CORD-19-Sentences  

CORD-19:e6fd10dbd99717ea319bed4c6dbc9d0a421e656c JSONTXT 8 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-108 Sentence denotes Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004
TextSentencer_T2 110-118 Sentence denotes Abstract
TextSentencer_T3 119-244 Sentence denotes Twenty-six avian infectious bronchitis (IB) viruses (IBV) were isolated from outbreaks in chickens in China between 1995 and.
TextSentencer_T4 245-352 Sentence denotes They were characterized by comparison with twenty-six Chinese reference strains and five other IBV strains.
TextSentencer_T5 353-436 Sentence denotes Chinese IBVs, which were mainly nephropathogenic, were placed into seven genotypes.
TextSentencer_T6 437-546 Sentence denotes Fourteen Chinese IBV isolates were placed in genotype I, having small evolutionary distances from each other.
TextSentencer_T7 547-619 Sentence denotes Genotype II included 6 strains that were isolated in the 1990s in China.
TextSentencer_T8 620-725 Sentence denotes Genotype III consisted of eight Chinese isolates that showed close relationship with Korean IBV isolates.
TextSentencer_T9 726-819 Sentence denotes Another eight IBV isolates clustered in genotype IV and showed larger evolutionary distances.
TextSentencer_T10 820-908 Sentence denotes The Massachusetts serotype was present in China in 1990s and was in a separate genotype.
TextSentencer_T11 909-1023 Sentence denotes Two isolates, HN99 and CK/CH/LHN/00I, which might be a reisolation of vaccine strains, clustered into genotype VI.
TextSentencer_T12 1024-1163 Sentence denotes Four Chinese IBV isolates formed another genotype and showed larger evolutionary distances from other Chinese IBV genotypes (genotype VII).
TextSentencer_T13 1164-1314 Sentence denotes IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%.
TextSentencer_T14 1315-1511 Sentence denotes The results showed that IBVs in China came from genetic changes both in IBV populations that existed before the advent of vaccination and in the viruses that were introduced through live vaccines.
TextSentencer_T15 1512-1580 Sentence denotes IBVs showing various genetic differences are cocirculating in China.
TextSentencer_T16 1582-1691 Sentence denotes Infectious bronchitis virus (IBV) is a highly infectious and contagious pathogen of chickens worldwide [11] .
TextSentencer_T17 1692-1862 Sentence denotes The primary tissue of IBV infection is the respiratory tract, though some isolates replicate in the kidney and oviduct, resulting in nephritis and reduced egg production.
TextSentencer_T18 1863-2079 Sentence denotes Generally, infectious bronchitis (IB) has been controlled with serotype-specific vaccines, but outbreaks of IB still occur, because vaccines offer little cross-protection between serologically distinct viruses [19] .
TextSentencer_T19 2080-2230 Sentence denotes A high mutation frequency and RNA recombination leads to the emergence of new viruses capable of causing disease in vaccinated chickens [31, 41, 35] .
TextSentencer_T20 2231-2376 Sentence denotes Although many countries share some common antigenic types, IBV strains within a geographic region are unique and distinct [1, 4, 15-17, 21, 47] .
TextSentencer_T21 2377-2535 Sentence denotes The identification of the circulating IBV field strains is extremely important for the selection of vaccine strains for the corresponding geographical region.
TextSentencer_T22 2536-2638 Sentence denotes IBV is the type species of the genus Coronavirus in the family Coronaviridae, order Nidovirales [11] .
TextSentencer_T23 2639-2937 Sentence denotes It is a pleomorphic enveloped virus and has a singlestranded RNA genome, approximately 27 kb in length, of positive polarity that specifies the production of three major structural proteins: the phosphorylated nucleocapsid (N) protein, the membrane (M) glycoprotein, and the spike (S) glycoprotein.
TextSentencer_T24 2938-3401 Sentence denotes The S glycoprotein of IBV, located on the outside of all virions, is responsible for fusion (virus envelope to cell membrane and cell membrane to cell membrane) and is translated as a precursor protein (S 0 ), then cleaved into a carboxy-terminal S2 subunit (approximately 625 amino acid residues), which anchors S in the virus envelope, and an amino-terminal S1 subunit (approximately 520 residues), believed to largely form the distal bulbous part of S [3, 7] .
TextSentencer_T25 3402-3709 Sentence denotes The S1 subunit of spike glycoprotein of IBV is responsible for inducing neutralizing and serotype-specific antibodies in chickens, and mutations in the antigenically important spike glycoprotein S1 subunit leads to the emergence and proliferation of variant serotypes [34] associated with disease outbreaks.
TextSentencer_T26 3710-3912 Sentence denotes Serotypic evolution in IBV is associated primarily with the sequences of the S1 glycoprotein, and the genetic diversity of IBV is mainly monitored by analysis of the S1 gene [2, 9, 10, 23, 27, 32, 42] .
TextSentencer_T27 3913-3979 Sentence denotes IBV strains have been isolated and identified since 1982 in China.
TextSentencer_T28 3980-4208 Sentence denotes The outbreaks of IB have been ongoing, and IB continues to be an economically important disease to the poultry industry, although vaccines based on Massachusetts (Mass) strains such as H120 and H52 have been used for many years.
TextSentencer_T29 4209-4338 Sentence denotes However, the epidemiological analysis of IBV isolates in China has not been thorough except for with a few strains [31, 28, 46] .
TextSentencer_T30 4339-4482 Sentence denotes The relationships between Chinese IBV isolates and foreign IBV isolates, especially Korean, Taiwanese and Japanese IBV isolates, are not known.
TextSentencer_T31 4483-4639 Sentence denotes The focus of this study was to determine the molecular typing of the spike glycoprotein S1 subunit of IBV isolated between the years 1995 and 2004 in China.
TextSentencer_T32 4640-4833 Sentence denotes This will determine the IBV type(s) which are necessary for understanding the epidemiology and evolution of IBVs, as well as isolation of the virus, which is important for improved vaccination.
TextSentencer_T33 4834-5163 Sentence denotes Twenty-six field IBVs were isolated from kidney, preventriculus, or oviduct of IB-suspected broilers or layers using specified pathogen-free (SPF) embryonated eggs between 1995 (Table 1) were pooled and 10% w/v tissue suspensions were made in 0.1% phosphate-buffered saline containing 100 u penicillin and 100 µg streptomycin/ml.
TextSentencer_T34 5164-5294 Sentence denotes After 12 h at 4 • C, 200 µl supernatant from the suspensions was inoculated into the allantonic cavity of 9-to 11-day-old embryos.
TextSentencer_T35 5295-5337 Sentence denotes Three to 5 eggs were used for each sample.
TextSentencer_T36 5338-5401 Sentence denotes The inoculated eggs were incubated at 37 • C and candled daily.
TextSentencer_T37 5402-5594 Sentence denotes Two to 7 blind passages were performed until the characteristic embryo changes such as the dwarfing, stunting, or curling of embryos were observed between 2 and 7 days after inoculation [12] .
TextSentencer_T38 5595-5692 Sentence denotes All allantoic fluids were harvested and tested for the presence of IBV using electron microscopy.
TextSentencer_T39 5694-5761 Sentence denotes Samples of allantoic fluids were submitted for electron microscopy.
TextSentencer_T40 5762-5948 Sentence denotes Briefly, after low-speed centrifugation at 1500 g for 30 min (Allegra TM 21R centrifuge; Beckman), the supernatant of the 1.5 ml allantoic fluids were centrifuged at 12 000 g for 30 min.
TextSentencer_T41 5949-6094 Sentence denotes The resulting pellet was resuspended in a minimal volume of deionized water and examined by negative contrast electron microscope (JEM-1200, EX).
TextSentencer_T42 6095-6234 Sentence denotes Genomic RNA was extracted from virus-inoculated allantoic fluid with TRIzol reagent (Invitrogen) following the manufacturer's instructions.
TextSentencer_T43 6235-6416 Sentence denotes The first-strand cDNA was synthesized according the procedures of a previous report [31] using S1Oligo3 [25] and genomic antisense IBV-212 oligonucleotide, 5 -ATACAAAATCTGCCATAA-3 .
TextSentencer_T44 6417-6618 Sentence denotes IBV-212 was designed based on a comparison and alignment of the GenBank sequences of several known Chinese IBV strains and situated in the downstream of S1Oligo3 which had 5 nt overlapped between them.
TextSentencer_T45 6619-6818 Sentence denotes The PCR profiles involved an initial denaturation for 5 min at 95 • C followed by 30 cycles of denaturation at 94 • C for 1 min, annealing at 50 • C for 1 min, and polymerization at 72 • C for 2 min.
TextSentencer_T46 6819-6884 Sentence denotes The final polymerization step was performed at 72 • C for 10 min.
TextSentencer_T47 6885-7015 Sentence denotes Owing to genetic variations among IBV isolates, it is difficult to design PCR primers that can be used to detect all IBV isolates.
TextSentencer_T48 7016-7306 Sentence denotes Therefore, three genome-sense oligonucleotides, S1Oligo5 [25] , S1Uni2 [1] , or IBV-87, 5 -TATTGATTAGAGATGTTGGG-3 , which was selected from conserved areas by aligning several known Chinese IBV sequences from GenBank, were used with S1Oligo3 [25] or IBV-212 as antisense primer ( Table 2 ).
TextSentencer_T49 7307-7388 Sentence denotes The PCR products were analyzed on a 1.0% agarose gel and were sequenced directly.
TextSentencer_T50 7389-7482 Sentence denotes In addition, PCR products were also sequenced after cloning into the pMD18-T vector (TaKaRa).
TextSentencer_T51 7483-7580 Sentence denotes Each region was sequenced at least three times from two PCR products from different RT reactions.
TextSentencer_T52 7581-7778 Sentence denotes The nucleotide and amino acid sequences of the S1 protein gene of the twenty-six IBV isolates were assembled, aligned, and compared with reference IBV strains using the MEGALIGN program in DNAStar.
TextSentencer_T53 7779-7956 Sentence denotes Phylogenetic analysis of the nucleotide sequences and the deduced amino acid sequences of the S1 protein gene was performed by the Clustal V method using DNAStar software [18] .
TextSentencer_T54 7957-8013 Sentence denotes Thirty-one reference strains were selected for molecular
TextSentencer_T55 8015-8323 Sentence denotes His-Arg-Arg-Arg-Arg DQ167137 CK/CH/LGD/96I S1Oligo5 + IBV-212 His-Arg-Arg-Arg-Arg DQ167136 CK/CH/LDL/97I IBV-87 + S1Oligo3 Arg-Arg-Thr-Gly-Arg DQ068701 CK/CH/LLN/98I S1Oligo5 + IBV-212 His-Arg-Arg-Arg-Arg DQ167145 CK/CH/LDL/98I IBV-87 + S1Oligo3 Arg-Arg-Thr-Gly-Arg DQ167132 CK/CH/LHLJ/99I S1Oligo5 + IBV-212
TextSentencer_T56 8324-8592 Sentence denotes IBV-87 + S1Oligo3 Arg-Arg-Thr-Gly-Arg DQ167130 CK/CH/LXJ/02I S1Oligo5 + IBV-212 His-Arg-Arg-Arg-Arg DQ167152 CK/CH/LHLJ/02I S1Oligo5 + S1Oligo3 His-Arg-Arg-Arg-Arg DQ167138 CK/CH/LSHH/03I S1Uni2 + S1Oligo3 His-Arg-His-Arg-Arg DQ167149 CK/CH/LSHH/03II S1Uni2 + S1Oligo3
TextSentencer_T57 8593-9157 Sentence denotes His-Arg-His-Arg-Arg DQ167150 CK/CH/LGD/03I S1Oligo5 + IBV-212 Arg-Arg-Phe-Arg-Arg DQ167133 CK/CH/LAH/03I S1Oligo5 + IBV-212 Arg-Arg-His-Ser-Arg DQ167128 CK/CH/LSD/03I S1Oligo5 + IBV-212 His-Arg-Arg-Arg-Arg DQ167148 CK/CH/LJL/04I S1Oligo5 + IBV-212 His-Arg-Arg-Arg-Arg DQ167144 CK/CH/LHLJ/04V S1Oligo5 + IBV-212 His-Arg-Arg-Arg-Arg DQ167139 CK/CH/LDL/04II S1Oligo5 + IBV-212 Arg-Arg-Tyr-Arg-Arg DQ167131 CK/CH/LGD/04II S1Oligo5 + IBV-212 Arg-Arg-Phe-Arg-Arg DQ167134 CK/CH/LGD/04III S1Oligo5 + IBV-212 Arg-Arg-Leu-Arg-Arg DQ167135 CK/CH/LHLJ/04XI S1Oligo5 + IBV-212
TextSentencer_T58 9158-9367 Sentence denotes His-Arg-Arg-Arg-Arg DQ167140 a Oligonucleotides used for amplifying S1 protein gene b Arg arginine, Phe phenylalanine, His histidine, Thr threonine, Gly glycine, Ser serine, Tyr tyrosine, Leu leucine analysis.
TextSentencer_T59 9368-9549 Sentence denotes Of these, twenty-six were Chinese IBV strains from the GenBank database, and they represented most of the Chinese IBV field isolates available through GenBank or other publications.
TextSentencer_T60 9550-9750 Sentence denotes A total of fifty-two Chinese IBV field isolates, including our twenty-six isolates, were chosen to give a representation based on geographic distribution, year of isolation, and phylogenetic position.
TextSentencer_T61 9751-9873 Sentence denotes In addition, two IBV strains, 3051/02 and T07/02, representing TW I and TW II IBV isolates in Taiwan [20] , were selected.
TextSentencer_T62 9874-9923 Sentence denotes A Korean IBV isolate, K069-01, was also selected.
TextSentencer_T63 9924-10039 Sentence denotes This IBV strain belonged to genotype III of Korean IBV strains, and this genotype was a major type of IBV in Korea.
TextSentencer_T64 10040-10153 Sentence denotes JP8127, a Japanese IBV strain, was also selected, and its S1 protein gene was compared with Chinese IBV isolates.
TextSentencer_T65 10154-10428 Sentence denotes IBV strains from the above 3 geographically different areas were selected because we were interested in knowing whether the IBV isolates in China were introduced from neighboring countries and continents or whether they arose by mutations of circulating Chinese IBV strains.
TextSentencer_T66 10429-10606 Sentence denotes Furthermore, the S1 protein gene of the H120 vaccine strain was selected and compared in this study because the vaccine was widely used for many years on poultry farms in China.
TextSentencer_T67 10607-10696 Sentence denotes The entire coding region of the S1 protein gene of these strains was chosen for analysis.
TextSentencer_T68 10698-10788 Sentence denotes The fifty-seven IBV strains, including our twenty-six isolates, were molecularly analyzed.
TextSentencer_T69 10789-10882 Sentence denotes The twenty-six IBV isolates in this study and their accession numbers are listed in Table 2 .
TextSentencer_T70 10883-10960 Sentence denotes The IBV reference strains and their accession numbers are listed in Table 3 .
TextSentencer_T71 10961-11047 Sentence denotes Twenty-six IBV strains were isolated from flocks that were suspected of IBV infection.
TextSentencer_T72 11048-11167 Sentence denotes The isolates were from flocks in different parts of China (Fig. 1 ) that showed clinical IB and had 5 to 60% mortality.
TextSentencer_T73 11168-11339 Sentence denotes The nephritis observed in all flocks was characterized by enlarged and pale kidneys, frequently with urate deposits in the tubules, and severe dehydration and weight loss.
TextSentencer_T74 11340-11492 Sentence denotes Typical signs, including dwarfing and death of the embryo, were observed in different passages when each isolate was inoculated into embryos (Table 1) .
TextSentencer_T75 11493-11687 Sentence denotes Diagnoses based on electron microscopy examination showed all isolates had typical coronavirus morphology and were free of other agents such as Newcastle disease virus (NDV) (results not shown).
TextSentencer_T76 11688-11801 Sentence denotes To assess the genetic relatedness among the IBV strains, a phylogenetic tree was performed with S1 protein genes.
TextSentencer_T77 11802-11835 Sentence denotes The results are shown in Fig. 2 .
TextSentencer_T78 11836-11969 Sentence denotes The fiftyseven IBV strains were separated into seven genotypes (I to VII) by phylogenetic analysis of the S1 protein genes (Fig. 2) .
TextSentencer_T79 11970-12109 Sentence denotes Genotype I consisted of fourteen Chinese strains having small evolutionary distances from each other as shown in the rooted tree (Fig. 2) .
TextSentencer_T80 12110-12182 Sentence denotes Genotype II included 6 strains that were isolated in the 1990s in China.
TextSentencer_T81 12183-12413 Sentence denotes Most of the Chinese IBV isolates included in genotype III were also isolated in the 1990s, except tl/CH/LDT3/03 and CK/CH/LGD/03I, which were both isolated in Guangdong province in 2003 from teal [29] and layer hens, respectively.
TextSentencer_T82 12414-12561 Sentence denotes The Korean IBV isolate, K069-01, which belonged to genotype III of Korean IBV strains [27] , was closely related to those isolates in genotype III.
TextSentencer_T83 12562-12681 Sentence denotes Six of eight IBV isolates displayed in genotype IV were isolated after 2000, and most of them came from southern China.
TextSentencer_T84 12682-12775 Sentence denotes Furthermore, isolates included in genotype IV showed larger evolutionary distances (Fig. 2 ).
TextSentencer_T85 12776-12920 Sentence denotes Ten Chinese IBV isolates formed the genotype V in which H120 was included, and none of our twenty-six isolates were grouped under this genotype.
TextSentencer_T86 12921-13094 Sentence denotes The isolates HN99 and CK/CH/LHN/00I, both isolated in Henan province in 1999 and 2000, respectively, together with a Japanese isolate, JP8127, were grouped into genotype VI.
TextSentencer_T87 13095-13200 Sentence denotes Our three IBV isolates recovered in Dalian, China, between 1997 and 2001, were grouped into genotype VII.
TextSentencer_T88 13201-13339 Sentence denotes A Chinese IBV isolate, J2, which was isolated from the proventricular tissues of infected chickens [46] , was also placed in genotype VII.
TextSentencer_T89 13340-13432 Sentence denotes Two IBV isolates, 3051/02 and T07/02, belonging to TW I and TW II, formed a unique genotype.
TextSentencer_T90 13434-13746 Sentence denotes Phylogenetic relationships, based on the sequence of the S1 subunit of the S protein gene, of our twenty-six isolates and thirty-one reference strains (the first 1669 nt, starting at the AUG translation initiation codon, of the S protein genes) using the MEGALIGN program DNAStar with the Clustal V method [18] .
TextSentencer_T91 13747-13780 Sentence denotes Our IBV isolates are in bold type
TextSentencer_T92 13781-13907 Sentence denotes The spike glycoprotein of IBV is translated as a precursor protein (S0) and then cleaved into two subunits S1 and S2 [9, 24] .
TextSentencer_T93 13908-14055 Sentence denotes Cleavage site motifs of the fifty-seven IBV strains are listed in Table 2 and Table 3 , and twelve different cleavage site sequences were observed.
TextSentencer_T94 14056-14150 Sentence denotes The most common cleavage recognition site observed (24 of 57 viruses) was Arg-Arg-Phe-Arg-Arg.
TextSentencer_T95 14151-14413 Sentence denotes Viruses with this cleavage recognition site are the H120 vaccine strain, one Korean strain, K069-01, Taiwan isolates 3015/ 02 and T07/02, ten Chinese Mass-type isolates, and ten other Chinese isolates included in genotype III (six strains) and IV (four strains).
TextSentencer_T96 14414-14466 Sentence denotes The second most common site was His-Arg-Arg-Arg-Arg.
TextSentencer_T97 14467-14574 Sentence denotes Viruses with this cleavage recognition site include twelve isolates in genotype I and three in genotype II.
TextSentencer_T98 14575-14636 Sentence denotes This recognition site was unique for virus isolates in China.
TextSentencer_T99 14637-14688 Sentence denotes The third most common site was Arg-Arg-Thr-Gly-Arg.
TextSentencer_T100 14689-14861 Sentence denotes Viruses with this cleavage recognition site were placed in genotype VII, which included our three isolates (CK/CH/LDL/97I, CK/CH/LDL/98I, and CK/CH/LDL/01I) and isolate J2.
TextSentencer_T101 14862-14929 Sentence denotes This cleavage recognition site was also unique to viruses in China.
TextSentencer_T102 14930-15053 Sentence denotes The JX/99/01, CK/CH/LAH/99I, and SC021202 viruses had a cleavage recognition site, Arg-Arg-His-Arg-Arg, as did D1466 [22] .
TextSentencer_T103 15054-15436 Sentence denotes Chinese IBV isolates HN99 and CK/CH/LHN/00I, which were grouped in genotype VI, had a cleavage recognition site, Arg-Arg-Ser-Arg-Arg, which was the most common site reported by Jackwood [22] , who had compared the cleavage recognition sites of fifty-five IBV isolates to determine if the site sequence correlates with host cell range, serotype, geographic origin, and pathogenicity.
TextSentencer_T104 15437-15780 Sentence denotes The CK/CH/LSHH/03I and CK/CH/LSHH/03II viruses had a unique cleavage recognition site, His-Arg-His-Arg-Arg, as did isolates BJ and BJY, Arg-Arg-Thr-Arg-Arg, CK/CH/LAH/03I, Arg-Arg-His-Ser-Arg, CK/CH/LDL/04II, Arg-Arg-Tyr-Arg-Arg, CK/CH/LGD/04III, Arg-Arg-Leu-Arg-Arg, BJS, His-Arg-Thr-Lys-Arg, and Japanese Strain, JP8127, Arg-Arg-Phe-Lys-Arg.
TextSentencer_T105 15781-15918 Sentence denotes The complete nucleotide and predicted amino acid sequences of the S1 protein of the fifty-seven IBV strains were determined and compared.
TextSentencer_T106 15919-16138 Sentence denotes Except for isolates in genotype V, which included the Mass-type strains, none of the Chinese IBV isolates examined in this study shared more than 83% amino acid similarity in the S1 protein with the H120 vaccine strain.
TextSentencer_T107 16139-16313 Sentence denotes The S1 protein genes, which varied from 0.2 to 26.7% among the strains examined, indicated that point mutations, deletions, and insertions contribute to the evolution of IBV.
TextSentencer_T108 16314-16717 Sentence denotes IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%, with the exceptions of isolate BJS (genotype II) and isolates in genotype IV, BJQ (genotype III) and isolates in genotype V, isolates between genotypes I and III, which showed amino acid similarities of 91-94.5%, 90.5-92%, and 93.2-95.6%, respectively.
TextSentencer_T109 16718-16906 Sentence denotes The overall predicted amino acid sequence comparisons of the entire S1 protein of fifty-seven IBV strains reflected that most of the sequence variations were concentrated in three regions.
TextSentencer_T110 16907-17069 Sentence denotes The first included residues 50-87, corresponding to the S1 protein of the H120 vaccine strain, in which the hypervariable region 1 (HVR1) is located [8, 37, 42] .
TextSentencer_T111 17070-17203 Sentence denotes The second contained amino acid sequences between residues 114-140, which encompasses the hypervariable region 2 (HVR2) [8, 37, 42] .
TextSentencer_T112 17204-17282 Sentence denotes The last included residues 273-293, in which the hypervariable region 3 (HVR3)
TextSentencer_T113 17284-17311 Sentence denotes a Amino acid abbreviations:
TextSentencer_T114 17312-17828 Sentence denotes S serine, D aspartic acid, G glycine, A alanine, N asparagine, H histidine, E glutamic acid, T threonine, Y tyrosine, P proline, Q glutamine, V valine, I isoleucine, K lysine, R arginine, M methionine; b positions of residues in deduced amino acid sequences of the S1 protein of the H120 vaccine strain; c positions of residues in deduced amino acid sequences of the S1 protein of the H120 vaccine strain between which the residue(s) of other IBVs was (were) inserted; d missing amino acid residues is present [39] .
TextSentencer_T115 17829-18081 Sentence denotes Furthermore, almost all of the Chinese IBV isolates contained deletions and insertions except for those of the Mass-type IBV, which were included in genotype V in this study, and had amino acid sequences similar to those of the H120 strain ( Table 4 ).
TextSentencer_T116 18082-18303 Sentence denotes The deletions and insertions, which occurred in the predicted amino acid sequences of the S1 proteins of fifty-seven IBV strains in this study, were correlated with the genotypes of S1 protein genes, as shown in Table 4 .
TextSentencer_T117 18304-18447 Sentence denotes In addition, the Korean strain, K069-01, shared most of the motifs of deletions and insertions with Chinese IBV field isolates in genotype III.
TextSentencer_T118 18448-18654 Sentence denotes In 1962, Winterfield and Hitchner reported a nephrosis condition associated with IB in the United States, and Cumming reported an IB outbreak causing severe kidney lesion in chickens in Australia [13, 43] .
TextSentencer_T119 18655-18760 Sentence denotes Since this time, various nephropathogenic strains of IBV have been identified throughout the world [33] .
TextSentencer_T120 18761-18929 Sentence denotes In China, IB with nephritis was first reported in 1982 and several nephropathogenic IBV strains have been isolated in different parts of China since then [31, 32, 44] .
TextSentencer_T121 18930-19161 Sentence denotes Of the twenty-six IBV isolates in this study, one was isolated from atrophic oviduct of a diseased layer hen, six from swollen proventricular tissues of infected chickens, and the rest from swollen kidneys of IB-suspected chickens.
TextSentencer_T122 19162-19308 Sentence denotes Although seven IBV strains were isolated from tissues other than kidney, the gross lesions of kidney in these diseased chickens were also obvious.
TextSentencer_T123 19309-19638 Sentence denotes Based on the fact that these IBV strains were isolated from 1995 to 2004 in China, we considered that IB was prevalent all the while in China, although vaccines based on Mass-type strains such as H120 and H52 have been used for many years on poultry farms, and nephropathogenic IBV was the major type of IBV circulating in China.
TextSentencer_T124 19639-19920 Sentence denotes Although the genetic basis of IBV pathogenicity is not known, the S1 protein gene of IBV has serotype-specific and neutralization-specific epitopes, and serotypic evolution and the genetic diversity of IBV is mainly monitored by analysis of the S1 gene [2, 9, 10, 23, 27, 32, 42] .
TextSentencer_T125 19921-20054 Sentence denotes In the present study, phylogenetic analysis of S1 genes showed that Chinese IBV isolates were grouped into seven genotypes (Fig. 2) .
TextSentencer_T126 20055-20321 Sentence denotes IBVs isolated ten years ago were included in the same genotype with the strains isolated recently (for example, CK/CH/LSC/95I and CK/CH/ LGD/03I in genotype III), indicating that this genotype may be indigenous and has been prevalent in China for at least ten years.
TextSentencer_T127 20322-20599 Sentence denotes Serotype differences among the genetically distinct IBVs generally correlated with variations in the HVR of the S1 protein gene [4, 8] and differences of as little as 5% between S1 sequences of IBV could result in poor cross-protection offered by currently used vaccines [19] .
TextSentencer_T128 20600-20923 Sentence denotes The low identities (<83%) of amino acid sequences between Chinese IBV isolates and H120, except for those of the Mass-type IBV, which were included in genotype V in this study, may account for the prevalence of the viruses during the past ten years in spite of the extensive use of Mass-type vaccines in the field in China.
TextSentencer_T129 20924-21008 Sentence denotes Hence, developing vaccines from local strains is necessary for IBV control in China.
TextSentencer_T130 21009-21402 Sentence denotes Although the number of basic residues around the spike glycoprotein cleavage recognition site of IBV does not appear to correlate with increased cleavability, host cell range, and increased virulence as it does with the envelope glycoproteins of orthomyxoviruses and paramyxoviruses, the sequences of cleavage recognition sites was correlated with geographic distribution of the viruses [22] .
TextSentencer_T131 21403-21666 Sentence denotes Nine spike glycoprotein cleavage recognition site sequences were found in viruses of genotypes I to IV, in which six were unique to isolates in China, indicating genetically distinct evolution from viruses in other countries by cleavage recognition site analysis.
TextSentencer_T132 21667-21960 Sentence denotes However, a Korean IBV strain, K069-01, shared the same cleavage recognition site sequence, Arg-Arg-Phe-Arg-Arg, with ten Chinese isolates included in subgenotypes III (six strains) and IV (four strains), ten Chinese Mass-type isolates (genotype V), and two Taiwan isolates, 3015/02 and T07/02.
TextSentencer_T133 21961-22122 Sentence denotes Furthermore, K069-01 and Chinese isolates in genotype III shared more than 90% amino acid identities and they were also grouped into the same genotype (Fig. 2) .
TextSentencer_T134 22123-22374 Sentence denotes K069-01 was clustered into genotype III of Korean IBV strains, which was the major type of IBV circulating in Korea, and isolates in this genotype induced 50% mortality in 1-day-old chicks as well as severe renal urate deposition on the kidneys [40] .
TextSentencer_T135 22375-22436 Sentence denotes This was similar to Chinese isolates in genotype I [29, 31] .
TextSentencer_T136 22437-22655 Sentence denotes Based on these facts, IBVs between Chinese genotype III and Korean genotype III had a close relationship, as did NDV [26] , owing to the increased trade of agricultural products including poultry between two countries.
TextSentencer_T137 22656-22891 Sentence denotes Unlike K069-01, isolates 3051/02 and T07/02, which represented TW I and TW II strains, respectively [20] , were clustered into a separate branch that was separated from the Chinese genotypes, indicating that they had different origins.
TextSentencer_T138 22892-22993 Sentence denotes Ten Chinese IBV strains were classified into the Mass serotype (genotype V by phylogenetic analysis).
TextSentencer_T139 22994-23210 Sentence denotes As in China, Mass-type IBVs were also present in other Asian countries, such as Korea [27, 40] , Japan [32, 38] , and Taiwan [20, 30] , although Mass-type vaccines were commonly used in these countries or continents.
TextSentencer_T140 23211-23346 Sentence denotes However, Chinese Mass-type strains were all isolated in the 1990s and were not the major IBV type circulating in recent years in China.
TextSentencer_T141 23347-23588 Sentence denotes Molecular studies have shown that a new serotype or variant can emerge as a result of only a few changes in the amino acid composition in the S1 part of the virus spike protein, with the majority of the virus genome remaining unchanged [6] .
TextSentencer_T142 23589-23836 Sentence denotes This could be due to immunologic pressure caused by the widespread use of vaccines, to recombination as a consequence of mixed infections, or to the decrease of dominant serotypes as a result of vaccination, allowing other field strains to emerge.
TextSentencer_T143 23837-24031 Sentence denotes To this study, the Mass-type viruses may have come from the vaccine strains by point mutation, although the possibility that some of them were reisolations of vaccine strains cannot be excluded.
TextSentencer_T144 24032-24196 Sentence denotes Two strains, HN99 and CK/CH/LHN/00I, both isolated in Henan province in China, together with a Japanese strain, JP8127, constituted a "novel" genotype VI (Fig. 2) .
TextSentencer_T145 24197-24361 Sentence denotes These two Chinese isolates did not show close similarity to any of the S1 protein sequences of other Chinese IBV isolates available through GenBank or publications.
TextSentencer_T146 24362-24568 Sentence denotes Interestingly, BLAST searches revealed significant similarity (99%) of S1 protein genes between isolate HN99 and a vaccine strain, JAAS (AY839140), which was from Australia and used in China to control IBV.
TextSentencer_T147 24569-24720 Sentence denotes The isolate CK/CH/LHN/00I shared 99% similarity in the S1 protein gene with another IBV vaccine strain, Jilin (AY839144), which was also used in China.
TextSentencer_T148 24721-24834 Sentence denotes When CK/CH/LHN/00I was inoculated experimentally into 15-day-old SPF chickens, no disease signs were apparent (S.
TextSentencer_T149 24835-24861 Sentence denotes Liu et al., unpub. data) .
TextSentencer_T150 24862-25045 Sentence denotes The spreading of a virus from one area or country to another could be due, at least in part, to its improper introduction by the trading of birds or by the use of attenuated vaccines.
TextSentencer_T151 25046-25367 Sentence denotes To our knowledge, no other IBV strains related to HN99 or CK/CH/LHN00I were isolated in recent years in China, and considering the pathogenicity and genetically close relationship between the two isolates and the corresponding vaccine strains, we speculated that the two isolates would be reisolations of vaccine strains.
TextSentencer_T152 25368-25486 Sentence denotes Isolate J2, which was very similar to Q1 and T3, was genetically distinct from most of the Chinese IBV isolates [45] .
TextSentencer_T153 25487-25629 Sentence denotes In this study, our three isolates (CK/CH/LDL/97I, CK/CH/LDL/98I, and CK/CH/LDL/01I) were clustered into the same group (genotype VII) with J2.
TextSentencer_T154 25630-25829 Sentence denotes Similar to J2, CK/CH/LDL/97I and CK/CH/LDL/98I were isolated in swollen proventriculars tissues of infected chickens, whereas CK/CH/LDL/01I was isolated from atrophic oviduct of a diseased layer hen.
TextSentencer_T155 25830-25956 Sentence denotes It was found that the gross lesions of the kidney in these diseased chickens were also obvious, as with isolate 2992/02 [20] .
TextSentencer_T156 25957-26066 Sentence denotes 2992/02 was isolated in Taiwan and was very similar to the J2 strain by comparison of S1 protein genes [20] .
TextSentencer_T157 26067-26352 Sentence denotes The diversity of the pathogenicity of IBV strains was expected; although the primary tissue of IBV infection is the respiratory tract, some isolates can grow in nonrespiratory organs such as the kidney, the female reproductive tract, intestine, and spleen of chickens [2, 14, 33, 36] .
TextSentencer_T158 26353-26569 Sentence denotes With the exception of the Massachusetts strain, a very interesting aspect of IBV epidemiology, as far as it is possible to know, is the presence and the spreading of the various IBV serotypes in different continents.
TextSentencer_T159 26570-26650 Sentence denotes About 20 emergent serotypes in North America did not spread to other continents.
TextSentencer_T160 26651-26746 Sentence denotes Similarly, the European, Australian, and Asiatic serotypes apparently did not spread elsewhere.
TextSentencer_T161 26747-26794 Sentence denotes In China, IBV epidemiology is more complicated.
TextSentencer_T162 26795-27003 Sentence denotes Besides genotypes I to IV and VII, the Mass-type IBV and IBV closely related to Australian classical strains were also present, indicating IBVs showing various genetic differences were cocirculating in China.