3.2. Influenza Viruses in Swine in Asia

3.2.1. China
China is considered the epicenter of influenza viruses [69]. 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]. 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]. 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]. 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].
First human-origin H1N1 and four human-origin H3N2 virus isolates in Chinese swine were retrieved during 2005–2006 [73]. 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]. Surprisingly, two isolates of equine influenza virus H3N8 were also detected in swine during December 2005 and January 2006 [74]. 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]. 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].
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]. 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. 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]. Further, a novel strain of avian-origin H4N1 virus was isolated from a Chinese swine in 2009 [80].
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]. 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]. Three reassortant H3N2 virus isolates having internal genes of A(H1N1)pdm09 virus were reported in swine between November 2010 and June 2011 [93].
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]. 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]. 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].
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]. 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. The wild birds visiting swine feeding sites at the swine farm were speculated to serve as the carrier for H9N2 virus [100]. 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. 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].
The IAV infection was also documented in 44 wild boars in Jilin province of China between April 2015 and February 2016 [101]. The first report of the IDV prevalence in Chinese swine documented 21 IDV positive swine in the Guangdong province in 2016 [44]. 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.

3.2.2. Hong Kong and Tibet
Hong Kong is a special administrative region while Tibet is an autonomous administrative region under the control of People’s Republic of China. The H1N1 and H3N2 virus isolates were successfully retrieved from apparently healthy swine in Hong Kong during July 1993–June 1994 [103]. 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].
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].

3.2.3. Bhutan
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].

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

3.2.5. Japan
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]. 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]. 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. The isolated H1N2 virus was believed to be a recombinant of H1N1 and H3N2 viruses [113]. Further 340 swine were diagnosed with H1N1 antibodies in Toyama Prefecture between 1978–1982. A lower seroprevalence was observed during the summer months while the seroprevalence was relatively higher during the winter season [114]. Again, one more H1N2 virus was isolated and characterized from the sows in Ehime Prefecture in September 1980 [115]. 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. This was the first report of the IAV infection in the imported swine [116].
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].
Several other reassortant H1N2 virus isolates were reported in Japanese swine after 1991 [119]. 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. One more H1N2 virus was detected in swine which was closely related to the Japanese H1N2 virus [120].
The immunohistochemistry identified lesions in the lungs of the sick swine infected with reassortant H1N2 virus [121]. Additionally, several H1N1 and H3N2 viruses have also been reported in Japanese swine between 1990 and 2017 [122,123]. 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. Further, one H3N2 virus isolate was determined to have genes of Japanese swine influenza and A(H1N1)pdm09 viruses [124]. These results reflected the occurrence of the reassortment events between Japanese swine influenza and A(H1N1)pdm09 viruses.
IAV seroprevalence has lately been reported in wild boars (Sus scrofa leucomystax) in Japan. 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. 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]. 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]. This reflected a past exposure of the Japanese wild boars to the IAV strains.

3.2.6. South Korea
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. 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]. 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. Additionally, four typical swine influenza H1N1 viruses were identified in swine [128].
Several H1N1, H1N2, and H3N2 viruses were detected in symptomatic South Korean swine after 2000 [129,130,131,132,133,134]. The IAV localization in the swine lung tissues was confirmed by immunohistochemistry [130]. 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].
Three H1N1 virus isolates closely related to US isolates of H1N1 were obtained from 45-day-old piglets in Korea in January 2005. The other swine farms in the proximity of this index farm were negative for the H1N1 virus [136]. 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].
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. These viruses had human-like H3 gene while other gene segments originated from swine influenza viruses within Korea. 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].
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]. The reassortment between A(H1N1)pdm09 and swine H1N2 viruses emerged into a novel reassortant H1N2 virus in swine [140]. 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]. 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]. More recently, a complete genome sequence of H1N1 virus was reported from a domestic swine in Korea in 2016 [143].

3.2.7. Thailand
The occurrence of IAV in Thai swine was first reported during November–December 1978. Active H3N2 infection was detected in one swine while several other swine had H3N2 antibodies [144]. Two H1N1 virus isolates from Thai swine were first recovered in January 1988 [145]. Several studies reported H1N1, A(H1N1)pdm09, H1N2, and H3N2 viruses in swine exhibiting respiratory disease symptoms between 2000 to 2014. 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].
The first evidence of H5N1 seroprevalence in Thai swine was documented in 2004 when eight H5N1 positive swine sera samples were identified [153]. Later ten H1N1 and two H3N2 virus isolates were retrieved from piglets aged between 4 to 12 weeks during 2008–2009 [154]. 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].
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. Interestingly, two farm owners, 46 swine handlers, four veterinarians, five farm cleaners and two farm office workers also reported IAV seroprevalence. 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].
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. 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].
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].
The reshuffling and reassortment of IAV internal genes were reported in Thai swine in February 2012. 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. 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].

3.2.8. Vietnam
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]. 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. 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].
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]. 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].

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

3.2.10. Lebanon
After an influenza outbreak on Lebanese poultry farms in 2005 the farmers fed the carcasses of the dead flocks to the swine. 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]. These results revealed the interspecies transmission of IAV among poultry, farm workers and swine.

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

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

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

3.2.14. Taiwan
The human to swine transmission of IAV was speculated after IAV antibodies were detected in 147 Taiwanese swine during June 1969–May 1970. The results were further confirmed with virus isolation which retrieved 13 IAV isolates [170]. 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].

3.2.15. Indonesia
An active IAV infection in 52 swine within four provinces in Indonesia was identified during 2005–2009. Interestingly, 39 H5N1 virus isolates were successfully retrieved and sequenced [172].

3.2.16. Sri Lanka
The first report of influenza in Sri Lankan swine was documented during 2004–2005 after one human-like H3N2 virus was identified. Later, A(H1N1)pdm09 virus isolates were identified in swine during 2009–2012. A spillover of these viruses from human to swine was speculated [173].

3.2.17. Kazakhstan
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. Interestingly, 10 of the human samples were also positive for IBV infection while the swine samples were negative for IBV [174].
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). 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. Horse to swine transmission of equine influenza virus H3N8 was reported in China. Additionally, avian-origin H7N2, H5N2 viruses were identified in South Korean swine while H5N1 was reported in Indonesian swine. Interestingly, after the swine were fed upon dead poultry carcasses in Lebanon the H9N2 virus was detected in Lebanese swine. 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).