin H3N2 viruses reported from Korea between 1987–1999 suggested the events of reverse zoonosis [127].

T206

25258-25477

Sentence

denotes

One unique H7N2 virus isolate was detected in swine which had seven gene segments originated from Hong Kong avian-origin H7N2 virus isolated in 1978 and the NS gene originated from Hong Kong H5N3 virus isolated in 1977.

T207

25478-25565

Sentence

denotes

Additionally, four typical swine influenza H1N1 viruses were identified in swine [128].

T208

25566-25688

Sentence

denotes

Several H1N1, H1N2, and H3N2 viruses were detected in symptomatic South Korean swine after 2000 [129,130,131,132,133,134].

T209

25689-25780

Sentence

denotes

The IAV localization in the swine lung tissues was confirmed by immunohistochemistry [130].

T210

25781-25977

Sentence

denotes

Total 35 avian-origin H5N2 viruses of Eurasian lineage were identified in swine in different South Korean provinces during 2004–2008 which suggested cross-species transmission of H5N2 virus [135].

T211

25978-26106

Sentence

denotes

Three H1N1 virus isolates closely related to US isolates of H1N1 were obtained from 45-day-old piglets in Korea in January 2005.

T212

26107-26204

Sentence

denotes

The other swine farms in the proximity of this index farm were negative for the H1N1 virus [136].

T213

26205-26539

Sentence

denotes

Further, one H1N1, two H1N2, and one H3N2 subtypes of IAV identical to the American strains based on their HA and NA gene sequences were obtained from swine nasal swab, lung, and thoracic fluid samples during 2005–2006 which suggested that there was no probability of arising of these IAV strains in Korea through recombination [137].

T214

26540-26757

Sentence

denotes

Two novel isolates of swine H3N1 virus with high genomic similarity to each other were retrieved from two different swine farms in Korea during March–April 2006 which would be due to a common origin of these isolates.

T215

26758-26874

Sentence

denotes

These viruses had human-like H3 gene while other gene segments originated from swine influenza viruses within Korea.

T216

26875-27046

Sentence

denotes

High reactivity of the 52 swine sera samples to H3N1 virus antibodies suggested a previous exposure and probability of the swine to swine transmission of H3N1 virus [138].

T217

27047-27217

Sentence

denotes

The human to swine transmission of A(H1N1)pdm09 virus was reported in Chungbuk province where 42 A(H1N1)pdm09 virus isolates were recovered from swine lung tissues [139].

T218

27218-27338

Sentence

denotes

The reassortment between A(H1N1)pdm09 and swine H1N2 viruses emerged into a novel reassortant H1N2 virus in swine [140].

T219

27339-27501

Sentence

denotes

A triple-reassortant H3N2 virus was identified in swine during December 2011–May 2012 which indicated the IAV reassortment was taking place in Korean swine [141].

T220

27502-27683

Sentence

denotes

A swine fever eradication campaign identified nine A(H1N1)pdm09, two classical H1N1 and one H1N2 viruses in wild boars which were hunted and killed in South Korea during 2012 [142].

T221

27684-27798

Sentence

denotes

More recently, a complete genome sequence of H1N1 virus was reported from a domestic swine in Korea in 2016 [143].

T222

27800-27806

Sentence

denotes

3.2.7.

T223

27807-27815

Sentence

denotes

Thailand

T224

27816-27901

Sentence

denotes

The occurrence of IAV in Thai swine was first reported during November–December 1978.

T225

27902-28002

Sentence

denotes

Active H3N2 infection was detected in one swine while several other swine had H3N2 antibodies [144].

T226

28003-28086

Sentence

denotes

Two H1N1 virus isolates from Thai swine were first recovered in January 1988 [145].

T227

28087-28225

Sentence

denotes

Several studies reported H1N1, A(H1N1)pdm09, H1N2, and H3N2 viruses in swine exhibiting respiratory disease symptoms between 2000 to 2014.

T228

28226-28377

Sentence

denotes

Intriguingly, one swine sample was found co-infected with four IAV subtypes including H1N1, H1N2, H3N1, and H3N2 viruses [146,147,148,149,150,151,152].

T229

28378-28523

Sentence

denotes

The first evidence of H5N1 seroprevalence in Thai swine was documented in 2004 when eight H5N1 positive swine sera samples were identified [153].

T230

28524-28645

Sentence

denotes

Later ten H1N1 and two H3N2 virus isolates were retrieved from piglets aged between 4 to 12 weeks during 2008–2009 [154].

T231

28646-28912

Sentence

denotes

Interestingly, most of the virus isolates retrieved in this study were obtained from 4 to 8 week-old piglets which was in agreement of a previous report stating that swine influenza viruses can be successfully retrieved from piglets less than ten weeks of age [155].

T232

28913-29048

Sentence

denotes

A zoonotic transmission of IAV was reported at a Thai swine farm where all the swine were found positive for either H1N1 or H1N2 virus.

T233

29049-29200

Sentence

denotes

Interestingly, two farm owners, 46 swine handlers, four veterinarians, five farm cleaners and two farm office workers also reported IAV seroprevalence.

T234

29201-29370

Sentence

denotes

This study claimed that there was transmission of swine influenza viruses from swine to human however the possibility of human to swine transmission was ruled out [156].

T235

29371-29523

Sentence

denotes

After a respiratory disease outbreak in nursery piglets, 15 nasal swabs were found positive for A(H1N1)pdm09 virus between December 2009 and March 2010.

T236

29524-29717

Sentence

denotes

Fifteen sera samples of the farm workers along with three sera from dogs and one serum obtained from a cat were negative for IAV, hence the interspecies transmission of IAV was ruled out [157].

T237

29718-29999

Sentence

denotes

The first report of active infection with reassortant H1N1 virus in Thai swine appeared in February 2010 but the follow up screenings conducted after two and three months, respectively confirmed the cessation of the active infection as the viral RNA was not detected anymore [158].

T238

30000-30100

Sentence

denotes

The reshuffling and reassortment of IAV internal genes were reported in Thai swine in February 2012.

T239

30101-30255

Sentence

denotes

The HA and NA genes of H1N1 virus isolates clustered with the Eurasian swine-like IAV lineage while the H3N2 viruses diverged and formed a separate group.

T240

30256-30410

Sentence

denotes

All the internal genes of H1N1 and H3N2 virus isolates appeared to be derived from A(H1N1)pdm09 viruses which confirmed the events of reassortments [159].

T241

30412-30418

Sentence

denotes

3.2.8.

T242

30419-30426

Sentence

denotes

Vietnam

T243

30427-30587

Sentence

denotes

The events of reverse zoonoses were suggested after the detection of A(H1N1)pdm09 virus seroprevalence in Vietnamese swine during October 2009–March 2010 [160].

T244

30588-30803

Sentence

denotes

One more evidence of reverse zoonosis was identified during February–March 2010 after six triple-reassortant H3N2 viruses having a novel cluster of the Triple Reassortant Internal Gene (TRIG) cassette were isolated.

T245

30804-31022

Sentence

denotes

The HA and NA genes of these reassortant H3N2 isolates originated from human H3N2 viruses reported between 2004–2006 while the other six internal genes had a high similarity with the Korean and American isolates [161].

T246

31023-31213

Sentence

denotes

Two more studies reported the H1N1, A(H1N1)pdm09, HIN2, and H3N2 virus isolates during February 2010–December 2013 from clinically healthy swine with no influenza disease symptoms [162,163].

T247

31214-31364

Sentence

denotes

Additionally, the antibodies for A(H1N1)pdm09 and H3N2 viruses were detected in swine which suggested a past exposure of swine to these viruses [163].

T248

31366-31372

Sentence

denotes

3.2.9.

T249

31373-31378

Sentence

denotes

India

T250

31379-31511

Sentence

denotes

A high seroprevalence of H1N1, H2N2 and H3N2 viruses was detected in human and swine sera in Calcutta, India during 1982–1990 [164].

T251

31512-31669

Sentence

denotes

The first active infection of IAV in Indian swine appeared in 2009 when A(H1N1)pdm09 virus isolates were reported from a swine farm located in Uttar Pradesh.

T252

31670-31857

Sentence

denotes

Interestingly, the retrieved A(H1N1)pdm09 virus sequences were similar to the North American and Korean viruses which might be either because of trade or long-distance transmission [165].

T253

31859-31866

Sentence

denotes

3.2.10.

T254

31867-31874

Sentence

denotes

Lebanon

T255

31875-31999

Sentence

denotes

After an influenza outbreak on Lebanese poultry farms in 2005 the farmers fed the carcasses of the dead flocks to the swine.

T256

32000-32210

Sentence

denotes

Intriguingly, a following investigation found that three swine were seropositive for the H9N2 virus while approximately one-third of the poultry farm workers were seropositive either for H1 or H9 viruses [166].

T257

32211-32309

Sentence

denotes

These results revealed the interspecies transmission of IAV among poultry, farm workers and swine.

T258

32311-32318

Sentence

denotes

3.2.11.

T259

32319-32327

Sentence

denotes

Malaysia

T260

32328-32467

Sentence

denotes

The seroprevalence of H1N1 and H3N2 viruses in four to six-month-old Malaysian swine at 41 swine farms was reported during May–August 2005.

T261

32468-32539

Sentence

denotes

Co-infections of H1N1 and H3N2 were detected in 29 swine samples [167].

T262

32541-32548

Sentence

denotes

3.2.12.

T263

32549-32553

Sentence

denotes

Laos

T264

32554-32698

Sentence

denotes

The seroprevalence of H3N2 virus in swine samples obtained from the slaughterhouses in Laos was reported between May 2008 to January 2009 [168].

T265

32700-32707

Sentence

denotes

3.2.13.

T266

32708-32714

Sentence

denotes

Russia

T267

32715-32815

Sentence

denotes

A full-length genome sequence of a reassortant H1N1 virus was reported from a Russian swine in 2016.

T268

32816-32961

Sentence

denotes

The HA and NA genes of this virus isolate shared 90% identity with the H1N1 viruses that were reported from humans in the USA in the 1980s [169].

T269

32963-32970

Sentence

denotes

3.2.14.

T270

32971-32977

Sentence

denotes

Taiwan

T271

32978-33116

Sentence

denotes

The human to swine transmission of IAV was speculated after IAV antibodies were detected in 147 Taiwanese swine during June 1969–May 1970.

T272

33117-33211

Sentence

denotes

The results were further confirmed with virus isolation which retrieved 13 IAV isolates [170].

T273

33212-33369

Sentence

denotes

More recently, IBV of Victoria/B lineage was detected in swine nasal swab samples collected from apparently healthy swine at three swine farms in 2014 [171].

T274

33371-33378

Sentence

denotes

3.2.15.

T275

33379-33388

Sentence

denotes

Indonesia

T276

33389-33492

Sentence

denotes

An active IAV infection in 52 swine within four provinces in Indonesia was identified during 2005–2009.

T277

33493-33579

Sentence

denotes

Interestingly, 39 H5N1 virus isolates were successfully retrieved and sequenced [172].

T278

33581-33588

Sentence

denotes

3.2.16.

T279

33589-33598

Sentence

denotes

Sri Lanka

T280

33599-33728

Sentence

denotes

The first report of influenza in Sri Lankan swine was documented during 2004–2005 after one human-like H3N2 virus was identified.

T281

33729-33806

Sentence

denotes

Later, A(H1N1)pdm09 virus isolates were identified in swine during 2009–2012.

T282

33807-33877

Sentence

denotes

A spillover of these viruses from human to swine was speculated [173].

T283

33879-33886

Sentence

denotes

3.2.17.

T284

33887-33897

Sentence

denotes

Kazakhstan

T285

33898-34071

Sentence

denotes

One recent investigation in Kazakhstan during 2017–2018 identified nine H1N1 and eight H3N2 viruses in human while seven H1N1 and four H3N2 viruses were identified in swine.

T286

34072-34200

Sentence

denotes

Interestingly, 10 of the human samples were also positive for IBV infection while the swine samples were negative for IBV [174].

T287

34201-34457

Sentence

denotes

In summary, the influenza viruses have been reported in swine in 16 Asian countries including China, Japan, Thailand, South Korea, Viet Nam, Cambodia, Taiwan, India, Bhutan, Russia, Laos, Malaysia, Lebanon, Indonesia, Kazakhstan, and Sri Lanka (Figure 4B).

T288

34458-34677

Sentence

denotes

Apart from the most common IAV strains of H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses, several avian-origin H5N1, H5N3, H4N1, H4N6, H4N8, H6N6, H7N9, H9N2, and H10N5 influenza viruses were also reported in Chinese swine.

T289

34678-34759

Sentence

denotes

Horse to swine transmission of equine influenza virus H3N8 was reported in China.

T290

34760-34888

Sentence

denotes

Additionally, avian-origin H7N2, H5N2 viruses were identified in South Korean swine while H5N1 was reported in Indonesian swine.

T291

34889-35014

Sentence

denotes

Interestingly, after the swine were fed upon dead poultry carcasses in Lebanon the H9N2 virus was detected in Lebanese swine.

T292

35015-35188

Sentence

denotes

The IBV was reported in Asian swine only in Taiwan while strains of ICV were reported in swine in China and Japan while IDV was recently reported in Chinese swine (Table 1).

T293

35190-35194

Sentence

denotes

3.3.

T294

35195-35234

Sentence

denotes

Influenza Viruses in Swine in Australia

T295

35235-35367

Sentence

denotes

Swine influenza was first reported in Australian swine only in 2009 after a swine farm owner reported coughing symptoms among swine.

T296

35368-35509

Sentence

denotes

Simultaneously, some of the human workers on the farm also developed influenza like symptoms and hence stayed out of the farm until recovery.

T297

35510-35641

Sentence

denotes

Later, the farm owner also developed similar symptoms following which he was tested for A(H1N1)pdm09 virus which resulted positive.

T298

35642-35852

Sentence

denotes

As a result, a representative number of swine showing coughing symptoms and loss in appetite were sampled for molecular diagnostics and serology which confirmed that 12 swine were positive for H1N1 virus [175].

T299

35853-36029

Sentence

denotes

Second report of IAV in Australian swine appeared on a Queensland farm in August 2009 when a veterinarian observed elevated temperature, coughing and loss of appetite in swine.

T300

36030-36181

Sentence

denotes

Simultaneously, two of the staff members on the farm exhibited influenza-like symptoms and hence were sampled for diagnostic testing using nasal swabs.

T301

36182-36289

Sentence

denotes

Interestingly, both the staff members and four of the swine were found positive for the A(H1N1)pdm09 virus.

T302

36290-36514

Sentence

denotes

Sequencing identified that the HA gene of A(H1N1)pdm09 virus retrieved from a staff member was identical to the virus retrieved from the swine which suggested transmission of A(H1N1)pdm09 virus between swine and human [176].

T303

36515-36718

Sentence

denotes

Third report of IAV in Australian swine appeared when a respiratory disease outbreak in swine and the farm workers occurred in Perth, Western Australia during 2012 which identified 43 IAV positive swine.

T304

36719-36857

Sentence

denotes

Sanger sequencing of HA and NA genes identified six novel HIN2, three novel H3N2, one A(H1N1)pdm09 and two seasonal H3N2 viruses in swine.

T305

36858-36955

Sentence

denotes

On the contrary, only one out of eight human workers were found positive for seasonal H3N2 virus.

T306

36956-37078

Sentence

denotes

This study could not conclude the event of zoonotic transmission of IAV between swine and human workers at the farm [177].

T307

37079-37278

Sentence

denotes

The fourth report of IAV was documented when 14 IAV positive swine were identified at a commercial swine farm in Western Australia during July–September 2012 and later during September–November 2016.

T308

37279-37360

Sentence

denotes

Additionally, 17 swine were determined to be IAV positive in southern Queensland.

T309

37361-37549

Sentence

denotes

The complete genomes of 10 IAV isolates retrieved in Western Australia and Queensland were successfully sequenced which identified seven H1N2, two human-like H3N2 and one H1N1 virus [178].

T310

37550-37678

Sentence

denotes

Overall, four reports of IAV outbreaks in swine in New South Wales, Queensland and Western Australia were available (Figure 4C).

T311

37679-37798

Sentence

denotes

The H1N1, H1N2, H3N2 and A(H1N1)pdm09 subtypes have been reported from Australian swine with relatively low prevalence.

T312

37800-37804

Sentence

denotes

3.4.

T313

37805-37841

Sentence

denotes

Influenza Viruses in Swine in Europe

T314

37843-37849

Sentence

denotes

3.4.1.

T315

37850-37857

Sentence

denotes

Belgium

T316

37858-38024

Sentence

denotes

The H1N1 virus was identified in swine lung tissues or trachea of two of the deceased sows after an influenza-like disease erupted at two swine farms in January 1979.

T317

38025-38130

Sentence

denotes

Interestingly, it was also reported that the identical virus was detected in wild ducks in Germany [179].

T318

38131-38354

Sentence

denotes

Since it was already established that H1N1 from wild ducks can successfully infect swine if inoculated via intranasal route [179] hence this observation suggested the transmission of H1N1 from wild ducks to the swine [180].

T319

38355-38508

Sentence

denotes

A second investigation isolated three avian-like H1N1, two H1N2 and twelve human-like H3N2 viruses from eight commercial swine farms in March 1999 [181].

T320

38510-38516

Sentence

denotes

3.4.2.

T321

38517-38524

Sentence

denotes

Denmark

T322

38525-38619

Sentence

denotes

Denmark has been running a passive surveillance program for IAV detection in swine since 2011.

T323

38620-38792

Sentence

denotes

The H1N2 virus having the H1 gene which evolved from H1N1 avian-like viruses and N2 gene which evolved from human H3N2 viruses was reported in swine during 2011–2013 [182].

T324

38793-38893

Sentence

denotes

This was an example of how IAV can evolve through reassortment and may emerge into a new IAV strain.

T325

38894-39096

Sentence

denotes

The other investigation included swine sampling at different time intervals to assess the persistence of IAV shedding in Danish swine which detected one avian-like H1N1 and 107 reassortant H1N2 viruses.

T326

39097-39198

Sentence

denotes

This study observed that most of the swine were shedding IAV right before achieving six weeks of age.

T327

39199-39284

Sentence

denotes

Surprisingly, a piglet as young as just three days was found infected with IAV [183].

T328

39285-39588

Sentence

denotes

Two H3N2 isolates having H3 genes from seasonal human influenza along with internal genes that originated from A(H1N1)pdm09 virus and NA genes from contemporary N2 swine influenza viruses that have been in circulation in Denmark were retrieved from young piglets at two locations during 2011–2014 [184].

T329

39589-39737

Sentence

denotes

H3N2 virus was also detected from piglets having respiratory illness and from sows with reproductive problems in commercial piggeries in 2014 [184].

T330

39739-39745

Sentence

denotes

3.4.3.

T331

39746-39760

Sentence

denotes

United Kingdom

T332

39761-39894

Sentence

denotes

The H3N2 virus antibodies were first detected in English swine in 1973 which revealed the past exposure of swine to H3N2 virus [185].

T333

39895-40020

Sentence

denotes

Later, the antibodies for H1N1 and H3N2 viruses were detected in swine at a slaughterhouse in England during 1991–1992 [186].

T334

40021-40144

Sentence

denotes

Interestingly, this serological investigation also reported the antibodies for IBV in eight and for ICV in 198 swine [186].

T335

40145-40487

Sentence

denotes

A molecular investigation identified a novel H1N7 virus in swine in England which had six of its RNA segments closely related to those of human viruses while two RNA segments were identical to those of equine viruses which concluded that the H1N7 strain may have evolved due to reassortment between human H1 and equine H7N7 viruses [187,188].

T336

40488-40744

Sentence

denotes

The first report of A(H1N1)pdm09 virus in English swine appeared in September 2009 when histology and immunofluorescence assays followed by molecular diagnostics and sequencing confirmed four A(H1N1)pdm09 virus infected swine in the Northern Ireland [189].

T337

40745-40972

Sentence

denotes

After this, 17 more A(H1N1)pdm09 virus isolates were reported in swine in England during September 2009–October 2010 which revealed that A(H1N1)pdm09 virus was in circulation in English swine during the 2009 flu pandemic [190].

T338

40973-41202

Sentence

denotes

The same year, four H1N2 virus isolates were reported in English swine which had six internal genes of A(H1N1)pdm09 virus along with HA and NA genes of H1N2 virus hence were identified as the novel reassortant H1N2 strains [191].

T339

41203-41307

Sentence

denotes

In a more recent study, two more IAV positive swine were identified in the United Kingdom in 2016 [192].

T340

41309-41315

Sentence

denotes

3.4.4.

T341

41316-41323

Sentence

denotes

Finland

T342

41324-41711

Sentence

denotes

However the first report of seroprevalence of H1N1 virus in Finnish swine appeared in 2008 during an investigation which detected H1N1 virus antibodies in swine at seven swine farms which further increased to 24 swine farms in 2009 [193] but the first isolate of avian-like swine H1N1 virus (indicative of active infection) was detected from the lung tissues of a swine in February 2009.

T343

41712-41801

Sentence

denotes

Later, the first A(H1N1)pdm09 virus in Finnish swine was detected in November 2009 [193].

T344

41802-41930

Sentence

denotes

Three more swine were identified with IAV antibodies during May 2011–January 2014 which was due to a past exposure to IAV [194].

T345

41932-41938

Sentence

denotes

3.4.5.

T346

41939-41945

Sentence

denotes

France

T347

41946-42171

Sentence

denotes

The H1N1 viruses in turkey and swine were identified after the swine influenza outbreak hit the turkey population in Brittany, France in February 1983 which suggested that IAV transmission happened from swine to turkey [195].

T348

42172-42302

Sentence

denotes

Later two strains of H1N2 virus were isolated from six swine exhibiting influenza-like illness in Brittany during 1987–1988 [196].

T349

42303-42436

Sentence

denotes

Another investigation reported H1N1, H1N2, and H3N2 viruses in swine herds experiencing respiratory disease in Brittany region [197].

T350

42437-42686

Sentence

denotes

A negative prevalence of IAV was reported in wild boars in Camargue during September 2009–November 2010 given that all the 315 nasal swabs obtained from either hunted or trapped wild boars along with all the sera samples were negative for IAV [198].

T351

42687-42811

Sentence

denotes

A more recent investigation reported the zoonotic transmission of A(H1N1)pdm09 virus from swine to a farmer in January 2018.

T352

42812-43060

Sentence

denotes

This farmer along with a veterinarian collected nasal swab samples from three pregnant sows exhibiting influenza-like illness on the swine farm and submitted to a local diagnostic laboratory for analysis which, as a result, were found IAV positive.

T353

43061-43152

Sentence

denotes

Few days later, the farmer and the veterinarian both developed the influenza-like symptoms.

T354

43153-43214

Sentence

denotes

The farmer was later diagnosed with A(H1N1)pdm09 virus [199].

T355

43216-43222

Sentence

denotes

3.4.6.

T356

43223-43230

Sentence

denotes

Germany

T357

43231-43325

Sentence

denotes

Sixty-five IAV positive wild boars were identified across five German states during 1997–2006.

T358

43326-43408

Sentence

denotes

Cloning and sequencing identified H1N1 and H3N2 viruses in these wild boars [200].

T359

43409-43522

Sentence

denotes

Later thirteen H1N1, three reassorted A(H1N1)pdm09 and four H1N2 viruses were detected in swine during 2009–2010.

T360

43523-43742

Sentence

denotes

Interestingly, the A(H1N1)pdm09 virus isolates had high similarity with the A(H1N1)pdm09 viruses reported earlier in humans within Germany which suggested a reverse zoonotic transmission of the A(H1N1)pdm09 virus [201].

T361

43743-44052

Sentence

denotes

A nationwide sero-surveillance identified 12,585 swine with H1N1, 9,566 swine with human-like H1N2, 12,220 swine with human-like H3N2 and 11,086 swine with A(H1N1)pdm09 virus antibodies during June 2009–December 2012 which reflected a high seroprevalence of influenza viruses in German swine population [202].

T362

44053-44165

Sentence

denotes

Later 273 IAV positive swine exhibiting influenza-like illness were detected between January 2010–December 2013.

T363

44166-44269

Sentence

denotes

Subtyping successfully distinguished 198 of 273 samples into H1N1, H1N2, H3N2 and A(H1N1)pdm09 viruses.

T364

44270-44388

Sentence

denotes

The H1N1 virus was the most widely occurring in German swine while A(H1N1)pdm09 virus had the lowest prevalence [203].

T365

44390-44396

Sentence

denotes

3.4.7.

T366

44397-44403

Sentence

denotes

Greece

T367

44404-44609

Sentence

denotes

The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were detected in swine sera samples collected from apparently healthy swine at 42 swine farms during 2002–2004 and from 46 swine farms during 2010–2012 [204].

T368

44611-44617

Sentence

denotes

3.4.8.

T369

44618-44623

Sentence

denotes

Italy

T370

44624-44783

Sentence

denotes

The seropositivity of Italian swine to H3N2 virus was first reported during December 1976–November 1977 when 24 swine were detected with H3N2 antibodies [205].

T371

44784-44949

Sentence

denotes

The first report of H1N1 active infection in Italian swine appeared during an influenza disease outbreak between 1977 to 1986 which identified 63 H1N1 viruses [206].

T372

44950-45085

Sentence

denotes

Further, four H3N2 viruses were detected in swine nasal swabs originated from three swine farms and an abattoir during 1981–1982 [207].

T373

45086-45160

Sentence

denotes

Later 47 H1N1 and 37 H3N2 viruses were detected in swine during 1992–1995.

T374

45161-45343

Sentence

denotes

Interestingly, four human sera samples were also positive for H1N1 and 77 samples were positive for H3N2 viruses which might be due to the transmission between human and swine [208].

T375

45344-45462

Sentence

denotes

Further IAV seroprevalence was detected in the age group of three-month to four-year old swine during 2002–2004 [209].

T376

45463-45633

Sentence

denotes

The first report of A(H1N1)pdm09 virus in Italian swine appeared after a respiratory disease outbreak in piggeries in Lombardia region of Northern Italy in November 2009.

T377

45634-45743

Sentence

denotes

Piglets experienced diarrhea and weight loss while the sows experienced reduction in reproduction rate [210].

T378

45744-45963

Sentence

denotes

Two more A(H1N1)pdm09 virus isolates were reported in female swine in Sicily in December 2009 [211] while five isolates of A(H1N1)pdm09 virus were identified in swine at three different locations during 2011–2012 [212].

T379

45964-46174

Sentence

denotes

A novel strain of reassorted H1N2 virus having 99–100% identity through six gene segments with A(H1N1)pdm09 virus along with HA and NA genes similar to H1N2 virus was reported in swine in Mantua Province [213].

T380

46175-46256

Sentence

denotes

Reassorted H1N2 viruses were again detected in 34 piglets during 2013–2014 [214].

T381

46257-46392

Sentence

denotes

Seroprevalence of Italian wild boars with one H1N1, ten H1N2, and one H3N2 viruses at two different locations was reported during 2012.

T382

46393-46512

Sentence

denotes

On the contrary, active infection was found only in three wild boars whose nasal swabs were positive for the IAV [215].

T383

46513-46657

Sentence

denotes

One more investigation reported active infection of IAV in 12 wild boars while 78 wild boars had IAV antibodies during July–December 2012 [216].

T384

46658-46768

Sentence

denotes

Further molecular and serological investigations detected avian-like H1N1 viruses in Italian wild boars [216].

T385

46769-46977

Sentence

denotes

The first complete genome sequence of IDV in Italian swine was retrieved from a symptomatic sow in 2015 which was identified to be closely related to the IDV sequence reported in Oklahoma swine in 2011 [217].

T386

46978-47188

Sentence

denotes

Further IDV prevalence in Italian swine was reported when 14, three and four swine were found positive for IDV antibodies in Veneto, Emilia Romagna and Lombardia regions, respectively during June 2015–May 2016.

T387

47189-47332

Sentence

denotes

As a result, swine clinical samples collected during 2013–2014 were investigated retrospectively for IDV prevalence but were reported negative.

T388

47333-47443

Sentence

denotes

An extended serological investigation detected IDV antibodies in 364 swine sera samples collected during 2015.

T389

47444-47546

Sentence

denotes

These findings suggested that IDV was in circulation in Italian swine population only after 2014 [45].

T390

47548-47554

Sentence

denotes

3.4.9.

T391

47555-47560

Sentence

denotes

Spain

T392

47561-47811

Sentence

denotes

Isolation and characterization of 12 H3N2, nine H1N1 and one H1N2 viruses reported the prevalence of influenza viruses for the first time in Spanish swine herds experiencing the respiratory illness and pneumonia during November 2001–April 2004 [218].

T393

47812-47947

Sentence

denotes

More strains of H1N1, H1N2 and H3N2 viruses were isolated, sequenced and characterized in Spanish swine during 2006–2011 [219,220,221].

T394

47948-48212

Sentence

denotes

Interestingly, five H1N1, three H1N2, and four H3N2 virus isolates retrieved between January 2010 and August 2011 had significant similarities with other European isolates which was an evidence of continent-wide transmission of these swine influenza viruses [220].

T395

48214-48221

Sentence

denotes

3.4.10.

T396

48222-48232

Sentence

denotes

Luxembourg

T397

48233-48406

Sentence

denotes

A molecular investigation reported a negative prevalence of IDV in swine in Luxembourg during 2009 but later successfully detected three IDV positive swine during 2014–2015.

T398

48407-48607

Sentence

denotes

Further, the serological investigation confirmed that swine in Luxembourg were free from IDV during 2012 but interestingly, IDV antibodies were detected in 17 swine samples collected during 2014–2015.

T399

48608-48859

Sentence

denotes

These observations suggested that IDV was not in circulation in swine in Luxembourg during 2009–2012 but became prevalent at a low frequency later during 2014–2015 [46] which was almost the same time IDV was reported in Italian swine populations [45].

T400

48861-48868

Sentence

denotes

3.4.11.

T401

48869-48884

Sentence

denotes

The Netherlands

T402

48885-49117

Sentence

denotes

A serological investigation of swine in the Netherlands identified 601 H1N1, 584 H1N2, and 229 H3N2 virus antibodies in 29 swine herds during January–May 1999 [222] with no further evidence of IAV in swine in the country after that.

T403

49119-49126

Sentence

denotes

3.4.12.

T404

49127-49133

Sentence

denotes

Norway

T405

49134-49426

Sentence

denotes

After the 18 swine which were experiencing influenza-like illness were found infected with A(H1N1)pdm09 virus on a Norwegian swine farm in October 2009 the surveillance was expanded to the 39 nearby swine farms which determined that 23 of these farms were positive for the A(H1N1)pdm09 virus.

T406

49427-49556

Sentence

denotes

Intriguingly, one human subject at the index farm who had influenza-like symptoms was also found positive for A(H1N1)pdm09 virus.

T407

49557-49701

Sentence

denotes

This study suggested that the symptoms first appeared in the human subject at the index farm and later the disease got transmitted to the swine.

T408

49702-49813

Sentence

denotes

Hence the findings of this study suggested the reverse zoonosis of the influenza virus from human to pig [223].

T409

49814-49962

Sentence

denotes

Further molecular and serological investigations identified 48 more swine herds that were positive for IAV during September 2009–October 2010 [224].

T410

49963-50149

Sentence

denotes

A more comprehensive nation-wide surveillance in Norwegian swine identified 16 A(H1N1)pdm09 virus positive swine herds during 2009 which later increased to 190 swine herds in 2010 [225].

T411

50150-50338

Sentence

denotes

Later 194 more swine were found infected with A(H1N1)pdm09 virus in Norway between April and July 2011 and reported that the IAV infected swine took longer to weigh 100 kg body mass [226].

T412

50340-50347

Sentence

denotes

3.4.13.

T413

50348-50354

Sentence

denotes

Poland

T414

50355-50505

Sentence

denotes

The first active IAV infection in swine in Poland was reported in 2010 when 21 oral fluid samples collected from three swine farms detected IAV [227].

T415

50506-50612

Sentence

denotes

Soon after, five avian-like H1N1 viruses were reported from the swine lung tissues during 2011–2013 [228].

T416

50613-50774

Sentence

denotes

Later a serological surveillance identified 1212 H1N1, 851 H1N2, 1012 H3N2, and 572 A(H1N1)pdm09 virus antibodies in swine during March 2011–February 2015 [229].

T417

50775-50941

Sentence

denotes

Surprisingly, 34 of these swine had antibodies against all four IAV subtypes i.e., H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses [229] suggesting the past co-infections.

T418

50943-50950

Sentence

denotes

3.4.14.

T419

50951-50965

Sentence

denotes

Czechoslovakia

T420

50966-51132

Sentence

denotes

The human-like H3N2 virus was isolated from a swine in Czechoslovakia during 1969–1972 [230]; however, no other reports ever appeared from the country in later years.

T421

51134-51141

Sentence

denotes

3.4.15.

T422

51142-51149

Sentence

denotes

Hungary

T423

51150-51269

Sentence

denotes

Complete genome of an H1N1 virus was reported from a Hungarian swine having fever and conjunctivitis in May 2011 [231].

T424

51270-51333

Sentence

denotes

This was the only report of H1N1 virus in the swine in Hungary.

T425

51335-51342

Sentence

denotes

3.4.16.

T426

51343-51393

Sentence

denotes

Multi-National Surveillances in European Countries

T427

51394-51704

Sentence

denotes

A large-scale investigation across seven European countries reported a high seroprevalence (˃62%) of IAV antibodies in swine populations of Belgium, Germany, Spain, Italy while a relatively lower (˂21.25%) seroprevalence was observed in swine populations of Czech Republic, Poland and Ireland during 2002–2003.

T428

51705-51894

Sentence

denotes

Antibodies against H1N1, H1N2, and H3N2 viruses were reported in swine from the European countries under surveillance except Poland where swine had antibodies against only H1N1 virus [232].

T429

51895-52061

Sentence

denotes

A virological surveillance across five European countries including Belgium, United Kingdom, Italy, France and Spain reported 169 IAV positive swine during 2006–2008.

T430

52062-52251

Sentence

denotes

The H1N1, H1N2, and H3N2 viruses were detected in swine from Belgium, Italy, and Spain while the samples from United Kingdom and France were found infected with H1N1 and H1N2 viruses [233].

T431

52252-52692

Sentence

denotes

Briefly, the virological and/or serological prevalence of influenza viruses in European countries (Figure 4D) identified the strains of H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses in swine populations of the United Kingdom, Ireland, Italy, Germany, France, Norway, Finland, Denmark, Belgium, Spain, Poland, Greece, Hungary, Netherlands, Czech Republic, and Czechoslovakia while the swine in Luxembourg and Italy were found infected with IDV.

T432

52694-52698

Sentence

denotes

3.5.

T433

52699-52742

Sentence

denotes

Influenza Viruses in Swine in North America

T434

52744-52750

Sentence

denotes

3.5.1.

T435

52751-52757

Sentence

denotes

Canada

T436

52758-52878

Sentence

denotes

Shortly after a respiratory disease outbreak in swine in Manitoba, an autopsy was done on a dead swine on March 1, 1967.

T437

52879-53042

Sentence

denotes

The histopathology confirmed the bronchitis in the deceased swine and a strain of IAV designated as “S/Manitoba/647/67” was characterized using IAV antisera [234].

T438

53043-53186

Sentence

denotes

The first report of H1N1 virus in Canadian swine appeared in Quebec during 1980s–1990s when five genotypes of H1N1 virus were identified [235].

T439

53187-53308

Sentence

denotes

Since then several studies have reported H1N1, H1N2 and H3N2 viruses in Canadian swine [236,237,238,239,240,241,242,243].

T440

53309-53491

Sentence

denotes

Another study reported nine isolates of swine influenza viruses with an antigenic variant from the sick swine having proliferative pneumonia in Quebec, Canada during 1990–1991 [244].

T441

53492-53653

Sentence

denotes

In a retrospective diagnosis, only one formalin-fixed paraffin embedded swine lung tissue collected during 1991 was found IAV positive with immunohistochemistry.

T442

53654-53785

Sentence

denotes

This investigation suggested that immunohistochemistry can be useful in retrospective diagnosis of the swine influenza virus [245].

T443

53786-53966

Sentence

denotes

The broncho-intestinal pneumonia in lung tissues of dead swine was reported on a swine farm which exhibited disease symptoms including coughing, weight loss, and labored breathing.

T444

53967-54172

Sentence

denotes

Interestingly, before the onset of the disease symptoms, this farm conducted a routine serological surveillance of influenza virus which identified H1N1 virus in only one of the twelve swine samples [246].

T445

54173-54295

Sentence

denotes

Following this surveillance, a three-month old swine from the same farm was found positive for avian influenza virus H4N6.

T446

54296-54356

Sentence

denotes

The complete genome of this H4N6 virus was reported in 1999.

T447

54357-54427

Sentence

denotes

This was the first ever report of an avian-origin H4N6 virus in swine.

T448

54428-54671

Sentence

denotes

The proximity of the swine farm to a natural lake where several wild bird species including waterfowls which were reported to visit frequently might be the reason behind the introduction of this avian influenza virus strain to the swine [246].

T449

54672-54828

Sentence

denotes

Later three avian-origin H3N3 influenza virus isolates were recovered from swine in eastern Ontario exhibiting weight loss and coughing during October 2001.

T450

54829-54937

Sentence

denotes

On a nearby farm located approximately 30 kms away, another H3N3 virus isolate was recovered from the swine.

T451

54938-55006

Sentence

denotes

There was no recorded movement of the swine between these two farms.

T452

55007-55110

Sentence

denotes

Since these were avian-origin H3N3 viruses hence the role of birds in transmission cannot be ruled out.

T453

55111-55260

Sentence

denotes

Later, on a third farm, where an influenza like disease had been affecting mainly the nursery piglets, an H1N1 virus was recovered in May 2002 [247].

T454

55261-55475

Sentence

denotes

Reassortant H1N1 and H1N2 viruses were detected in swine nasal swab or lung tissue samples obtained from three-week old piglets and sows exhibiting typical influenza-like symptoms in Ontario during 2003–2004 [248].

T455

55476-55646

Sentence

denotes

First triple-reassortant (avian/classical swine/human triple-reassortant) H3N2 viruses from four swine and one human nasal samples were identified in Ontario during 2005.

T456

55647-55850

Sentence

denotes

The phylogenetic analysis determined that all the virus sequences were 100% identical to each other which apparently emerged from triple-reassortant H3N2 viruses reported in US based swine in 1988 [249].

T457

55851-56010

Sentence

denotes

One more report of triple-reassortant H3N2 (trH3N2) viruses appeared on the swine farms located in Saint-Hyacinthe, Assomption and Saint-Foy during early 2009.

T458

56011-56158

Sentence

denotes

The trH3N2 viruses identified in this study were determined to be closely related to North American/Canadian trH3N2 viruses reported earlier [250].

T459

56159-56362

Sentence

denotes

Later A(H1N1)pdm09 and H1N1 viruses having internal genes of triple reassortant H3N2 virus were reported in swine in four provinces including Manitoba, Alberta, Saskatchewan and Quebec during 2009 [251].

T460

56363-56512

Sentence

denotes

The first evidence of A(H1N1)pdm09 virus in Canadian swine appeared in 2009 after the human workers at a swine farm developed influenza-like illness.

T461

56513-56625

Sentence

denotes

The investigation identified that two farm workers along with 56 swine were positive for the A(H1N1)pdm09 virus.

T462

56626-56701

Sentence

denotes

Transmission of A(H1N1)pdm09 virus from human to swine was suggested [252].

T463

56702-56839

Sentence

denotes

The same year 17 more swine were detected with A(H1N1)pdm09 virus after a respiratory disease outbreak hit the Alberta swine farms [253].

T464

56840-57001

Sentence

denotes

A reverse zoonotic transmission of A(H1N1)pdm09 virus to swine from a human subject who visited Mexico and returned to the swine farm was reported in April 2009.

T465

57002-57165

Sentence

denotes

As a result, ten swine having severe disease were sacrificed for necropsy which identified lesions in the bronchioles corresponding to the influenza virus disease.

T466

57166-57231

Sentence

denotes

Virus isolation and sequencing identified the A(H1N1)pdm09 virus.

T467

57232-57404

Sentence

denotes

Additionally, A(H1N1)pdm09 virus was identified in two more human subjects who were exposed to the swine hence indicated the occurrence of zoonoses on the swine farm [254].

T468

57405-57509

Sentence

denotes

Later during summer 2009, ten more A(H1N1)pdm09 viruses from five swine herds in Manitoba were reported.

T469

57510-57628

Sentence

denotes

Virus shedding was observed up to 20 days post-infection after the appearance of the clinical symptoms in swine [255].

T470

57629-57860

Sentence

denotes

This observation was in agreement of a previous report which documented the experimental infection of swine in the laboratory and determined that virus shedding occurs until 11th day after appearance of the clinical symptoms [256].

T471

57861-58025

Sentence

denotes

Another investigation reported nine A(H1N1)pdm09 and four H3N2 viruses after an influenza-like disease outbreak on a Quebec based swine farm in December 2010 [257].

T472

58026-58321

Sentence

denotes

The effect of microclimatic conditions on the transmission dynamics of swine IAV in the barns was studied which observed that high relative humidity in the environment during summer months suppresses the aerosol transmission of the droplets which in turn decreases the transmission of IAV [240].

T473

58322-58594

Sentence

denotes

The high relative humidity in the environment would facilitate the generation of larger droplets which do not tend to shrink easily and hence are less likely to be aerosol transmitted to a longer distance as they fall on the ground quickly after their formation [240,258].

T474

58595-58681

Sentence

denotes

As a result, a lower transmission of IAV is observed usually during the summer months.

T475

58682-58800

Sentence

denotes

On the contrary, the IAV transmission increases during winter months when relative humidity is relatively lower [258].

T476

58802-58808

Sentence

denotes

3.5.2.

T477

58809-58822

Sentence

denotes

United States

T478

58823-58952

Sentence

denotes

The IAV was first isolated from the nasal discharge of a swine in the United States in 1931 [34] and from the human in 1933 [35].

T479

58953-59230

Sentence

denotes

The first report of human-origin IAV in swine appeared in the United States on 24 May 1937 after an unexpected result was observed when the serum sample of a sick swine obtained from a State Prison Farm located in New Jersey neutralized the antibodies of human influenza virus.

T480

59231-59361

Sentence

denotes

A series of investigations made a strikingly new observation that swine had suffered from a human strain of influenza virus [259].

T481

59362-59517

Sentence

denotes

Serological investigations conducted during 1950s suggested that the weight loss and mortalities among swine were due to swine influenza viruses [260,261].

T482

59518-59642

Sentence

denotes

Swine influenza viruses were isolated from febrile swine at nine occasions during 1965–1968 in Wisconsin and Nebraska [262].

T483

59643-59756

Sentence

denotes

Additionally, swine influenza antibodies were also detected in swine sera samples collected from six farms [262].

T484

59757-60030

Sentence

denotes

A virological surveillance conducted in Memphis, Tennessee and Madison, Wisconsin during May 1976 to June 1977 successfully isolated 478 influenza viruses from swine nasal swabs collected at abattoirs; approximately 300 of which were characterized to be swine H1N1 viruses.

T485

60031-60163

Sentence

denotes

Additionally, the serological surveillance identified that 21% of the 9400 swine sera samples had swine H1N1 virus antibodies [263].

T486

60164-60312

Sentence

denotes

A small percentage (1.4%) of swine sera samples were found positive for the swine H3N2 viruses which was further confirmed by virus isolation [263].

T487

60313-60434

Sentence

denotes

Interestingly, this study identified inter-species transmission of swine influenza viruses between human and swine [263].

T488

60435-60578

Sentence

denotes

A novel swine-origin H1N1 virus termed as “A/New Jersey/76 (Hsw1N1)” was detected at Fort Dix Army training camp in New Jersey in January 1976.

T489

60579-60639

Sentence

denotes

The outbreak was localized and was limited to Fort Dix only.

T490

60640-60804

Sentence

denotes

As a result, 230 soldiers were found infected with this novel virus; 13 of which had severe respiratory disease with one death due to viral pneumonia [264,265,266].

T491

60805-60964

Sentence

denotes

Since this novel swine-origin H1N1 virus quickly disappeared from Fort Dix hence the epidemiology and the origin of the disease could not be ascertained [264].

T492

60965-61083

Sentence

denotes

The H1N1 and H3N2 virus antibodies were detected in swine sera collected from an abattoir in North-West United States.

T493

61084-61180

Sentence

denotes

Interestingly, a higher IAV seroprevalence was observed during the Fall and early winter months.

T494

61181-61314

Sentence

denotes

Virus isolation and sequencing identified that the H1N1 viruses were closely related to the classical H1 swine influenza virus [267].

T495

61315-61471

Sentence

denotes

Classical swine-like H1N1 and triple-reassortant H3N2 viruses were identified in swine samples collected across 23 states in the USA during 1998–1999 [268].

T496

61472-61648

Sentence

denotes

The Minnesota Veterinary Diagnostic Laboratory (MVDL) detected large number of H1N1, H1N2 and H3N2 subtypes of IAV in swine samples during 1998–2001 and again during 2007–2009.

T497

61649-61742

Sentence

denotes

Interestingly, some of the samples were co-infected with H1N1 and H3N2 viruses [269,270,271].

T498

61743-61968

Sentence

denotes

A second-generation reassortant H1N2 virus having genes from a reassortant H3N2 and classical H1 swine influenza viruses was obtained from the lung tissue samples of a dead sow at an Indiana swine farm in November 1999 [272].

T499

61969-62152

Sentence

denotes

A novel subtype of H3N1 virus termed as “A/Swine/Minnesota/00395/2004 (H3N1)” was identified during a severe respiratory disease outbreak on a swine farm in Minnesota in October 2004.

T500

62153-62444

Sentence

denotes

Sequencing observed that the HA gene of this strain was closely related to swine influenza H3N2 virus while the NA gene was related to classical H1N1 virus which suggested that the novel H3N1 virus emerged due to reassortment between H1N1 and H3N2 viruses in the Midwest United States [273].

T501

62445-62674

Sentence

denotes

Further an H2N3 subtype of IAV which may have emerged as a result of a reassortment between avian and swine influenza viruses was identified on a commercial swine farm in Minnesota in April 2006 and again in September 2006 [274].

T502

62675-62926

Sentence

denotes

The first evidence of A(H1N1)pdm09 virus infection in US swine appeared when four A(H1N1)pdm09 and one triple-reassortant H1N2 viruses were identified and characterized in the exhibition swine in the states of Minnesota and South Dakota in 2009 [275].

T503

62927-63144

Sentence

denotes

During last ten years, a large number of H1N1, H1N2, H3N2, A(H1N1)pdm09 along with reassortant IAV subtypes have been reported in the US swine populations [243,276,277,278,279,280,281,282,283,284,285,286,287,288,289].

T504

63145-63261

Sentence

denotes

The United States has a large feral swine population which is considered a reservoir of H1N1 and H3N2 viruses [290].

T505

63262-63527

Sentence

denotes

The swine-like H1N1, avian-like H1N1, swine-like H1N2, swine-like H3N2, human-like H3N2, A(H1N1)pdm09 along with avian-like H6N2 and H7N2 viruses were identified in feral swine samples collected across 35 states in the USA between October 2009–September 2013 [291].

T506

63528-63824

Sentence

denotes

Histological examination of the lung tissues obtained from two backyard piglets suffering from pneumonia and weight loss in Colorado in November 2010 suggested that the piglets were infected with swine influenza virus which were later confirmed to be infected with IAV subtype A(H1N1)pdm09 virus.

T507

63825-64060

Sentence

denotes

Since the piglets were raised at the house of a pharmacist hence a possible human to swine transmission was speculated given the possibility of an occupational exposure of the pharmacist to the A(H1N1)pdm09 virus at the pharmacy [292].

T508

64061-64225

Sentence

denotes

The first report of IBV infection in swine appeared when swine in the Midwest United States were found infected with IBV lineages of Yagamata/B and Victoria/B [37].

T509

64226-64359

Sentence

denotes

This was a new finding because initially IBV was thought to have a host range limited to human, pheasants, horses and seal [1,2,3,4].

T510

64360-64480

Sentence

denotes

A novel strain of swine influenza virus was detected in Oklahoma swine exhibiting influenza-like symptoms in April 2011.

T511

64481-64561

Sentence

denotes

The nasal swab samples taken from the swine were negative for the IAV infection.

T512

64562-64702

Sentence

denotes

Hence the virus isolation was attempted in swine testicle cells; the cells in culture showed influenza-like cytopathic effects by third day.

T513

64703-64851

Sentence

denotes

Electron microscopic observations revealed particles typical of a virus of Orthomyxoviridae family, but the RT-PCR was negative for the IBV and ICV.

T514

64852-64975

Sentence

denotes

After ultracentrifugation was used for virus isolation, the genome of the virus was sequenced using Ion Torrent sequencing.

T515

64976-65197

Sentence

denotes

The genome sequence analysis along with genetic and biochemical investigations revealed that the isolated virus was a novel Orthomyxovirus having 50% overall identity at amino acid level with human influenza C virus [43].

T516

65198-65419

Sentence

denotes

Since this novel virus was genetically and antigenically distinct from ICV therefore, later was proposed to be categorized as a new genus of Orthomyxoviridae family which was later accepted as influenza D virus (IDV) [5].

T517

65420-65548

Sentence

denotes

Later, two feral swine which were shot dead in a cotton field in Texas in June 2011 were found infected with A(H1N1)pdm09 virus.

T518

65549-65736

Sentence

denotes

The significant identity of A(H1N1)pdm09 virus isolated from these two feral swine with human A(H1N1)pdm09 virus suggested a possible transmission between human and the feral swine [290].

T519

65737-66015

Sentence

denotes

Another study reported seroprevalence of H3N2 virus in one feral swine from Mississippi and in five feral swine from the state of California in 2005 but a negative seroprevalence was reported in the feral swine samples obtained from the states of Florida, Oklahoma and Missouri.

T520

66016-66195

Sentence

denotes

Additionally, the seroprevalence of IAV was reported in feral swine from Texas where a total of 68 out of 472 feral swine sera were found positive for H3N2 and H1N1 viruses [293].

T521

66196-66429

Sentence

denotes

Another investigation detected H3N2 virus RNA in only one feral swine from a pool of samples collected across 31 states in the USA during 2011–2012 which indicated a negligible active influenza infection in US feral swine population.

T522

66430-66708

Sentence

denotes

On the contrary, ELISA identified IAV antibodies in 182 feral swine samples while the serological subtyping identified H3N2 virus antibodies in 76 feral swine samples collected from 19 states which indicated a significant past exposure of US feral swine to the H3N2 virus [294].

T523

66709-66953

Sentence

denotes

Further, seroprevalence of IDV was reported in 49 feral swine samples collected from Oklahoma, Texas, Hawaii and North Carolina during October 2012–September 2013 which provided the first evidence of past IDV infections in US feral swine [295].

T524

66954-67143

Sentence

denotes

A study investigating virus shedding in nursery piglets found that all 81 piglets under investigation were shedding H3N2 virus starting seventh day of arrival into the barns until 29th day.

T525

67144-67209

Sentence

denotes

Shedding was still observed in some piglets until 39th day [296].

T526

67210-67400

Sentence

denotes

Interestingly, 48 of these nursery piglets were also identified shedding H1N1 virus starting at the third day of arrival into the barns until 41st day over a 53-day observation period [296].

T527

67401-67502

Sentence

denotes

This was the new information which identified that young nursery piglets could get infected with IAV.

T528

67503-67702

Sentence

denotes

The oral fluid samples collected from 25 neonatal piglets at four Oklahoma based swine farms during May–August 2014 [297] were found infected with different IAV subtypes including H1, N1, H3, and N2.

T529

67703-67785

Sentence

denotes

This study supported the use of swine oral fluid samples in IAV diagnostics [285].

T530

67786-67933

Sentence

denotes

The swine oral fluid samples were also collected in North and South Carolina during June to August 2014 using the cotton rope hanging method [298].

T531

67934-68103

Sentence

denotes

In this method of sampling, swine are encouraged to chew the rope, as a result, saliva accumulates on the rope which is later squeezed to collect the sample aseptically.

T532

68104-68303

Sentence

denotes

One of the benefits of this method of sampling is that each sample does not represent an individual swine but rather represents multiple swine that chewed the rope while hanging inside the pen [298].

T533

68304-68497

Sentence

denotes

Another benefit of this sampling method is that swine oral samples may contain contaminants like feed and feces but this method minimizes the chances of such contaminations in the sample [299].

T534

68498-68733

Sentence

denotes

Another investigation carried out metagenomic sequencing of swine nasal and rectal swabs obtained from apparently healthy swine which identified 11 IAV positive swine at three abattoirs and a buying station in USA in August 2015 [300].

T535

68734-68895

Sentence

denotes

In a striking observation, an avian-lineage H4N6 virus was isolated and sequenced from 7–8-month-old gilts on a Missouri based swine farm in December 2015 [301].

T536

68896-69052

Sentence

denotes

The investigators collected more samples at different time points for next few months at the same farm to assess the transmission of H4N6 virus among swine.

T537

69053-69228

Sentence

denotes

No other samples were found positive for the H4N6 virus which suggested that the H4N6 virus did not transmit from swine-to-swine and therefore disappeared from the index farm.

T538

69229-69316

Sentence

denotes

Interestingly, this extended study identified three H1N1 viruses infecting swine [301].

T539

69317-69576

Sentence

denotes

One large-scale study identified that 23 percent (2 947/12,814) of the swine samples were positive for the IAV in Mid-West United States between July 2011–March 2017, however, sequencing could identify only 173 H1 and H3 subtypes among positive samples [302].

T540

69577-69823

Sentence

denotes

A human to swine transmission of IAV was suggested when two human-like H3N2 virus isolates were identified from an Oklahoma based swine farm in 2017 which had high similarity with the human-like H3N2 viruses reported earlier from Baltimore [303].

T541

69825-69831

Sentence

denotes

3.5.3.

T542

69832-69838

Sentence

denotes

Mexico

T543

69839-69913

Sentence

denotes

Maya people represent ethnolinguistic groups in South and Central America.

T544

69914-70030

Sentence

denotes

The practice of household swine keeping put the Maya people at high risk of contracting the swine influenza viruses.

T545

70031-70278

Sentence

denotes

Thirty-one sera samples collected from the Maya people in Mexico were identified having antibodies against H1N1 and H3N2 viruses while 93 other sera had antibodies against the H3 subtype of IAV, representing a past exposure to these viruses [304].

T546

70279-70539

Sentence

denotes

However, this study did not include swine samples for investigation but since swine were household animals in their backyard hence the IAV seroprevalence of the Maya people could be because of a past transmission of these viruses from the backyard swine [304].

T547

70540-70706

Sentence

denotes

A retrospective study identified antibodies against swine-like H1N1, A(H1N1)pdm09, H3N2, and human-like H1N1 viruses in backyard swine in Mexico between 2000 to 2009.

T548

70707-70871

Sentence

denotes

This investigation retrospectively determined that the classical-swine H1N1 virus was most widely present in Mexican swine before the 2009 influenza pandemic [305].

T549

70872-71062

Sentence

denotes

Further, a significant number of swine experiencing respiratory illness had H1N1 or H3N2 virus antibodies in commercial piggeries in Sonora Province of Mexico during October 2008–March 2009.

T550

71063-71230

Sentence

denotes

The molecular diagnostics and subtyping determined four H1 and two H3 viruses while 19 other IAV positive samples could not be subtyped given the low viral load [306].

T551

71231-71355

Sentence

denotes

During the influenza virus pandemic in Mexico in 2009, A(H1N1)pdm09 virus was first identified in a single swine nasal swab.

T552

71356-71452

Sentence

denotes

Additionally, H3N2, A(H1N1)pdm09 and IBV viruses were detected in four symptomatic humans [307].

T553

71453-71628

Sentence

denotes

The A(H1N1)pdm09 virus isolate retrieved from the swine was believed to be the first from the sister lineage of the pandemic influenza virus isolates reported in Mexico [307].

T554

71629-71731

Sentence

denotes

Further 59 IAV isolates were retrieved from Mexican swine having respiratory illness during 2010–2014.

T555

71732-71822

Sentence

denotes

Intriguingly, this study identified 13 reassorted genotypes of IAV in Mexican swine [308].

T556

71823-72109

Sentence

denotes

This investigation also reported that IAV introduction into Mexican swine may have occurred through three different routes; human to swine transmission; reassortment between human-like H3N2 and A(H1N1)pdm09 virus; and through the long-distance movement of the swine from USA and Europe.

T557

72110-72300

Sentence

denotes

A periodic introduction of IAV in Mexican swine occurred with the import of American and European swine to Mexico over two decades in 1980s and 1990s before the 2009 influenza pandemic [33].

T558

72301-72391

Sentence

denotes

Fifty-eight IAV whole genome sequences were retrieved from Mexican swine during 2010–2014.

T559

72392-72475

Sentence

denotes

Genome sequence analysis identified classical H1N1, H3N2, and A(H1N1)pdm09 viruses.

T560

72476-72630

Sentence

denotes

Interestingly, the data obtained in this study suggested independent evolution of IAV in the Mexican swine population in different regions of the country.

T561

72631-72756

Sentence

denotes

Phylogeny determined that Mexico City was the source of the 2009 influenza pandemic which erupted during March–May 2009 [33].

T562

72757-72910

Sentence

denotes

Later a reassortant H1N2 virus which had the genes from human and swine influenza viruses was isolated and sequenced from a swine in November 2014 [309].

T563

72912-72918

Sentence

denotes

3.5.4.

T564

72919-72928

Sentence

denotes

Guatemala

T565

72929-73127

Sentence

denotes

The molecular diagnostics identified a total of 104 IAV positive commercial and backyard swine in Guatemala during 2010–2011 which resulted into three A(H1N1)pdm09 and one H3N2 virus isolates [310].

T566

73129-73135

Sentence

denotes

3.5.5.

T567

73136-73140

Sentence

denotes

Cuba

T568

73141-73325

Sentence

denotes

The first report of A(H1N1)pdm09 virus in commercial piggeries in Cuba appeared in November 2010 when 24 swine were found positive for A(H1N1)pdm09 virus across five swine farms [311].

T569

73326-73474

Sentence

denotes

Further, five more IAV positive swine were detected in Pinar del Rio province of Western Cuba having respiratory illness and interstitial pneumonia.

T570

73475-73628

Sentence

denotes

However only one IAV positive sample could be successfully subtyped as A(H1N1)pdm09 virus having reassorted internal genes, all except the NA gene [312].

T571

73630-73636

Sentence

denotes

3.5.6.

T572

73637-73656

Sentence

denotes

Trinidad and Tobago

T573

73657-73841

Sentence

denotes

In a more recent investigation, a high seroprevalence of IAV (114/309) was detected in swine in Trinidad and Tobago which later identified H3N2 and A(H1N1)pdm09 viruses in swine [313].

T574

73842-73950

Sentence

denotes

In summary, the H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were reported in North American swine population.

T575

73951-74156

Sentence

denotes

Interestingly, the avian influenza virus strain H4N6 was detected in US based swine while H3N3 and H4N6 were identified in the Canadian swine and H5N2 was reported in the Mexican swine in 2018 (Figure 4E).

T576

74157-74228

Sentence

denotes

Mexico City was identified to be the origin of 2009 influenza pandemic.

T577

74229-74340

Sentence

denotes

It was also ascertained that A(H1N1)pdm09 virus was present in Mexican swine well before 2009 pandemic erupted.

T578

74342-74346

Sentence

denotes

3.6.

T579

74347-74360

Sentence

denotes

South America

T580

74362-74368

Sentence

denotes

3.6.1.

T581

74369-74378

Sentence

denotes

Argentina

T582

74379-74553

Sentence

denotes

After influenza virus outbreak hit a swine farm in Buenos Aires in November 2008, one of the five dead swine were diagnosed with viral pneumonia through immunohistochemistry.

T583

74554-74722

Sentence

denotes

A full genome of H3N2 virus sharing 96–98% nucleotide sequence identity with H3N2 viruses reported in North America during 2000–2003 was recovered from the swine [314].

T584

74723-74940

Sentence

denotes

An H1N1 virus was reported from a swine after a swine farm manager along with his spouse experienced influenza-like symptoms few days before the outbreak erupted in the swine at a Buenos Aires based farm in June 2009.

T585

74941-75015

Sentence

denotes

The influenza disease symptoms lasted for about a week in nursery piglets.

T586

75016-75185

Sentence

denotes

Immunohistochemistry identified necrotizing bronchiolitis in four of the swine post-mortem samples while one sample had severe inflammation in the bronchiolar epithelia.

T587

75186-75387

Sentence

denotes

The serological investigation detected IAV antibodies in most of the sera samples collected after 15 days of onset of clinical symptoms however the active infection was reduced to only six swine [315].

T588

75388-75687

Sentence

denotes

The third investigation carried out histopathology which identified lung lesions compatible to the influenza virus infection in nine swine necropsy samples at a Buenos Aires based swine farm in October 2009 and later in eight swine necropsy samples originated from a Santa Fe based farm in May 2010.

T589

75688-75916

Sentence

denotes

The swine at Buenos Aires farm were found infected with H1N1 virus while the swine at the Santa Fe farm retrieved one H1N2 and three human-like reassortant A(H1N1)pdm09 virus isolates which had triple reassortant internal genes.

T590

75917-76016

Sentence

denotes

This was the first report of human-like reassortant A(H1N1)pdm09 virus in swine in Argentina [316].

T591

76017-76256

Sentence

denotes

Later two more investigations using histopathology, immunohistochemistry, serology, and molecular analyses reported H1N2, H3N2, and reassortant H3N2 viruses with A(H1N1)pdm09 internal genes in swine in Argentina during 2011–2012 [317,318].

T592

76258-76264

Sentence

denotes

3.6.2.

T593

76265-76271

Sentence

denotes

Brazil

T594

76272-76515

Sentence

denotes

Several H1N1, H1N2, H3N2, human-like H1N1, and A(H1N1)pdm09 viruses have been identified in Brazilian swine from the Minas Gerais, Parana, Rio Grande do Sul and Sao Paulo provinces in Brazil during and after 2009 [319,320,321,322,323,324,325].

T595

76516-76646

Sentence

denotes

A technician who visited a Minas Gerais swine farm experiencing influenza outbreak developed similar respiratory disease symptoms.

T596

76647-76900

Sentence

denotes

The nasal swab sample was obtained from the technician, as a result, one A(H1N1)pdm09 virus was isolated which was closely related to the A(H1N1)pdm09 viruses reported from the swine herd in the Minas Gerais which was recently visited by the technician.

T597

76901-77028

Sentence

denotes

Hence it was concluded that a zoonotic transmission from swine to the technician occurred at the Minas Gerais swine farm [326].

T598

77029-77251

Sentence

denotes

An immunohistochemical investigation demonstrated microscopic lesions suggesting broncho-interstitial pneumonia in the lung tissues of four severely sick piglets at a swine farm located in Parana province in February 2011.

T599

77252-77308

Sentence

denotes

The A(H1N1)pdm09 viruses were isolated from two piglets.

T600

77309-77379

Sentence

denotes

Additionally, a novel reassortant H1N2 virus was also recovered [327].

T601

77380-77481

Sentence

denotes

One more investigation identified that A(H1N1)pdm09 virus was the most prevalent IAV subtype in sows.

T602

77482-77601

Sentence

denotes

The co-infections of sows with A(H1N1)pdm09, H1N2, or H3N2 subtypes were also documented in Rio Grande do Sul province.

T603

77602-77748

Sentence

denotes

These findings were noteworthy because the coinfections may trigger reassortments and thus may facilitate emergence of novel strains of IAV [328].

T604

77749-77862

Sentence

denotes

Later two more H1N2 viruses were isolated and characterized from swine in Rio Grande do Sul province during 2013.

T605

77863-78067

Sentence

denotes

The sequences of both the isolates had high nucleotide similarity to each other in different genome segments in the range of 98.9% to 100% which suggested a common source of origin of both isolates [329].

T606

78069-78075

Sentence

denotes

3.6.3.

T607

78076-78084

Sentence

denotes

Colombia

T608

78085-78179

Sentence

denotes

The A(H1N1)pdm09 virus was identified in seven swine farms in Colombia during 2008–2009 [330].

T609

78181-78187

Sentence

denotes

3.6.4.

T610

78188-78192

Sentence

denotes

Peru

T611

78193-78302

Sentence

denotes

The A(H1N1)pdm09 virus antibodies were detected in 110 backyard swine in Peru during March 2009–October 2011.

T612

78303-78511

Sentence

denotes

Total four A(H1N1)pdm09 virus isolates were retrieved and sequenced which determined that there were at least two separate events of A(H1N1)pdm09 virus transmission from human to backyard swine in Peru [331].

T613

78513-78519

Sentence

denotes

3.6.5.

T614

78520-78525

Sentence

denotes

Chile

T615

78526-78624

Sentence

denotes

The backyard productive systems (BPS) for raising swine, cattle, and poultry are popular in Chile.

T616

78625-78901

Sentence

denotes

A molecular investigation reported a negative active IAV infection across 113 BPS units within ten counties in Chile during 2012–2014 but the serological investigation detected IAV antibodies in swine at two BPS units which suggested a past exposure of swine to the IAV [332].

T617

78902-79065

Sentence

denotes

Interestingly, the HA gene sequence of an H12 virus was obtained from a domestic Muscovy duck at one of the BPS which appeared to have originated from a wild bird.

T618

79066-79154

Sentence

denotes

This suggested a spillover of the IAV from wild reservoir to the domestic poultry [332].

T619

79155-79310

Sentence

denotes

Another study reported the prevalence of H1N2 virus in swine reared at 40 different BPS having poultry and swine in El Yali wetland during 2013–2014 [333].

T620

79311-79464

Sentence

denotes

One more study identified four swine sera samples (4/64; 6.3%) that were found positive for IAV antibodies collected from different BPS in Central Chile.

T621

79465-79568

Sentence

denotes

One pool of swine nasal swab samples (1/39; 2.6%) was also detected IAV positive with real-time RT-PCR.

T622

79569-79704

Sentence

denotes

Interestingly, 7.9% chicken, 4.3% ducks and 11.1% geese samples collected from 329 BPS in Central Chile also had active IAV infections.

T623

79705-79827

Sentence

denotes

The breeding practice of poultry and swine in the BPS was determined to be a major risk factor for IAV transmission [334].

T624

79828-80025

Sentence

denotes

Briefly, the IAV strains of H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses have been reported from the swine in Argentina and Brazil while A(H1N1)pdm09 virus was reported in swine in Colombia and Peru.

T625

80026-80089

Sentence

denotes

Swine in Chile were found infected with H1N2 virus (Figure 4F).

T626

80090-80217

Sentence

denotes

In summary, total 281 research articles were identified which reported several influenza viruses in swine populations globally.

T627

80218-80398

Sentence

denotes

The highest number of studies were reported from Asia (n = 107), followed by North America (n = 76), Europe (n = 55), South America (n = 21), Africa (n = 18) and Australia (n = 4).

T628

80399-80530

Sentence

denotes

The highest number of reports per country were documented in United States (n = 40) followed by China (n = 39) and Canada (n = 24).

T629

80531-80617

Sentence

denotes

Until February 2020, influenza viruses have been reported from 53 countries worldwide.

T630

80618-80753

Sentence

denotes

Four subtypes of IAV including H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were most frequently detected in swine populations (Table 1).

T631

80754-81051

Sentence

denotes

Most of the large-scale studies used serological investigations including ELISA, hemagglutinin inhibition (HI), neuraminidase inhibition (NI), virus neutralization (VN), or microneutralization (MN) assays for the determination of the seroprevalence and subtyping of the influenza viruses in swine.

T632

81052-81138

Sentence

denotes

Several investigations used virus isolation for the confirmation and subtyping of IAV.

T633

81139-81286

Sentence

denotes

Most of the virological investigations used one-step real-time RT-PCR and/or reverse-transcription PCR for influenza virus detection and subtyping.

T634

81287-81485

Sentence

denotes

Sanger sequencing or next-generation sequencing using MiSeq or Ion Torrent sequencing successfully generated the influenza virus sequences from the swine samples for epidemiological interpretations.

T635

81486-81686

Sentence

denotes

Histological examinations including immunohistochemistry or immunofluorescence were used to examine the swine lung or other internal organ tissue samples for the influenza virus diagnostics (Table 2).

T636

81688-81690

Sentence

denotes

4.

T637

81691-81701

Sentence

denotes

Discussion

T638

81702-81832

Sentence

denotes

As of February 2020, influenza viruses have been identified and reported in swine from 53 countries worldwide (Table 1; Figure 3).

T639

81833-82028

Sentence

denotes

The influenza viruses have been detected in different sample types including swine sera, nasal, tracheal, oropharyngeal, nasopharyngeal swabs as well as oral fluids collected from the live swine.

T640

82029-82109

Sentence

denotes

Nasal and snout wipes, lung homogenates and fecal slurry samples were also used.

T641

82110-82348

Sentence

denotes

Additionally, the lung as well as other internal organ tissues (Table 2) obtained from either dead or sacrificed swine have also been used for the detection of IAV symptoms i.e., lesions in lungs, pneumonia, bronchitis, bronchiolitis etc.

T642

82349-82508

Sentence

denotes

Various methods have been used for the detection of influenza viruses in swine samples depending on the sample type, sample numbers and objective of the study.

T643

82509-82835

Sentence

denotes

Virus isolation methods, using either MDCK, Caco-2, HRT18, or swine testicle cells or the pathogen free embryonated chicken eggs, although considered the gold standard [335,336,337] have largely been taken over lately by the sequencing approaches which tend to provide a considerably faster identification of the IAV subtypes.

T644

82836-83084

Sentence

denotes

The additional benefit of sequencing over virus isolation is that the sequences would be useful for analyzing the influenza virus outbreak clusters [338], virus evolution or reassortment [339] using phylogenetic analyses in different gene segments.

T645

83085-83272

Sentence

denotes

A recent study reported that next-generation sequencing can be useful in the influenza virus diagnosis and for the identification of the novel virulence markers and drug resistance [340].

T646

83273-83419

Sentence

denotes

Most of the studies have used real-time RT-PCR with matrix-gene specific oligonucleotide primers and TaqMan probe for IAV detection [308,341,342].

T647

83420-83534

Sentence

denotes

The conserved sequences of the matrix-gene specific primers can detect any IAV subtype in the swine samples [343].

T648

83535-83857

Sentence

denotes

Most of the studies used subtype-specific real-time RT-PCR for the IAV subtyping, however, few studies opted for the conventional approach of reverse-transcription PCR followed by Sanger sequencing for amplification of the HA and/or NA genes for retrieving the sequences for phylogenetic analyses to identify the subtypes.

T649

83858-84003

Sentence

denotes

Although the real-time RT-PCR is a powerful and rapid tool for the subtyping of IAV strains, it is more expensive than reverse-transcription PCR.

T650

84004-84298

Sentence

denotes

A few studies have reported reverse-transcription PCR based amplification of all the eight gene segments of IAV to generate the whole genome sequences [33,91,128,231] but in most cases, the whole genome sequences were generated using MiSeq next-generation sequencing approach [150,214,325,329].

T651

84299-84426

Sentence

denotes

A great advantage of this sequencing approach is that it can identify novel influenza viruses in the swine samples [80,90,301].

T652

84427-84594

Sentence

denotes

Most of the serological investigations used one or more methods for influenza virus detection and subtyping in the swine samples e.g., ELISA, HI, NI, MN, or VN assays.

T653

84595-84715

Sentence

denotes

The serological methods are useful in large-scale surveillances for screening large number of samples in a limited time.

T654

84716-84942

Sentence

denotes

However, the molecular detection assays are more reliable than the serological methods given the higher sensitivity, but the serological assays are rapid and affordable hence are preferred for large-scale surveillance studies.

T655

84943-85094

Sentence

denotes

The molecular and serological investigations report either active infections (viral RNA) or past exposures (antibodies) in swine samples, respectively.

T656

85095-85261

Sentence

denotes

The molecular detection approaches followed by sequencing are largely used for the research focusing on the influenza virus epidemiology [73,78,82,87,94,128,146,150].

T657

85262-85510

Sentence

denotes

Several studies used histological examinations e.g., immunohistochemistry or immunofluorescence to identify the IAV symptoms in lung or other internal organs of either dead or severely sick swine sacrificed for the investigations [130,189,315,318].

T658

85511-85638

Sentence

denotes

Immunohistochemistry provides a rapid and affordable diagnosis of the influenza virus disease using swine tissue samples [344].

T659

85639-85771

Sentence

denotes

One major benefit of immunohistochemistry is that it can be used in the retrospective analysis of the archived tissue samples [245].

T660

85772-86092

Sentence

denotes

A large number of investigations have reported sub-clinical influenza virus infections in asymptomatic (apparently healthy) swine [78,103,150,161,171,278,300], indicating that influenza infections can go undetected while the swine may be shedding virus and hence may infect other swine and farm workers in contact [183].

T661

86093-86314

Sentence

denotes

Intriguingly, most of the swine samples processed in Australia, Europe, and North America were obtained from the symptomatic swine while most of the Chinese swine samples were collected from asymptomatic swine (Figure 5).

T662

86315-86654

Sentence

denotes

Symptomatic swine may exhibit mild or severe influenza like symptoms [59,202,252], including fever, coughing, sneezing, pneumonia, bronchitis, reduced appetite, diarrhea, nasal and/or ocular discharge, conjunctivitis, weakness, anorexia, prostration, weight loss, abortion in sows, and mortality in some cases [89,224,231,239,248,282,318].

T663

86655-86767

Sentence

denotes

Most studies where the swine were severely infected reported reduced appetite and weight loss [129,246,247,292].

T664

86768-86914

Sentence

denotes

Due to IAV infection, the swine takes longer to weigh 100 kg body mass [226], hence the IAV disease burden affects the swine farmers economically.

T665

86915-87068

Sentence

denotes

Varying rates of mortality of swine due to IAV infections were reported from around the world ranging from 0.5% to 30% [138,206,213,218,221,273,296,327].

T666

87069-87327

Sentence

denotes

This wide difference in mortality rate could be due to novel virus strains emerged through reassortments within the swine [273,315,327] or inter-species transmission, e.g., avian to swine transmission, resulting into severe disease outbreaks [27,80,119,133].

T667

87328-87545

Sentence

denotes

One example of the emergence of a novel influenza virus strain is the emergence of A(H1N1)pdm09 strain due to reassortment between avian and swine IAV strains in swine which resulted into 2009 influenza pandemic [33].

T668

87546-87775

Sentence

denotes

Additionally, the emergence of IAV subtype H1N2 is another classic example of influenza virus reassortment which resulted into severe disease outbreaks in Japanese and Korean swine populations during 1990s and 2000s [27,121,140].

T669

87776-87898

Sentence

denotes

Strains of IAV can infect the swine of any age group; piglets as young as one week may become infected with IAV naturally.

T670

87899-88164

Sentence

denotes

Interestingly, a study in Denmark observed a piglet as young as just three days was infected with IAV despite having maternally derived IAV antibodies [183], suggesting that the infection might have occurred from the infected sow which was shedding the virus [183].

T671

88165-88366

Sentence

denotes

However, the symptoms of the influenza-like illness in swine may last only for one week but the virus shedding may still persist until 41 days after appearance of the influenza-like symptoms [183,296].

T672

88367-88540

Sentence

denotes

This phenomenon may have serious implications in influenza virus spill over to the non-infected swine as well as to the exposed farm workers due to prolonged virus shedding.

T673

88541-88743

Sentence

denotes

Three other studies observed virus shedding in swine and reported that the virus shedding may persist until the 11 day [256], 20 day [255], or 29 day [296] after onset of the clinical symptoms in swine.

T674

88744-88863

Sentence

denotes

This variation in the duration of the virus shedding might be strain dependent, which needs to be further investigated.

T675

88864-89115

Sentence

denotes

A higher rate of virus shedding and IAV prevalence was reported during the fall and early winter months than summer season because the high relative humidity present in the environment during summer decreases the transmission of influenza virus [267].

T676

89116-89343

Sentence

denotes

The high relative humidity in summer facilitates the generation of larger droplets which are less likely to be aerosol transmitted to a longer distance as they tend to fall on the ground quickly after their formation [240,258].

T677

89344-89492

Sentence

denotes

Several cases of inter-species transmission were identified which documented transmission of IAV between human and swine or between birds and swine.

T678

89493-89834

Sentence

denotes

The occurrence of the avian influenza virus strains in swine in China (H5N1, H9N2, H4N1, H4N6, H5N3, H10N5, H4N8, H6N6, H7N9), United States (H4N6, H6N2, H7N2), Canada (H4N6, H3N3), South Korea (H7N2, H5N2), Nigeria (H5N1), and Egypt (H5N1, H5N2, H9N2 ) serve as the evidence of interspecies transmission of avian influenza viruses to swine.

T679

89835-89974

Sentence

denotes

The first evidence of avian influenza virus active infection in swine appeared in 1999 in Canada when H4N6 virus was isolated from a swine.

T680

89975-90102

Sentence

denotes

Later several other avian-origin IAV strains were detected and sequenced in swine in China, Canada, and South Korea (Figure 6).

T681

90103-90360

Sentence

denotes

Various studies have spotted wild birds visiting the swine farms or in the vicinity which suggested that wild birds may have served as the carriers for the introduction of the different avian-origin IAV subtypes to the swine populations [59,80,100,246,332].

T682

90361-90577

Sentence

denotes

The highest number of avian-origin IAV strains were reported in Chinese swine which shows frequent avian-swine interaction in China, a country that has historically been an epicenter for influenza virus disease [69].

T683

90578-90690

Sentence

denotes

Egypt is recognized as a “hot spot” for the influenza virus reassortment due to its geographical location [345].

T684

90691-90921

Sentence

denotes

The role of migratory wild birds in the introduction of avian influenza in Egypt has been already established [346,347], and the highly pathogenic strains of the IAV have previously been detected in migratory birds in Egypt [348].

T685

90922-91219

Sentence

denotes

Since migratory wild birds were reported to harbor in the vicinity of Cairo [60] therefore, the probability of the migratory bird–swine interaction in the regions remain high which very well explains the occurrence of highly and low pathogenic strains of avian-origin IAV in swine in Cairo, Egypt.

T686

91220-91463

Sentence

denotes

Given the “mixing vessel” nature of the swine, the occurrence of avian-origin IAV strains in swine is alarming in terms of IAV reassortment and evolution which may trigger the emergence of novel IAV strains of pandemic potential in the future.

T687

91464-91775

Sentence

denotes

Further, the multiple reports of double or triple reassortant IAV strains in swine are evidence that IAV co-infections may facilitate the antigenic diversity of the influenza viruses; and as a result, new HA and NA subtypes of IAV may be continually added to the existing 18 HA and 11 NA subtypes in the future.

T688

91776-91955

Sentence

denotes

Intriguingly, the frequency of the occurrence of double or triple-reassortant IAV strains in swine has dramatically increased in the recent decades [76,81,87,109,161,250,268,278].

T689

91956-92186

Sentence

denotes

One unique example of the reassortment and evolution of the pandemic strain of IAV in swine was the emergence of A(H1N1)pdm09 virus in swine in Mexico which evolved due to the reassortment between avian and swine IAV strains [33].

T690

92187-92526

Sentence

denotes

While an overwhelming majority of investigations reported IAV in the swine across the world (Figure 7A), there were only a few reports which documented either active infections or past exposures of the swine to the influenza virus types IBV [37,171,186,277] (Figure 7B), ICV [38,117,186] (Figure 7C) or IDV [5,43,44,45,46,217] (Figure 7D).

T691

92527-92745

Sentence

denotes

A low prevalence of IBV was observed in swine given that only one study reported the IBV antibodies in swine samples in England during 1991–1992 [186] with no evidence of further spill over to other European countries.

T692

92746-92849

Sentence

denotes

The active infection of IBV was later reported in US swine when two IBV isolates were obtained in 2009.

T693

92850-93053

Sentence

denotes

A recent study from Taiwan reported three strains of the Victoria/B lineage of IBV in naturally infected swine in 2014 [171], again there was no further report of dissemination to nearby Asian countries.

T694

93054-93136

Sentence

denotes

The IBV infected swine were apparently healthy with no signs of influenza disease.

T695

93137-93319

Sentence

denotes

The first report of ICV appeared in Chinese swine after the virus was isolated from apparently healthy swine in 1981 in a routine diagnostic procedure at an abattoir in Beijing [38].

T696

93320-93476

Sentence

denotes

Later ICV seroprevalence was reported in English and Japanese swine during 1980s–1990s [117,186] with no further evidence of circulation anymore thereafter.

T697

93477-93646

Sentence

denotes

The IDV was first detected and characterized in 2011 in Oklahoma based swine in the United States which appeared to have made a species jump from cattle to swine [5,43].

T698

93647-93830

Sentence

denotes

Interestingly, a complete IDV genome was retrieved from a symptomatic sow in Italy in 2015 which was found closely related to the IDV genome reported in 2011 from Oklahoma, USA [217].

T699

93831-93932

Sentence

denotes

This might have happened due to the trade of the cattle or swine between Italy and the United States.

T700

93933-94163

Sentence

denotes

A recent study from China identified IDV sequences which shared a high similarity (99%–100%) with the IDV sequences reported earlier from the cattle in China [102] which was another evidence of bovine to swine transmission of IDV.

T701

94164-94310

Sentence

denotes

The IDV has been in circulation in swine in the current decade with reports emerging from swine in Italy, Luxembourg, China and the United States.

T702

94311-94507

Sentence

denotes

In summary, IAV was first isolated from a swine in USA in 1930 [34,349] and later antibodies for the human influenza viruses were reported in swine at the State Prison of New Jersey in 1937 [259].

T703

94508-94672

Sentence

denotes

More IAV outbreaks and cases in swine in North America were reported during 1981–2000; the frequency has now dramatically fallen in the last two decades (Figure 8).

T704

94673-94783

Sentence

denotes

This might be due to improved swine influenza surveillance and vaccination in North America in recent decades.

T705

94784-94936

Sentence

denotes

The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were reported from the commercial, backyard, exhibition, feral swine and wild boars in the United States.

T706

94937-95133

Sentence

denotes

As of February 2020, the highest number of reports of influenza virus infections in swine in a country were documented in the United States (n = 40) followed by China (n = 39) and Canada (n = 24).

T707

95134-95264

Sentence

denotes

The highest number of IAV positive swine samples were reported in the United States (36128/200384) followed by China (5031/90760).

T708

95265-95411

Sentence

denotes

One of the factors behind the higher number of IAV cases in swine in the United States compared to China would be related to the disease symptoms.

T709

95412-95655

Sentence

denotes

A majority of the North American swine samples that were screened for the IAV infections had either mild or severe symptoms of influenza-like illness which would have made it visually easier to identify IAV infected swine in the United States.

T710

95656-95864

Sentence

denotes

On the contrary, a smaller number of Chinese swine exhibited influenza-like disease symptoms while a large proportion of the Chinese swine population appeared to have sub-clinical infections with no symptoms.

T711

95865-95980

Sentence

denotes

This would have made it difficult for identifying the influenza virus infected swine during surveillances in China.

T712

95981-96116

Sentence

denotes

The first report of IDV in 2011 in Oklahoma swine reflected the antigenic diversity and evolution of influenza viruses in the US swine.

T713

96117-96374

Sentence

denotes

However, the recent influenza virus disease prevalence in North American swine appeared to have declined, nevertheless, given the large swine population of the continent, the surveillance should continue to track the influenza virus diversity and evolution.

T714

96375-96647

Sentence

denotes

The first serological evidence of IAV in European swine was documented from the Czechoslovakia during 1969–1972, but the first H1N1 virus in European swine was isolated in Belgium in 1979 which was apparently transmitted from wild ducks in Germany to the swine in Belgium.

T715

96648-96801

Sentence

denotes

Since then several H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses have been detected in commercial and backyard swine as well as in wild boars within Europe.

T716

96802-96967

Sentence

denotes

The incidence of IAV in European swine has increased several folds in the past two decades with a relatively high number of IAV positive swine samples (19644/49814).

T717

96968-97077

Sentence

denotes

Most of the IAV positive European swine were reported having influenza-like symptoms at the time of sampling.

T718

97078-97245

Sentence

denotes

Germany reported the highest number of IAV positive swine in Europe where the pork industry is considered the third largest globally after China and the United States.

T719

97246-97547

Sentence

denotes

Importantly, the IDV was more recently identified in the European swine, first in Italy in 2015, and later a retrospective study identified IDV infection in swine samples collected in Luxembourg during 2014–2015 which indicated that the circulation of IDV in European swine took place only after 2014.

T720

97548-97615

Sentence

denotes

The evidence has suggested the bovine to swine transmission of IDV.

T721

97616-97833

Sentence

denotes

This observation is interesting because until recently more emphasis has been given to the avian-swine interaction and the bovine–swine interactions have been neglected from the influenza virus spill over perspective.

T722

97834-97979

Sentence

denotes

The first occurrence of IAV in Asian swine can be traced back to 1969, but the IAV prevalence has increased multi-fold in the recent two decades.

T723

97980-98088

Sentence

denotes

The IAV subtypes H1N1, H1N2, H3N2, and A(H1N1)pdm09 have become endemic in swine in several Asian countries.

T724

98089-98257

Sentence

denotes

The highly pathogenic avian-origin IAV strains of H5N1 and H7N9 have been reported from Chinese swine while H5N1 has been documented in swine in Viet Nam and Indonesia.

T725

98258-98337

Sentence

denotes

The highly pathogenic strains of H5N2 have been reported in South Korean swine.

T726

98338-98453

Sentence

denotes

Several LPAIV strains including H4N1, H4N6, H4N8, H6N6, H9N2, and H10N5 have also been documented in Chinese swine.

T727

98454-98618

Sentence

denotes

The studies suggested a frequent interaction between wild birds and swine in China which appeared to have transmitted avian-origin IAV strains in the Chinese swine.

T728

98619-98744

Sentence

denotes

Occurrence of equine influenza virus H3N8 in Chinese swine further expanded the genetic diversity of swine influenza viruses.

T729

98745-98955

Sentence

denotes

Despite an avian to human transmission of certain avian influenza virus strains including H5N1 virus, only a limited human to human transmission of avian influenza viruses was established in the past [350,351].

T730

98956-99243

Sentence

denotes

With the passage of these avian-origin IAV strains in a mammalian host like swine, a high probability remains of these avian influenza virus strains to adapt and gain the ability of the human to human transmission, if happens, the consequences would be devastating for the public health.

T731

99244-99395

Sentence

denotes

Australian swine were free from influenza virus until the year 2009 when a New South Wales swine farm reported an influenza-like outbreak in the swine.

T732

99396-99500

Sentence

denotes

The zoonotic transmission of the A(H1N1)pdm09 virus was reported to the farm workers and the farm owner.

T733

99501-99629

Sentence

denotes

Until now, there have only been four IAV reports in Australian swine which reflects a low prevalence of IAV in Australian swine.

T734

99630-99744

Sentence

denotes

New Zealand is yet to officially report the influenza virus prevalence in swine and remains free from the disease.

T735

99745-99919

Sentence

denotes

A retrospective study identified that the A(H1N1)pdm09 virus was present in Mexican swine as early as 2000, well before the influenza pandemic occurred during March–May 2009.

T736

99920-100138

Sentence

denotes

A high genetic diversity of IAV in Mexican swine due to live swine imports from North America and Europe during 1980s laid the foundation of the emergence of zoonotic strain of A(H1N1)pdm09 virus in Mexican swine [33].

T737

100139-100247

Sentence

denotes

The highest number of IAV positive swine in Central America were reported from Mexico followed by Guatemala.

T738

100248-100413

Sentence

denotes

Interestingly, a report of the highly pathogenic H5N2 virus in Mexican swine in 2018 further triggers the alarm in the context of a potential novel IAV reassortment.

T739

100414-100569

Sentence

denotes

Outbreaks of IAV in the South American swine populations occurred during the last two decades, with the highest prevalence reported in the Brazilian swine.

T740

100570-100722

Sentence

denotes

A considerable proportion of cases showed sub-clinical infections with no symptoms which might have made it more difficult to detect the infected swine.

T741

100723-100841

Sentence

denotes

The reports of IAV active infections or the seroprevalence appeared in the African swine only during last two decades.

T742

100842-100971

Sentence

denotes

Until February 2020, IAV have been detected in swine in Cameroon, Nigeria, Egypt, Kenya, Reunion Island, Uganda, Togo, and Ghana.

T743

100972-101175

Sentence

denotes

However, South Africa has a considerable swine population [352], but currently there is no published report on the prevalence of active IAV or other influenza virus infections in the South African swine.

T744

101176-101314

Sentence

denotes

This might be because of the lack of an active surveillance for the detection of the influenza virus disease in the swine in South Africa.

T745

101316-101318

Sentence

denotes

5.

T746

101319-101330

Sentence

denotes

Conclusions

T747

101331-101577

Sentence

denotes

The reports of reassortant, double-reassortant and triple-reassortant influenza viruses in Asian, North American and European swine strengthens the concept of swine being the “mixing vessel” in terms of influenza virus reassortment and evolution.

T748

101578-101822

Sentence

denotes

The multiple reports of avian-origin IAV strains including highly pathogenic H5N1, H5N2 and H7N9 in swine are alarming given the fact that the avian-origin strains may adapt in swine to facilitate the emergence of a reassortant pandemic strain.

T749

101823-101967

Sentence

denotes

The highest number of influenza virus studies in swine population have been reported from the United States (n = 40) followed by China (n = 39).

T750

101968-102043

Sentence

denotes

Also, the United States reported the highest numbers of IAV cases in swine.

T751

102044-102193

Sentence

denotes

Due to widespread active surveillance, the United States has significantly brought down the influenza virus disease in swine in the last two decades.

T752

102194-102295

Sentence

denotes

Conversely, the IAV disease burden has increased multi-fold in Chinese swine in the last two decades.

T753

102296-102494

Sentence

denotes

Additionally, the occurrence of several high- and low-pathogenic avian-origin IAV strains in the Chinese swine population may put the country at greater risk of an influenza pandemic for the future.

T754

102495-102811

Sentence

denotes

Given the “mixing vessel” nature of swine physiology, the occurrence of several avian-origin IAV strains and multiple reports of double-reassortant and triple-reassortant IAV subtypes in Chinese swine are alarming because reassortments in swine may facilitate the emergence of a new IAV strain of pandemic potential.

T755

102812-103050

Sentence

denotes

In the background of the current Corona virus pandemic (COVID-19) which originated in China, the presence of avian-origin IAV strains in Chinese swine must be considered a serious threat for the future and hence must be dealt accordingly.

T756

103051-103345

Sentence

denotes

An active nationwide swine surveillance similar to that of North America which as a result, has brought down the current prevalence of influenza virus in the North American swine, should be in place in the rest of the world to safeguard the public health and the economics of the swine farming.

T757

103346-103525

Sentence

denotes

A better and active worldwide swine influenza surveillance would be useful for upgrading the current diagnostic protocols and vaccines to prevent future influenza virus outbreaks.

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