Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination
Identifieur interne : 000738 ( Pmc/Curation ); précédent : 000737; suivant : 000739Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination
Auteurs : Mohamed S. H. Hassan ; Davor Ojkic ; Carla S. Coffin ; Susan C. Cork ; Frank Van Der Meer ; Mohamed Faizal Abdul-CareemSource :
- Viruses [ 1999-4915 ] ; 2019.
Abstract
Infectious bronchitis virus (IBV) infection in chickens can lead to an economically important disease, namely, infectious bronchitis (IB). New IBV variants are continuously emerging, which complicates vaccination-based IB control. In this study, five IBVs were isolated from clinical samples submitted to a diagnostic laboratory in Ontario, Canada, and subjected to detailed molecular characterization. Analysis of the spike (S)1 gene showed that these five IBVs were highly related to the Delmarva (DMV/1639) strain (~97.0% nucleotide sequence similarity) that was firstly isolated from an IB outbreak in the Delmarva peninsula, United States of America (USA), in 2011. However, the complete genomic sequence analysis showed a 93.5–93.7% similarity with the Connecticut (Conn) vaccine strain, suggesting that Conn-like viruses contributed to the evolution of the five Canadian IBV/DMV isolates. A SimPlot analysis of the complete genomic sequence showed evidence of recombination for at least three different IBV strains, including a Conn vaccine-like strain, a 4/91 vaccine-like strain, and one strain that is yet-unidentified. The unidentified strain may have contributed the genomic regions of the S, 3, and membrane (M) genes of the five Canadian IBV/DMV isolates. The study outcomes add to the existing knowledge about involvement of recombination in IBV evolution.
Url:
DOI: 10.3390/v11111054
PubMed: 31766215
PubMed Central: 6893544
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Hassan</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author><author><name sortKey="Ojkic, Davor" sort="Ojkic, Davor" uniqKey="Ojkic D" first="Davor" last="Ojkic">Davor Ojkic</name><affiliation><nlm:aff id="af2-viruses-11-01054">Animal Health Laboratory, University of Guelph, Guelph, ON N1G 2W1, Canada;<email>dojkic@uoguelph.ca</email></nlm:aff></affiliation></author><author><name sortKey="Coffin, Carla S" sort="Coffin, Carla S" uniqKey="Coffin C" first="Carla S." last="Coffin">Carla S. Coffin</name><affiliation><nlm:aff id="af3-viruses-11-01054">Cumming School of Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>cscoffin@ucalgary.ca</email></nlm:aff></affiliation></author><author><name sortKey="Cork, Susan C" sort="Cork, Susan C" uniqKey="Cork S" first="Susan C." last="Cork">Susan C. Cork</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author><author><name sortKey="Van Der Meer, Frank" sort="Van Der Meer, Frank" uniqKey="Van Der Meer F" first="Frank" last="Van Der Meer">Frank Van Der Meer</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author><author><name sortKey="Abdul Careem, Mohamed Faizal" sort="Abdul Careem, Mohamed Faizal" uniqKey="Abdul Careem M" first="Mohamed Faizal" last="Abdul-Careem">Mohamed Faizal Abdul-Careem</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31766215</idno><idno type="pmc">6893544</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893544</idno><idno type="RBID">PMC:6893544</idno><idno type="doi">10.3390/v11111054</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000738</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000738</idno><idno type="wicri:Area/Pmc/Curation">000738</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000738</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination</title><author><name sortKey="Hassan, Mohamed S H" sort="Hassan, Mohamed S H" uniqKey="Hassan M" first="Mohamed S. H." last="Hassan">Mohamed S. H. Hassan</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author><author><name sortKey="Ojkic, Davor" sort="Ojkic, Davor" uniqKey="Ojkic D" first="Davor" last="Ojkic">Davor Ojkic</name><affiliation><nlm:aff id="af2-viruses-11-01054">Animal Health Laboratory, University of Guelph, Guelph, ON N1G 2W1, Canada;<email>dojkic@uoguelph.ca</email></nlm:aff></affiliation></author><author><name sortKey="Coffin, Carla S" sort="Coffin, Carla S" uniqKey="Coffin C" first="Carla S." last="Coffin">Carla S. Coffin</name><affiliation><nlm:aff id="af3-viruses-11-01054">Cumming School of Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>cscoffin@ucalgary.ca</email></nlm:aff></affiliation></author><author><name sortKey="Cork, Susan C" sort="Cork, Susan C" uniqKey="Cork S" first="Susan C." last="Cork">Susan C. Cork</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author><author><name sortKey="Van Der Meer, Frank" sort="Van Der Meer, Frank" uniqKey="Van Der Meer F" first="Frank" last="Van Der Meer">Frank Van Der Meer</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author><author><name sortKey="Abdul Careem, Mohamed Faizal" sort="Abdul Careem, Mohamed Faizal" uniqKey="Abdul Careem M" first="Mohamed Faizal" last="Abdul-Careem">Mohamed Faizal Abdul-Careem</name><affiliation><nlm:aff id="af1-viruses-11-01054">Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</nlm:aff></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Infectious bronchitis virus (IBV) infection in chickens can lead to an economically important disease, namely, infectious bronchitis (IB). New IBV variants are continuously emerging, which complicates vaccination-based IB control. In this study, five IBVs were isolated from clinical samples submitted to a diagnostic laboratory in Ontario, Canada, and subjected to detailed molecular characterization. Analysis of the spike (S)1 gene showed that these five IBVs were highly related to the Delmarva (DMV/1639) strain (~97.0% nucleotide sequence similarity) that was firstly isolated from an IB outbreak in the Delmarva peninsula, United States of America (USA), in 2011. However, the complete genomic sequence analysis showed a 93.5–93.7% similarity with the Connecticut (Conn) vaccine strain, suggesting that Conn-like viruses contributed to the evolution of the five Canadian IBV/DMV isolates. A SimPlot analysis of the complete genomic sequence showed evidence of recombination for at least three different IBV strains, including a Conn vaccine-like strain, a 4/91 vaccine-like strain, and one strain that is yet-unidentified. The unidentified strain may have contributed the genomic regions of the S, 3, and membrane (M) genes of the five Canadian IBV/DMV isolates. The study outcomes add to the existing knowledge about involvement of recombination in IBV evolution.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jackwood, M W" uniqKey="Jackwood M">M.W. Jackwood</name></author><author><name sortKey="De Wit, S" uniqKey="De Wit S">S. de Wit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cavanagh, D" uniqKey="Cavanagh D">D. Cavanagh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fehr, A R" uniqKey="Fehr A">A.R. Fehr</name></author><author><name sortKey="Perlman, S" uniqKey="Perlman S">S. Perlman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Armesto, M" uniqKey="Armesto M">M. Armesto</name></author><author><name sortKey="Cavanagh, D" uniqKey="Cavanagh D">D. Cavanagh</name></author><author><name sortKey="Britton, P" uniqKey="Britton P">P. Britton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quinteros, J A" uniqKey="Quinteros J">J.A. Quinteros</name></author><author><name sortKey="Markham, P F" uniqKey="Markham P">P.F. Markham</name></author><author><name sortKey="Lee, S W" uniqKey="Lee S">S.-W. Lee</name></author><author><name sortKey="Hewson, K A" uniqKey="Hewson K">K.A. Hewson</name></author><author><name sortKey="Hartley, C A" uniqKey="Hartley C">C.A. Hartley</name></author><author><name sortKey="Legione, A R" uniqKey="Legione A">A.R. Legione</name></author><author><name sortKey="Coppo, M J" uniqKey="Coppo M">M.J. Coppo</name></author><author><name sortKey="Vaz, P K" uniqKey="Vaz P">P.K. Vaz</name></author><author><name sortKey="Browning, G F" uniqKey="Browning G">G.F. Browning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wickramasinghe, I N" uniqKey="Wickramasinghe I">I.N. Wickramasinghe</name></author><author><name sortKey="Van Beurden, S J" uniqKey="Van Beurden S">S.J. van Beurden</name></author><author><name sortKey="Weerts, E A" uniqKey="Weerts E">E.A. Weerts</name></author><author><name sortKey="Verheije, M H" uniqKey="Verheije M">M.H. Verheije</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Valastro, V" uniqKey="Valastro V">V. Valastro</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Britton, P" uniqKey="Britton P">P. Britton</name></author><author><name sortKey="Fusaro, A" uniqKey="Fusaro A">A. Fusaro</name></author><author><name sortKey="Jackwood, M W" uniqKey="Jackwood M">M.W. Jackwood</name></author><author><name sortKey="Cattoli, G" uniqKey="Cattoli G">G. Cattoli</name></author><author><name sortKey="Monne, I" uniqKey="Monne I">I. Monne</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jackwood, M W" uniqKey="Jackwood M">M.W. Jackwood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ammayappan, A" uniqKey="Ammayappan A">A. Ammayappan</name></author><author><name sortKey="Upadhyay, C" uniqKey="Upadhyay C">C. Upadhyay</name></author><author><name sortKey="Gelb, J" uniqKey="Gelb J">J. Gelb</name></author><author><name sortKey="Vakharia, V N" uniqKey="Vakharia V">V.N. Vakharia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lim, T H" uniqKey="Lim T">T.H. Lim</name></author><author><name sortKey="Lee, H J" uniqKey="Lee H">H.J. Lee</name></author><author><name sortKey="Lee, D H" uniqKey="Lee D">D.H. Lee</name></author><author><name sortKey="Lee, Y N" uniqKey="Lee Y">Y.N. Lee</name></author><author><name sortKey="Park, J K" uniqKey="Park J">J.K. Park</name></author><author><name sortKey="Youn, H N" uniqKey="Youn H">H.N. Youn</name></author><author><name sortKey="Kim, M S" uniqKey="Kim M">M.S. Kim</name></author><author><name sortKey="Lee, J B" uniqKey="Lee J">J.B. Lee</name></author><author><name sortKey="Park, S Y" uniqKey="Park S">S.Y. Park</name></author><author><name sortKey="Choi, I S" uniqKey="Choi I">I.S. Choi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moreno, A" uniqKey="Moreno A">A. Moreno</name></author><author><name sortKey="Franzo, G" uniqKey="Franzo G">G. Franzo</name></author><author><name sortKey="Massi, P" uniqKey="Massi P">P. Massi</name></author><author><name sortKey="Tosi, G" uniqKey="Tosi G">G. Tosi</name></author><author><name sortKey="Blanco, A" uniqKey="Blanco A">A. Blanco</name></author><author><name sortKey="Antilles, N" uniqKey="Antilles N">N. Antilles</name></author><author><name sortKey="Biarnes, M" uniqKey="Biarnes M">M. Biarnes</name></author><author><name sortKey="Majo, N" uniqKey="Majo N">N. Majo</name></author><author><name sortKey="Nofrarias, M" uniqKey="Nofrarias M">M. Nofrarias</name></author><author><name sortKey="Dolz, R" uniqKey="Dolz R">R. Dolz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, S" uniqKey="Zhou S">S. Zhou</name></author><author><name sortKey="Tang, M" uniqKey="Tang M">M. Tang</name></author><author><name sortKey="Jiang, Y" uniqKey="Jiang Y">Y. Jiang</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author><author><name sortKey="Shen, X" uniqKey="Shen X">X. Shen</name></author><author><name sortKey="Li, J" uniqKey="Li J">J. Li</name></author><author><name sortKey="Dai, Y" uniqKey="Dai Y">Y. Dai</name></author><author><name sortKey="Zou, J" uniqKey="Zou J">J. Zou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, T" uniqKey="Zhang T">T. Zhang</name></author><author><name sortKey="Han, Z" uniqKey="Han Z">Z. Han</name></author><author><name sortKey="Xu, Q" uniqKey="Xu Q">Q. Xu</name></author><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q. Wang</name></author><author><name sortKey="Gao, M" uniqKey="Gao M">M. Gao</name></author><author><name sortKey="Wu, W" uniqKey="Wu W">W. Wu</name></author><author><name sortKey="Shao, Y" uniqKey="Shao Y">Y. Shao</name></author><author><name sortKey="Li, H" uniqKey="Li H">H. Li</name></author><author><name sortKey="Kong, X" uniqKey="Kong X">X. Kong</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S. Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, X" uniqKey="Liu X">X. Liu</name></author><author><name sortKey="Ma, H" uniqKey="Ma H">H. Ma</name></author><author><name sortKey="Xu, Q" uniqKey="Xu Q">Q. Xu</name></author><author><name sortKey="Sun, N" uniqKey="Sun N">N. Sun</name></author><author><name sortKey="Han, Z" uniqKey="Han Z">Z. Han</name></author><author><name sortKey="Sun, C" uniqKey="Sun C">C. Sun</name></author><author><name sortKey="Guo, H" uniqKey="Guo H">H. Guo</name></author><author><name sortKey="Shao, Y" uniqKey="Shao Y">Y. Shao</name></author><author><name sortKey="Kong, X" uniqKey="Kong X">X. Kong</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S. Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, E" uniqKey="Martin E">E. Martin</name></author><author><name sortKey="Brash, M" uniqKey="Brash M">M. Brash</name></author><author><name sortKey="Stalker, M" uniqKey="Stalker M">M. Stalker</name></author><author><name sortKey="Ojkic, D" uniqKey="Ojkic D">D. Ojkic</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Petrik, M" uniqKey="Petrik M">M. Petrik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grgic, H" uniqKey="Grgic H">H. Grgic</name></author><author><name sortKey="Hunter, D B" uniqKey="Hunter D">D.B. Hunter</name></author><author><name sortKey="Hunton, P" uniqKey="Hunton P">P. Hunton</name></author><author><name sortKey="Nagy, E" uniqKey="Nagy E">E. Nagy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, E A" uniqKey="Martin E">E.A. Martin</name></author><author><name sortKey="Brash, M L" uniqKey="Brash M">M.L. Brash</name></author><author><name sortKey="Hoyland, S K" uniqKey="Hoyland S">S.K. Hoyland</name></author><author><name sortKey="Coventry, J M" uniqKey="Coventry J">J.M. Coventry</name></author><author><name sortKey="Sandrock, C" uniqKey="Sandrock C">C. Sandrock</name></author><author><name sortKey="Guerin, M T" uniqKey="Guerin M">M.T. Guerin</name></author><author><name sortKey="Ojkic, D" uniqKey="Ojkic D">D. Ojkic</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amarasinghe, A" uniqKey="Amarasinghe A">A. Amarasinghe</name></author><author><name sortKey="Popowich, S" uniqKey="Popowich S">S. Popowich</name></author><author><name sortKey="De Silva Senapathi, U" uniqKey="De Silva Senapathi U">U. De Silva Senapathi</name></author><author><name sortKey="Abdul Cader, M S" uniqKey="Abdul Cader M">M.S. Abdul-Cader</name></author><author><name sortKey="Marshall, F" uniqKey="Marshall F">F. Marshall</name></author><author><name sortKey="Van Der Meer, F" uniqKey="Van Der Meer F">F. van der Meer</name></author><author><name sortKey="Cork, S C" uniqKey="Cork S">S.C. Cork</name></author><author><name sortKey="Gomis, S" uniqKey="Gomis S">S. Gomis</name></author><author><name sortKey="Abdul Careem, M F" uniqKey="Abdul Careem M">M.F. Abdul-Careem</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amarasinghe, A" uniqKey="Amarasinghe A">A. Amarasinghe</name></author><author><name sortKey="De Silva Senapathi, U" uniqKey="De Silva Senapathi U">U. De Silva Senapathi</name></author><author><name sortKey="Abdul Cader, M S" uniqKey="Abdul Cader M">M.S. Abdul-Cader</name></author><author><name sortKey="Popowich, S" uniqKey="Popowich S">S. Popowich</name></author><author><name sortKey="Marshall, F" uniqKey="Marshall F">F. Marshall</name></author><author><name sortKey="Cork, S C" uniqKey="Cork S">S.C. Cork</name></author><author><name sortKey="Van Der Meer, F" uniqKey="Van Der Meer F">F. van der Meer</name></author><author><name sortKey="Gomis, S" uniqKey="Gomis S">S. Gomis</name></author><author><name sortKey="Abdul Careem, M F" uniqKey="Abdul Careem M">M.F. Abdul-Careem</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kameka, A M" uniqKey="Kameka A">A.M. Kameka</name></author><author><name sortKey="Haddadi, S" uniqKey="Haddadi S">S. Haddadi</name></author><author><name sortKey="Kim, D S" uniqKey="Kim D">D.S. Kim</name></author><author><name sortKey="Cork, S C" uniqKey="Cork S">S.C. Cork</name></author><author><name sortKey="Abdul Careem, M F" uniqKey="Abdul Careem M">M.F. Abdul-Careem</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grgic, H" uniqKey="Grgic H">H. Grgic</name></author><author><name sortKey="Hunter, D B" uniqKey="Hunter D">D.B. Hunter</name></author><author><name sortKey="Hunton, P" uniqKey="Hunton P">P. Hunton</name></author><author><name sortKey="Nagy, E" uniqKey="Nagy E">E. Nagy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smati, R" uniqKey="Smati R">R. Smati</name></author><author><name sortKey="Silim, A" uniqKey="Silim A">A. Silim</name></author><author><name sortKey="Guertin, C" uniqKey="Guertin C">C. Guertin</name></author><author><name sortKey="Henrichon, M" uniqKey="Henrichon M">M. Henrichon</name></author><author><name sortKey="Marandi, M" uniqKey="Marandi M">M. Marandi</name></author><author><name sortKey="Arella, M" uniqKey="Arella M">M. Arella</name></author><author><name sortKey="Merzouki, A" uniqKey="Merzouki A">A. Merzouki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sievers, F" uniqKey="Sievers F">F. Sievers</name></author><author><name sortKey="Wilm, A" uniqKey="Wilm A">A. Wilm</name></author><author><name sortKey="Dineen, D" uniqKey="Dineen D">D. Dineen</name></author><author><name sortKey="Gibson, T J" uniqKey="Gibson T">T.J. Gibson</name></author><author><name sortKey="Karplus, K" uniqKey="Karplus K">K. Karplus</name></author><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Lopez, R" uniqKey="Lopez R">R. Lopez</name></author><author><name sortKey="Mcwilliam, H" uniqKey="Mcwilliam H">H. McWilliam</name></author><author><name sortKey="Remmert, M" uniqKey="Remmert M">M. Remmert</name></author><author><name sortKey="Soding, J" uniqKey="Soding J">J. Soding</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stamatakis, A" uniqKey="Stamatakis A">A. Stamatakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Godzik, A" uniqKey="Godzik A">A. Godzik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katoh, K" uniqKey="Katoh K">K. Katoh</name></author><author><name sortKey="Standley, D M" uniqKey="Standley D">D.M. Standley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goraichuk, I V" uniqKey="Goraichuk I">I.V. Goraichuk</name></author><author><name sortKey="Kulkarni, A B" uniqKey="Kulkarni A">A.B. Kulkarni</name></author><author><name sortKey="Williams Coplin, D" uniqKey="Williams Coplin D">D. Williams-Coplin</name></author><author><name sortKey="Suarez, D L" uniqKey="Suarez D">D.L. Suarez</name></author><author><name sortKey="Afonso, C L" uniqKey="Afonso C">C.L. Afonso</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lole, K S" uniqKey="Lole K">K.S. Lole</name></author><author><name sortKey="Bollinger, R C" uniqKey="Bollinger R">R.C. Bollinger</name></author><author><name sortKey="Paranjape, R S" uniqKey="Paranjape R">R.S. Paranjape</name></author><author><name sortKey="Gadkari, D" uniqKey="Gadkari D">D. Gadkari</name></author><author><name sortKey="Kulkarni, S S" uniqKey="Kulkarni S">S.S. Kulkarni</name></author><author><name sortKey="Novak, N G" uniqKey="Novak N">N.G. Novak</name></author><author><name sortKey="Ingersoll, R" uniqKey="Ingersoll R">R. Ingersoll</name></author><author><name sortKey="Sheppard, H W" uniqKey="Sheppard H">H.W. Sheppard</name></author><author><name sortKey="Ray, S C" uniqKey="Ray S">S.C. Ray</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guindon, S" uniqKey="Guindon S">S. Guindon</name></author><author><name sortKey="Dufayard, J F" uniqKey="Dufayard J">J.-F. Dufayard</name></author><author><name sortKey="Lefort, V" uniqKey="Lefort V">V. Lefort</name></author><author><name sortKey="Anisimova, M" uniqKey="Anisimova M">M. Anisimova</name></author><author><name sortKey="Hordijk, W" uniqKey="Hordijk W">W. Hordijk</name></author><author><name sortKey="Gascuel, O" uniqKey="Gascuel O">O. Gascuel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gelb, J" uniqKey="Gelb J">J. Gelb</name></author><author><name sortKey="Ladman, B S" uniqKey="Ladman B">B.S. Ladman</name></author><author><name sortKey="Pope, C R" uniqKey="Pope C">C.R. Pope</name></author><author><name sortKey="Ruano, J M" uniqKey="Ruano J">J.M. Ruano</name></author><author><name sortKey="Brannick, E M" uniqKey="Brannick E">E.M. Brannick</name></author><author><name sortKey="Bautista, D A" uniqKey="Bautista D">D.A. Bautista</name></author><author><name sortKey="Coughlin, C M" uniqKey="Coughlin C">C.M. Coughlin</name></author><author><name sortKey="Preskenis, L A" uniqKey="Preskenis L">L.A. Preskenis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mckinley, E T" uniqKey="Mckinley E">E.T. McKinley</name></author><author><name sortKey="Hilt, D A" uniqKey="Hilt D">D.A. Hilt</name></author><author><name sortKey="Jackwood, M W" uniqKey="Jackwood M">M.W. Jackwood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Reddy, V R" uniqKey="Reddy V">V.R. Reddy</name></author><author><name sortKey="Theuns, S" uniqKey="Theuns S">S. Theuns</name></author><author><name sortKey="Roukaerts, I D" uniqKey="Roukaerts I">I.D. Roukaerts</name></author><author><name sortKey="Zeller, M" uniqKey="Zeller M">M. Zeller</name></author><author><name sortKey="Matthijnssens, J" uniqKey="Matthijnssens J">J. Matthijnssens</name></author><author><name sortKey="Nauwynck, H J" uniqKey="Nauwynck H">H.J. Nauwynck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feng, K Y" uniqKey="Feng K">K.Y. Feng</name></author><author><name sortKey="Chen, T" uniqKey="Chen T">T. Chen</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X. Zhang</name></author><author><name sortKey="Shao, G M" uniqKey="Shao G">G.M. Shao</name></author><author><name sortKey="Cao, Y" uniqKey="Cao Y">Y. Cao</name></author><author><name sortKey="Chen, D K" uniqKey="Chen D">D.K. Chen</name></author><author><name sortKey="Lin, W C" uniqKey="Lin W">W.C. Lin</name></author><author><name sortKey="Chen, F" uniqKey="Chen F">F. Chen</name></author><author><name sortKey="Xie, Q M" uniqKey="Xie Q">Q.M. Xie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abozeid, H H" uniqKey="Abozeid H">H.H. Abozeid</name></author><author><name sortKey="Paldurai, A" uniqKey="Paldurai A">A. Paldurai</name></author><author><name sortKey="Khattar, S K" uniqKey="Khattar S">S.K. Khattar</name></author><author><name sortKey="Afifi, M A" uniqKey="Afifi M">M.A. Afifi</name></author><author><name sortKey="El Kady, M F" uniqKey="El Kady M">M.F. El-Kady</name></author><author><name sortKey="El Deeb, A H" uniqKey="El Deeb A">A.H. El-Deeb</name></author><author><name sortKey="Samal, S K" uniqKey="Samal S">S.K. Samal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hewson, K A" uniqKey="Hewson K">K.A. Hewson</name></author><author><name sortKey="Ignjatovic, J" uniqKey="Ignjatovic J">J. Ignjatovic</name></author><author><name sortKey="Browning, G F" uniqKey="Browning G">G.F. Browning</name></author><author><name sortKey="Devlin, J M" uniqKey="Devlin J">J.M. Devlin</name></author><author><name sortKey="Noormohammadi, A H" uniqKey="Noormohammadi A">A.H. Noormohammadi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mardani, K" uniqKey="Mardani K">K. Mardani</name></author><author><name sortKey="Noormohammadi, A H" uniqKey="Noormohammadi A">A.H. Noormohammadi</name></author><author><name sortKey="Hooper, P" uniqKey="Hooper P">P. Hooper</name></author><author><name sortKey="Ignjatovic, J" uniqKey="Ignjatovic J">J. Ignjatovic</name></author><author><name sortKey="Browning, G F" uniqKey="Browning G">G.F. Browning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, S" uniqKey="Liu S">S. Liu</name></author><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q. Zhang</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name></author><author><name sortKey="Han, Z" uniqKey="Han Z">Z. Han</name></author><author><name sortKey="Shao, Y" uniqKey="Shao Y">Y. Shao</name></author><author><name sortKey="Kong, X" uniqKey="Kong X">X. Kong</name></author><author><name sortKey="Tong, G" uniqKey="Tong G">G. Tong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Beurden, S J" uniqKey="Van Beurden S">S.J. Van Beurden</name></author><author><name sortKey="Berends, A J" uniqKey="Berends A">A.J. Berends</name></author><author><name sortKey="Kramer Kuhl, A" uniqKey="Kramer Kuhl A">A. Kramer-Kuhl</name></author><author><name sortKey="Spekreijse, D" uniqKey="Spekreijse D">D. Spekreijse</name></author><author><name sortKey="Chenard, G" uniqKey="Chenard G">G. Chenard</name></author><author><name sortKey="Philipp, H C" uniqKey="Philipp H">H.C. Philipp</name></author><author><name sortKey="Mundt, E" uniqKey="Mundt E">E. Mundt</name></author><author><name sortKey="Rottier, P J M" uniqKey="Rottier P">P.J.M. Rottier</name></author><author><name sortKey="Verheije, M H" uniqKey="Verheije M">M.H. Verheije</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Y" uniqKey="Yang Y">Y. Yang</name></author><author><name sortKey="Zhang, L" uniqKey="Zhang L">L. Zhang</name></author><author><name sortKey="Geng, H" uniqKey="Geng H">H. Geng</name></author><author><name sortKey="Deng, Y" uniqKey="Deng Y">Y. Deng</name></author><author><name sortKey="Huang, B" uniqKey="Huang B">B. Huang</name></author><author><name sortKey="Guo, Y" uniqKey="Guo Y">Y. Guo</name></author><author><name sortKey="Zhao, Z" uniqKey="Zhao Z">Z. Zhao</name></author><author><name sortKey="Tan, W" uniqKey="Tan W">W. Tan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ye, Z" uniqKey="Ye Z">Z. Ye</name></author><author><name sortKey="Wong, C K" uniqKey="Wong C">C.K. Wong</name></author><author><name sortKey="Li, P" uniqKey="Li P">P. Li</name></author><author><name sortKey="Xie, Y" uniqKey="Xie Y">Y. Xie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sjaak De Wit, J J" uniqKey="Sjaak De Wit J">J.J. Sjaak de Wit</name></author><author><name sortKey="Cook, J K" uniqKey="Cook J">J.K. Cook</name></author><author><name sortKey="Van Der Heijden, H M" uniqKey="Van Der Heijden H">H.M. van der Heijden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hughes, L A" uniqKey="Hughes L">L.A. Hughes</name></author><author><name sortKey="Savage, C" uniqKey="Savage C">C. Savage</name></author><author><name sortKey="Naylor, C" uniqKey="Naylor C">C. Naylor</name></author><author><name sortKey="Bennett, M" uniqKey="Bennett M">M. Bennett</name></author><author><name sortKey="Chantrey, J" uniqKey="Chantrey J">J. Chantrey</name></author><author><name sortKey="Jones, R" uniqKey="Jones R">R. Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ziegler, A F" uniqKey="Ziegler A">A.F. Ziegler</name></author><author><name sortKey="Ladman, B S" uniqKey="Ladman B">B.S. Ladman</name></author><author><name sortKey="Dunn, P A" uniqKey="Dunn P">P.A. Dunn</name></author><author><name sortKey="Schneider, A" uniqKey="Schneider A">A. Schneider</name></author><author><name sortKey="Davison, S" uniqKey="Davison S">S. Davison</name></author><author><name sortKey="Miller, P G" uniqKey="Miller P">P.G. Miller</name></author><author><name sortKey="Lu, H" uniqKey="Lu H">H. Lu</name></author><author><name sortKey="Weinstock, D" uniqKey="Weinstock D">D. Weinstock</name></author><author><name sortKey="Salem, M" uniqKey="Salem M">M. Salem</name></author><author><name sortKey="Eckroade, R J" uniqKey="Eckroade R">R.J. Eckroade</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simon Loriere, E" uniqKey="Simon Loriere E">E. Simon-Loriere</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thor, S W" uniqKey="Thor S">S.W. Thor</name></author><author><name sortKey="Hilt, D A" uniqKey="Hilt D">D.A. Hilt</name></author><author><name sortKey="Kissinger, J C" uniqKey="Kissinger J">J.C. Kissinger</name></author><author><name sortKey="Paterson, A H" uniqKey="Paterson A">A.H. Paterson</name></author><author><name sortKey="Jackwood, M W" uniqKey="Jackwood M">M.W. Jackwood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Khanh, N P" uniqKey="Khanh N">N.P. Khanh</name></author><author><name sortKey="Tan, S W" uniqKey="Tan S">S.W. Tan</name></author><author><name sortKey="Yeap, S K" uniqKey="Yeap S">S.K. Yeap</name></author><author><name sortKey="Satharasinghe, D A" uniqKey="Satharasinghe D">D.A. Satharasinghe</name></author><author><name sortKey="Hair Bejo, M" uniqKey="Hair Bejo M">M. Hair-Bejo</name></author><author><name sortKey="Bich, T N" uniqKey="Bich T">T.N. Bich</name></author><author><name sortKey="Omar, A R" uniqKey="Omar A">A.R. Omar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Naguib, M M" uniqKey="Naguib M">M.M. Naguib</name></author><author><name sortKey="Hoper, D" uniqKey="Hoper D">D. Hoper</name></author><author><name sortKey="Arafa, A S" uniqKey="Arafa A">A.S. Arafa</name></author><author><name sortKey="Setta, A M" uniqKey="Setta A">A.M. Setta</name></author><author><name sortKey="Abed, M" uniqKey="Abed M">M. Abed</name></author><author><name sortKey="Monne, I" uniqKey="Monne I">I. Monne</name></author><author><name sortKey="Beer, M" uniqKey="Beer M">M. Beer</name></author><author><name sortKey="Harder, T C" uniqKey="Harder T">T.C. Harder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, L" uniqKey="Xu L">L. Xu</name></author><author><name sortKey="Ren, M" uniqKey="Ren M">M. Ren</name></author><author><name sortKey="Sheng, J" uniqKey="Sheng J">J. Sheng</name></author><author><name sortKey="Ma, T" uniqKey="Ma T">T. Ma</name></author><author><name sortKey="Han, Z" uniqKey="Han Z">Z. Han</name></author><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y. Zhao</name></author><author><name sortKey="Sun, J" uniqKey="Sun J">J. Sun</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S. Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mckinley, E T" uniqKey="Mckinley E">E.T. McKinley</name></author><author><name sortKey="Jackwood, M W" uniqKey="Jackwood M">M.W. Jackwood</name></author><author><name sortKey="Hilt, D A" uniqKey="Hilt D">D.A. Hilt</name></author><author><name sortKey="Kissinger, J C" uniqKey="Kissinger J">J.C. Kissinger</name></author><author><name sortKey="Robertson, J S" uniqKey="Robertson J">J.S. Robertson</name></author><author><name sortKey="Lemke, C" uniqKey="Lemke C">C. Lemke</name></author><author><name sortKey="Paterson, A H" uniqKey="Paterson A">A.H. Paterson</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Viruses</journal-id><journal-id journal-id-type="iso-abbrev">Viruses</journal-id><journal-id journal-id-type="publisher-id">viruses</journal-id><journal-title-group><journal-title>Viruses</journal-title></journal-title-group><issn pub-type="epub">1999-4915</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31766215</article-id><article-id pub-id-type="pmc">6893544</article-id><article-id pub-id-type="doi">10.3390/v11111054</article-id><article-id pub-id-type="publisher-id">viruses-11-01054</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination</article-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-7424-5305</contrib-id><name><surname>Hassan</surname><given-names>Mohamed S. H.</given-names></name><xref ref-type="aff" rid="af1-viruses-11-01054">1</xref></contrib><contrib contrib-type="author"><name><surname>Ojkic</surname><given-names>Davor</given-names></name><xref ref-type="aff" rid="af2-viruses-11-01054">2</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-1472-0901</contrib-id><name><surname>Coffin</surname><given-names>Carla S.</given-names></name><xref ref-type="aff" rid="af3-viruses-11-01054">3</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0002-8200-3584</contrib-id><name><surname>Cork</surname><given-names>Susan C.</given-names></name><xref ref-type="aff" rid="af1-viruses-11-01054">1</xref></contrib><contrib contrib-type="author"><name><surname>van der Meer</surname><given-names>Frank</given-names></name><xref ref-type="aff" rid="af1-viruses-11-01054">1</xref></contrib><contrib contrib-type="author"><name><surname>Abdul-Careem</surname><given-names>Mohamed Faizal</given-names></name><xref ref-type="aff" rid="af1-viruses-11-01054">1</xref><xref rid="c1-viruses-11-01054" ref-type="corresp">*</xref></contrib></contrib-group><aff id="af1-viruses-11-01054"><label>1</label>Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>msh.hassan@ucalgary.ca</email> (M.S.H.H.);<email>sccork@ucalgary.ca</email> (S.C.C.);<email>fjvander@ucalgary.ca</email> (F.v.d.M.)</aff><aff id="af2-viruses-11-01054"><label>2</label>Animal Health Laboratory, University of Guelph, Guelph, ON N1G 2W1, Canada;<email>dojkic@uoguelph.ca</email></aff><aff id="af3-viruses-11-01054"><label>3</label>Cumming School of Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada;<email>cscoffin@ucalgary.ca</email></aff><author-notes><corresp id="c1-viruses-11-01054"><label>*</label>Correspondence: <email>faizal.abdulcareem@ucalgary.ca</email>; Tel.: +403-220-4462; Fax: +403-210-9740</corresp></author-notes><pub-date pub-type="epub"><day>13</day><month>11</month><year>2019</year></pub-date><pub-date pub-type="collection"><month>11</month><year>2019</year></pub-date><volume>11</volume><issue>11</issue><elocation-id>1054</elocation-id><history><date date-type="received"><day>16</day><month>10</month><year>2019</year></date><date date-type="accepted"><day>11</day><month>11</month><year>2019</year></date></history><permissions><copyright-statement>© 2019 by the authors.</copyright-statement><copyright-year>2019</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><p>Infectious bronchitis virus (IBV) infection in chickens can lead to an economically important disease, namely, infectious bronchitis (IB). New IBV variants are continuously emerging, which complicates vaccination-based IB control. In this study, five IBVs were isolated from clinical samples submitted to a diagnostic laboratory in Ontario, Canada, and subjected to detailed molecular characterization. Analysis of the spike (S)1 gene showed that these five IBVs were highly related to the Delmarva (DMV/1639) strain (~97.0% nucleotide sequence similarity) that was firstly isolated from an IB outbreak in the Delmarva peninsula, United States of America (USA), in 2011. However, the complete genomic sequence analysis showed a 93.5–93.7% similarity with the Connecticut (Conn) vaccine strain, suggesting that Conn-like viruses contributed to the evolution of the five Canadian IBV/DMV isolates. A SimPlot analysis of the complete genomic sequence showed evidence of recombination for at least three different IBV strains, including a Conn vaccine-like strain, a 4/91 vaccine-like strain, and one strain that is yet-unidentified. The unidentified strain may have contributed the genomic regions of the S, 3, and membrane (M) genes of the five Canadian IBV/DMV isolates. The study outcomes add to the existing knowledge about involvement of recombination in IBV evolution.</p></abstract><kwd-group><kwd>Infectious bronchitis virus (IBV)</kwd><kwd>recombination</kwd><kwd>complete genome sequence</kwd><kwd>phylogenetic analysis</kwd><kwd>chicken</kwd><kwd>Canada</kwd></kwd-group></article-meta></front><floats-group><fig id="viruses-11-01054-f001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Randomized accelerated maximum likelihood (RAxML) phylogenetic tree based on the complete nucleotide sequences of S1 genes of our five IBV isolates and 86 reference sequences. All genotypes of representative IBV strains are indicated on the right side. Our five IBV isolates are marked in red color.</p></caption><graphic xlink:href="viruses-11-01054-g001"></graphic></fig><fig id="viruses-11-01054-f002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Sequence alignment of open reading frame (ORF) 6b from our five IBV isolates. The deletion in gene 6b of isolate IBV/Ck/Can/18-048192T results in a truncated 6b protein. Sequences of isolates IBV/Ck/Can/17-035614, IBV/Ck/Can/17-036989, IBV/Ck/Can/18-048430, and IBV/Ck/Can/18-049707, as representatives of the normal 6b gene, were compared. The ATGs with a single underline in boldface are the start codons of 6b gene. TGA and TAGs in boxes are the termination codons of 6b gene in IBV/Ck/Can/18-048192T and the other four isolates, respectively. A 13-nucleotide sequence was deleted in isolate IBV/Ck/Can/18-048192T (represented as –).</p></caption><graphic xlink:href="viruses-11-01054-g002"></graphic></fig><fig id="viruses-11-01054-f003" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Alignment of the complete genome sequences of our five IBV isolates, the Connecticut vaccine, and 4/91 vaccine strains, which was performed using MAFFT. Nucleotide sequence disagreements at the indicated positions are shown in black, while nucleotide sequence agreements are shown in gray.</p></caption><graphic xlink:href="viruses-11-01054-g003"></graphic></fig><fig id="viruses-11-01054-f004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Alignment of the complete genome sequences of isolate GA9977/2019, the Connecticut vaccine, and 4/91 vaccine strains, which was performed using MAFFT. Nucleotide sequence disagreements at indicated positions are shown in black, while nucleotide sequence agreements are shown in gray.</p></caption><graphic xlink:href="viruses-11-01054-g004"></graphic></fig><fig id="viruses-11-01054-f005" orientation="portrait" position="float"><label>Figure 5</label><caption><p>(<bold>a</bold>) Recombination analysis by SimPlot of the complete genome sequences of IBV/Ck/Can/18-049707, the Connecticut vaccine, and the 4/91 vaccine strains. Breakpoints are indicated by the vertical red lines. The SimPlot was created using a window size of 1000 nt and a step size of 50 nt. Isolate IBV/Ck/Can/18-049707 was used as the query sequence. (<bold>b</bold>) Percentages of nucleotide sequence identity among our five IBV isolates, the Connecticut vaccine, the 4/91 vaccine, and H120 (as a representative of the Massachusetts type, the second major live vaccine available in Canada) according to the genome fragments indicated by SimPlot. Genome positions were determined according to isolate IBV/Ck/Can/18-049707 in the alignment. (<bold>c</bold>) Phylogenetic analysis of genome positions 1–1911, 1912–3735, 3736–12043, 12044–20120, 20121–25100, and 25,101–3′ end of the complete genome among our five IBV isolates, Connecticut vaccine, 4/91 vaccine, Arkansas DPI (GQ504720), H120 (FJ888351), JMK (GU393338), Iowa 97 (GU393337), Delaware 072 (Gu393332) and ck/CH/LDL/05II (kx364298). The trees were constructed using the maximum likelihood method in PhyML. Our five IBV isolates are marked in red color.</p></caption><graphic xlink:href="viruses-11-01054-g005a"></graphic><graphic xlink:href="viruses-11-01054-g005b"></graphic></fig><table-wrap id="viruses-11-01054-t001" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-01054-t001_Table 1</object-id><label>Table 1</label><caption><p>History of the five infectious bronchitis virus (IBV) isolates used in this study.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">IBV Isolate</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Type of Sample</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Commodity</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Age</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Size of the Flock</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Main Complaint</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">IBV/Ck/Can/17-035614</td><td align="center" valign="middle" rowspan="1" colspan="1">Cecal tonsils</td><td align="center" valign="middle" rowspan="1" colspan="1">Layers</td><td align="center" valign="middle" rowspan="1" colspan="1">6 weeks</td><td align="center" valign="middle" rowspan="1" colspan="1">100,000</td><td align="center" valign="middle" rowspan="1" colspan="1">Uneven flock</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">IBV/Ck/Can/17-036989</td><td align="center" valign="middle" rowspan="1" colspan="1">Kidneys</td><td align="center" valign="middle" rowspan="1" colspan="1">Layers</td><td align="center" valign="middle" rowspan="1" colspan="1">22 weeks</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">Drop in egg production</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">IBV/Ck/Can/18-048192T</td><td align="center" valign="middle" rowspan="1" colspan="1">Trachea</td><td align="center" valign="middle" rowspan="1" colspan="1">Broilers</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">IBV/Ck/Can/18-048430</td><td align="center" valign="middle" rowspan="1" colspan="1">Tracheal swab</td><td align="center" valign="middle" rowspan="1" colspan="1">Broilers</td><td align="center" valign="middle" rowspan="1" colspan="1">34 days</td><td align="center" valign="middle" rowspan="1" colspan="1">9408</td><td align="center" valign="middle" rowspan="1" colspan="1">Routine sampling</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">IBV/Ck/Can/18-049707</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Cecal tonsils</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Broiler breeders</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">41 weeks</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">20,358</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Increased mortality</td></tr></tbody></table><table-wrap-foot><fn><p>NA = Not available.</p></fn></table-wrap-foot></table-wrap><table-wrap id="viruses-11-01054-t002" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-01054-t002_Table 2</object-id><label>Table 2</label><caption><p>Percent S1 amino acid and nucleotide sequence identity values for the five IBV isolates used in this study and other strains that are circulating in Canada.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin" rowspan="1" colspan="1"></th><th colspan="15" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">Nucleotide Identity (%)</th></tr><tr><th align="center" valign="middle" rowspan="1" colspan="1"></th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">18-048192T</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">18-049707</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">18-048430</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">17-036989</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">17-035614</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">DMV/1639</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">PA/Wolg/98</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Qu-mv</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Conn </th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Mass</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4/91</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">CAL1737</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">CU_82792</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">DE/072</th></tr></thead><tbody><tr><td rowspan="15" align="center" valign="middle" style="border-bottom:solid thin" colspan="1"><bold>Amino Acid Identity (%)</bold></td><td align="center" valign="middle" rowspan="1" colspan="1"><bold>18-048192T</bold></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.5</td><td align="center" valign="middle" rowspan="1" colspan="1">99.8</td><td align="center" valign="middle" rowspan="1" colspan="1">99.4</td><td align="center" valign="middle" rowspan="1" colspan="1">99.7</td><td align="center" valign="middle" rowspan="1" colspan="1">96.5</td><td align="center" valign="middle" rowspan="1" colspan="1">90.1</td><td align="center" valign="middle" rowspan="1" colspan="1">78.8</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">76.0</td><td align="center" valign="middle" rowspan="1" colspan="1">76.5</td><td align="center" valign="middle" rowspan="1" colspan="1">56.4</td><td align="center" valign="middle" rowspan="1" colspan="1">55.8</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>18-049707</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">99.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" rowspan="1" colspan="1">99.9</td><td align="center" valign="middle" rowspan="1" colspan="1">99.7</td><td align="center" valign="middle" rowspan="1" colspan="1">96.5</td><td align="center" valign="middle" rowspan="1" colspan="1">90.1</td><td align="center" valign="middle" rowspan="1" colspan="1">78.6</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">75.8</td><td align="center" valign="middle" rowspan="1" colspan="1">76.2</td><td align="center" valign="middle" rowspan="1" colspan="1">56.3</td><td align="center" valign="middle" rowspan="1" colspan="1">55.6</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>18-048430</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" rowspan="1" colspan="1">99.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.5</td><td align="center" valign="middle" rowspan="1" colspan="1">99.8</td><td align="center" valign="middle" rowspan="1" colspan="1">96.4</td><td align="center" valign="middle" rowspan="1" colspan="1">89.9</td><td align="center" valign="middle" rowspan="1" colspan="1">78.7</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">75.3</td><td align="center" valign="middle" rowspan="1" colspan="1">76.4</td><td align="center" valign="middle" rowspan="1" colspan="1">56.4</td><td align="center" valign="middle" rowspan="1" colspan="1">55.8</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>17-036989</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">99.1</td><td align="center" valign="middle" rowspan="1" colspan="1">99.8</td><td align="center" valign="middle" rowspan="1" colspan="1">99.1</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" rowspan="1" colspan="1">96.4</td><td align="center" valign="middle" rowspan="1" colspan="1">90.0</td><td align="center" valign="middle" rowspan="1" colspan="1">78.5</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">75.7</td><td align="center" valign="middle" rowspan="1" colspan="1">75.5</td><td align="center" valign="middle" rowspan="1" colspan="1">55.3</td><td align="center" valign="middle" rowspan="1" colspan="1">55.6</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>17-035614</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">99.4</td><td align="center" valign="middle" rowspan="1" colspan="1">99.4</td><td align="center" valign="middle" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" rowspan="1" colspan="1">99.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">96.7</td><td align="center" valign="middle" rowspan="1" colspan="1">89.9</td><td align="center" valign="middle" rowspan="1" colspan="1">78.6</td><td align="center" valign="middle" rowspan="1" colspan="1">77.3</td><td align="center" valign="middle" rowspan="1" colspan="1">77.3</td><td align="center" valign="middle" rowspan="1" colspan="1">75.8</td><td align="center" valign="middle" rowspan="1" colspan="1">76.1</td><td align="center" valign="middle" rowspan="1" colspan="1">56.3</td><td align="center" valign="middle" rowspan="1" colspan="1">55.6</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>DMV/1639</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">94.8</td><td align="center" valign="middle" rowspan="1" colspan="1">95.2</td><td align="center" valign="middle" rowspan="1" colspan="1">95.0</td><td align="center" valign="middle" rowspan="1" colspan="1">95.0</td><td align="center" valign="middle" rowspan="1" colspan="1">95.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">91.1</td><td align="center" valign="middle" rowspan="1" colspan="1">79.7</td><td align="center" valign="middle" rowspan="1" colspan="1">78.4</td><td align="center" valign="middle" rowspan="1" colspan="1">78.4</td><td align="center" valign="middle" rowspan="1" colspan="1">76.2</td><td align="center" valign="middle" rowspan="1" colspan="1">75.1</td><td align="center" valign="middle" rowspan="1" colspan="1">56.0</td><td align="center" valign="middle" rowspan="1" colspan="1">55.3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>PA/Wolg/98</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">87.5</td><td align="center" valign="middle" rowspan="1" colspan="1">87.3</td><td align="center" valign="middle" rowspan="1" colspan="1">87.1</td><td align="center" valign="middle" rowspan="1" colspan="1">87.1</td><td align="center" valign="middle" rowspan="1" colspan="1">87.1</td><td align="center" valign="middle" rowspan="1" colspan="1">87.5</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">79.6</td><td align="center" valign="middle" rowspan="1" colspan="1">78.6</td><td align="center" valign="middle" rowspan="1" colspan="1">78.6</td><td align="center" valign="middle" rowspan="1" colspan="1">76.3</td><td align="center" valign="middle" rowspan="1" colspan="1">76.1</td><td align="center" valign="middle" rowspan="1" colspan="1">56.5</td><td align="center" valign="middle" rowspan="1" colspan="1">56.0</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>Qu-mv</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">76.3</td><td align="center" valign="middle" rowspan="1" colspan="1">76.1</td><td align="center" valign="middle" rowspan="1" colspan="1">76.1</td><td align="center" valign="middle" rowspan="1" colspan="1">75.9</td><td align="center" valign="middle" rowspan="1" colspan="1">75.9</td><td align="center" valign="middle" rowspan="1" colspan="1">75.9</td><td align="center" valign="middle" rowspan="1" colspan="1">76.1</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">78.6</td><td align="center" valign="middle" rowspan="1" colspan="1">79.3</td><td align="center" valign="middle" rowspan="1" colspan="1">77.0</td><td align="center" valign="middle" rowspan="1" colspan="1">75.9</td><td align="center" valign="middle" rowspan="1" colspan="1">57.2</td><td align="center" valign="middle" rowspan="1" colspan="1">56.8</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>Conn 46</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">75.5</td><td align="center" valign="middle" rowspan="1" colspan="1">76.9</td><td align="center" valign="middle" rowspan="1" colspan="1">75.6</td><td align="center" valign="middle" rowspan="1" colspan="1">75.5</td><td align="center" valign="middle" rowspan="1" colspan="1">75.6</td><td align="center" valign="middle" rowspan="1" colspan="1">75.3</td><td align="center" valign="middle" rowspan="1" colspan="1">75.7</td><td align="center" valign="middle" rowspan="1" colspan="1">74.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">95.1</td><td align="center" valign="middle" rowspan="1" colspan="1">77.6</td><td align="center" valign="middle" rowspan="1" colspan="1">80.3</td><td align="center" valign="middle" rowspan="1" colspan="1">58.7</td><td align="center" valign="middle" rowspan="1" colspan="1">57.9</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>M41</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">73.0</td><td align="center" valign="middle" rowspan="1" colspan="1">73.3</td><td align="center" valign="middle" rowspan="1" colspan="1">73.2</td><td align="center" valign="middle" rowspan="1" colspan="1">73.2</td><td align="center" valign="middle" rowspan="1" colspan="1">73.3</td><td align="center" valign="middle" rowspan="1" colspan="1">73.4</td><td align="center" valign="middle" rowspan="1" colspan="1">73.9</td><td align="center" valign="middle" rowspan="1" colspan="1">74.2</td><td align="center" valign="middle" rowspan="1" colspan="1">90.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">78.3</td><td align="center" valign="middle" rowspan="1" colspan="1">80.6</td><td align="center" valign="middle" rowspan="1" colspan="1">58.6</td><td align="center" valign="middle" rowspan="1" colspan="1">57.9</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>4/91</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">75.5</td><td align="center" valign="middle" rowspan="1" colspan="1">75.5</td><td align="center" valign="middle" rowspan="1" colspan="1">75.3</td><td align="center" valign="middle" rowspan="1" colspan="1">75.3</td><td align="center" valign="middle" rowspan="1" colspan="1">75.3</td><td align="center" valign="middle" rowspan="1" colspan="1">74.7</td><td align="center" valign="middle" rowspan="1" colspan="1">74.4</td><td align="center" valign="middle" rowspan="1" colspan="1">75.1</td><td align="center" valign="middle" rowspan="1" colspan="1">73.9</td><td align="center" valign="middle" rowspan="1" colspan="1">73.8</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">77.2</td><td align="center" valign="middle" rowspan="1" colspan="1">56.2</td><td align="center" valign="middle" rowspan="1" colspan="1">55.8</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>CAL1737</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">72.8</td><td align="center" valign="middle" rowspan="1" colspan="1">72.8</td><td align="center" valign="middle" rowspan="1" colspan="1">72.7</td><td align="center" valign="middle" rowspan="1" colspan="1">72.7</td><td align="center" valign="middle" rowspan="1" colspan="1">72.8</td><td align="center" valign="middle" rowspan="1" colspan="1">71.2</td><td align="center" valign="middle" rowspan="1" colspan="1">71.6</td><td align="center" valign="middle" rowspan="1" colspan="1">72.3</td><td align="center" valign="middle" rowspan="1" colspan="1">77.6</td><td align="center" valign="middle" rowspan="1" colspan="1">78.3</td><td align="center" valign="middle" rowspan="1" colspan="1">74.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">57.6</td><td align="center" valign="middle" rowspan="1" colspan="1">57.2</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>CU_82792</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">45.2</td><td align="center" valign="middle" rowspan="1" colspan="1">45.5</td><td align="center" valign="middle" rowspan="1" colspan="1">45.4</td><td align="center" valign="middle" rowspan="1" colspan="1">45.5</td><td align="center" valign="middle" rowspan="1" colspan="1">45.4</td><td align="center" valign="middle" rowspan="1" colspan="1">44.6</td><td align="center" valign="middle" rowspan="1" colspan="1">46.1</td><td align="center" valign="middle" rowspan="1" colspan="1">48..0</td><td align="center" valign="middle" rowspan="1" colspan="1">48.4</td><td align="center" valign="middle" rowspan="1" colspan="1">49.3</td><td align="center" valign="middle" rowspan="1" colspan="1">45.3</td><td align="center" valign="middle" rowspan="1" colspan="1">47.1</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">96.3</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><bold>DE/072</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.7</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.0</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">46.6</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">47.8</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">48.8</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">49.5</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">45.5</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">48.0</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">93.6</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot><fn><p>Our five IBV isolates are denoted in boldface.</p></fn></table-wrap-foot></table-wrap><table-wrap id="viruses-11-01054-t003" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-01054-t003_Table 3</object-id><label>Table 3</label><caption><p>Genome features of the five IBV isolates used in this study.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1"></th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">IBV/Ck/Can/17-035614</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">IBV/Ck/Can/17-036989</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">IBV/Ck/Can/18-048192T</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">IBV/Ck/Can/18-048430</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">IBV/Ck/Can/18-049707</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>5′UTR</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">1–530 (530 nt)</td><td align="center" valign="middle" rowspan="1" colspan="1">1–528 (528 nt)</td><td align="center" valign="middle" rowspan="1" colspan="1">1–528 (528 nt)</td><td align="center" valign="middle" rowspan="1" colspan="1">1–528 (528 nt)</td><td align="center" valign="middle" rowspan="1" colspan="1">1–528 (528 nt)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>1a</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">531–12,419 (11889 nt<sup>a</sup>-3962 aa<sup>b</sup>)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–12,417 (11889 nt-3962 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–12,360 (11832 nt-3943 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–12,393 (11865 nt-3954 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–12,417 (11889 nt-3962 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>1ab</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">531–20,452 (19922 nt-6639 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–20,450 (19922 nt-6639 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–20,393 (19865 nt-6620 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–20,426 (19898 nt-6631 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">529–20,450 (19922 nt-6639 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>S</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">20,403–23,903 (3501 nt-1166 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">20,401–23,901 (3501 nt-1166 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">20,344–23,844 (3501 nt-1166 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">20,377–23,877 (3501 nt-1166 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">20,401–23,901 (3501 nt-1166 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>3a</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">23,903–24,076 (174 nt-57 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">23,901–24,074 (174 nt-57 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">23,844–24,017 (174 nt-57 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">23,877–24,050 (174 nt-57 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">23,901–24,074 (174 nt-57 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>3b</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">24,076–24,270 (195 nt-64 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,074–24,268 (195 nt-64 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,017–24,211 (195 nt-64 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,050–24,244 (195 nt-64 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,074–24,268 (195 nt-64 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>E</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">24,251–24,580 (330 nt-109 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,249–24,578 (330 nt-109 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,192–24,521 (330 nt-109 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,225–24,554 (330 nt-109 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,249–24,578 (330 nt-109 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>M</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">24,552–25,229 (678 nt-225 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,550–25,227 (678 nt-225 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,493–25,170 (678 nt-225 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,526–25,203 (678 nt-225 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">24,550–25,227 (678 nt-225 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>4b</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">25,230–25,514 (285 nt-94 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,228–25,512 (285 nt-94 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,171–25,455 (285 nt-94 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,204–25,488 (285 nt-94 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,228–25,512 (285 nt-94 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>4c</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">25,435–25,605 (171 nt-56 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,433–25,603 (171 nt-56 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,376–25,546 (171 nt-56 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,409–25,579 (171 nt-56 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,433–25,603 (171 nt-56 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>5a</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">25,589–25,786 (198 nt-65 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,587–25,784 (198 nt-65 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,530–25,727 (198 nt-65 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,563–25,760 (198 nt-65 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,587–25,784 (198 nt-65 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>5b</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">25,783–26,031 (249 nt-82 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,781–26,029 (249 nt-82 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,724–25,972 (249 nt-82 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,757–26,005 (249 nt-82 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,781–26,029 (249 nt-82 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>N</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">25,974–27,203 (1230 nt-409 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,972–27,201 (1230 nt-409 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,915–27,144 (1230 nt-409 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,948–27,177 (1230 nt-409 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">25,972–27,201 (1230 nt-409 aa)</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><bold>6b</bold></td><td align="center" valign="middle" rowspan="1" colspan="1">27,212–27,436 (225 nt-74 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">27,210–27,434 (225 nt-74 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">27,153–27296 (144 nt-47 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">27,186–27,410 (225 nt-74 aa)</td><td align="center" valign="middle" rowspan="1" colspan="1">27210–27,434 (225 nt-74 aa)</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"><bold>3′UTR</bold></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">27,437–27,710 (274 nt)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">27,435–27,708 (274 nt)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">27,297–27,638 (342 nt)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">27,411–27,684 (274 nt)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">27,435–27,708 (274 nt)</td></tr></tbody></table><table-wrap-foot><fn><p><sup>a</sup>: Nucleotide length; <sup>b</sup>: Amino acid length.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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