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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular characterization of whole genome sequence of infectious bronchitis virus 624I genotype confirms the close relationship with Q1 genotype</title><author><name sortKey="Laconi, Andrea" sort="Laconi, Andrea" uniqKey="Laconi A" first="Andrea" last="Laconi">Andrea Laconi</name><affiliation><nlm:aff id="tbed13000-aff-0001"></nlm:aff></affiliation><affiliation><nlm:aff id="tbed13000-aff-0002"></nlm:aff></affiliation></author><author><name sortKey="Listorti, Valeria" sort="Listorti, Valeria" uniqKey="Listorti V" first="Valeria" last="Listorti">Valeria Listorti</name><affiliation><nlm:aff id="tbed13000-aff-0003"></nlm:aff></affiliation></author><author><name sortKey="Franzo, Giovanni" sort="Franzo, Giovanni" uniqKey="Franzo G" first="Giovanni" last="Franzo">Giovanni Franzo</name><affiliation><nlm:aff id="tbed13000-aff-0004"></nlm:aff></affiliation></author><author><name sortKey="Cecchinato, Mattia" sort="Cecchinato, Mattia" uniqKey="Cecchinato M" first="Mattia" last="Cecchinato">Mattia Cecchinato</name><affiliation><nlm:aff id="tbed13000-aff-0004"></nlm:aff></affiliation></author><author><name sortKey="Naylor, Clive" sort="Naylor, Clive" uniqKey="Naylor C" first="Clive" last="Naylor">Clive Naylor</name><affiliation><nlm:aff id="tbed13000-aff-0002"></nlm:aff></affiliation></author><author><name sortKey="Lupini, Caterina" sort="Lupini, Caterina" uniqKey="Lupini C" first="Caterina" last="Lupini">Caterina Lupini</name><affiliation><nlm:aff id="tbed13000-aff-0003"></nlm:aff></affiliation></author><author><name sortKey="Catelli, Elena" sort="Catelli, Elena" uniqKey="Catelli E" first="Elena" last="Catelli">Elena Catelli</name><affiliation><nlm:aff id="tbed13000-aff-0003"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">30126059</idno><idno type="pmc">7168539</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168539</idno><idno type="RBID">PMC:7168539</idno><idno type="doi">10.1111/tbed.13000</idno><date when="2018">2018</date><idno type="wicri:Area/Pmc/Corpus">000832</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000832</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular characterization of whole genome sequence of infectious bronchitis virus 624I genotype confirms the close relationship with Q1 genotype</title><author><name sortKey="Laconi, Andrea" sort="Laconi, Andrea" uniqKey="Laconi A" first="Andrea" last="Laconi">Andrea Laconi</name><affiliation><nlm:aff id="tbed13000-aff-0001"></nlm:aff></affiliation><affiliation><nlm:aff id="tbed13000-aff-0002"></nlm:aff></affiliation></author><author><name sortKey="Listorti, Valeria" sort="Listorti, Valeria" uniqKey="Listorti V" first="Valeria" last="Listorti">Valeria Listorti</name><affiliation><nlm:aff id="tbed13000-aff-0003"></nlm:aff></affiliation></author><author><name sortKey="Franzo, Giovanni" sort="Franzo, Giovanni" uniqKey="Franzo G" first="Giovanni" last="Franzo">Giovanni Franzo</name><affiliation><nlm:aff id="tbed13000-aff-0004"></nlm:aff></affiliation></author><author><name sortKey="Cecchinato, Mattia" sort="Cecchinato, Mattia" uniqKey="Cecchinato M" first="Mattia" last="Cecchinato">Mattia Cecchinato</name><affiliation><nlm:aff id="tbed13000-aff-0004"></nlm:aff></affiliation></author><author><name sortKey="Naylor, Clive" sort="Naylor, Clive" uniqKey="Naylor C" first="Clive" last="Naylor">Clive Naylor</name><affiliation><nlm:aff id="tbed13000-aff-0002"></nlm:aff></affiliation></author><author><name sortKey="Lupini, Caterina" sort="Lupini, Caterina" uniqKey="Lupini C" first="Caterina" last="Lupini">Caterina Lupini</name><affiliation><nlm:aff id="tbed13000-aff-0003"></nlm:aff></affiliation></author><author><name sortKey="Catelli, Elena" sort="Catelli, Elena" uniqKey="Catelli E" first="Elena" last="Catelli">Elena Catelli</name><affiliation><nlm:aff id="tbed13000-aff-0003"></nlm:aff></affiliation></author></analytic><series><title level="j">Transboundary and Emerging Diseases</title><idno type="ISSN">1865-1674</idno><idno type="eISSN">1865-1682</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Infectious Bronchitis virus (<styled-content style="fixed-case" toggle="no">IBV</styled-content>) genotype Q1 was detected for the first time in China in 1996, and then spread worldwide. The first report of Q1 genotype in Italy occurred in 2011 and a deep molecular investigation of a Q1 isolated in Italy in 2013 has led to speculation regarding the origin of this genotype. Phylogenetic analysis of the <italic>S1</italic> sequence of a Q1 Italian strain revealed a close relationship with sequences of the 624I strains circulating in Italy in the early 1990s and this led to the idea that 624I was an ancestor of the Q1 genotype. Despite the fact that most heterogeneity of <styled-content style="fixed-case" toggle="no">IBV</styled-content>s occurs in the <italic>S1</italic> gene, the sequence analysis of this gene alone was not sufficient to confirm or deny this hypothesis. In the present study, an Italian 624I (gammaCoV/AvCov/Ck/Italy/<styled-content style="fixed-case" toggle="no">IP</styled-content>14425/96) was fully sequenced for the first time and compared to all available complete Q1 genome sequences. This analysis confirmed the genetic correlation between GammaCoV/AvCov/Ck/Italy/<styled-content style="fixed-case" toggle="no">IP</styled-content>14425/96 and Q1 strains, suggesting a common origin between 624I and Q1 genotypes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Swayne, G" uniqKey="Swayne G">G. Swayne</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></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">Transbound Emerg Dis</journal-id><journal-id journal-id-type="iso-abbrev">Transbound Emerg Dis</journal-id><journal-id journal-id-type="doi">10.1111/(ISSN)1865-1682</journal-id><journal-id journal-id-type="publisher-id">TBED</journal-id><journal-title-group><journal-title>Transboundary and Emerging Diseases</journal-title></journal-title-group><issn pub-type="ppub">1865-1674</issn><issn pub-type="epub">1865-1682</issn><publisher><publisher-name>John Wiley and Sons Inc.</publisher-name><publisher-loc>Hoboken</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">30126059</article-id><article-id pub-id-type="pmc">7168539</article-id><article-id pub-id-type="doi">10.1111/tbed.13000</article-id><article-id pub-id-type="publisher-id">TBED13000</article-id><article-categories><subj-group subj-group-type="overline"><subject>Original Article</subject></subj-group><subj-group subj-group-type="heading"><subject>Original Articles</subject></subj-group></article-categories><title-group><article-title>Molecular characterization of whole genome sequence of infectious bronchitis virus 624I genotype confirms the close relationship with Q1 genotype</article-title><alt-title alt-title-type="left-running-head">LACONI et al.</alt-title></title-group><contrib-group><contrib id="tbed13000-cr-0001" contrib-type="author" corresp="yes"><name><surname>Laconi</surname><given-names>Andrea</given-names></name><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-0102-7021</contrib-id><xref ref-type="aff" rid="tbed13000-aff-0001"><sup>1</sup></xref><xref ref-type="aff" rid="tbed13000-aff-0002"><sup>2</sup></xref><address><email>a.laconi@uu.nl</email><email>a.laconi85@gmail.com</email></address></contrib><contrib id="tbed13000-cr-0002" contrib-type="author"><name><surname>Listorti</surname><given-names>Valeria</given-names></name><xref ref-type="aff" rid="tbed13000-aff-0003"><sup>3</sup></xref></contrib><contrib id="tbed13000-cr-0003" contrib-type="author"><name><surname>Franzo</surname><given-names>Giovanni</given-names></name><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-2991-217X</contrib-id><xref ref-type="aff" rid="tbed13000-aff-0004"><sup>4</sup></xref></contrib><contrib id="tbed13000-cr-0004" contrib-type="author"><name><surname>Cecchinato</surname><given-names>Mattia</given-names></name><xref ref-type="aff" rid="tbed13000-aff-0004"><sup>4</sup></xref></contrib><contrib id="tbed13000-cr-0005" contrib-type="author"><name><surname>Naylor</surname><given-names>Clive</given-names></name><xref ref-type="aff" rid="tbed13000-aff-0002"><sup>2</sup></xref></contrib><contrib id="tbed13000-cr-0006" contrib-type="author"><name><surname>Lupini</surname><given-names>Caterina</given-names></name><xref ref-type="aff" rid="tbed13000-aff-0003"><sup>3</sup></xref></contrib><contrib id="tbed13000-cr-0007" contrib-type="author"><name><surname>Catelli</surname><given-names>Elena</given-names></name><xref ref-type="aff" rid="tbed13000-aff-0003"><sup>3</sup></xref></contrib></contrib-group><aff id="tbed13000-aff-0001"><label><sup>1</sup></label><named-content content-type="organisation-division">Department of Pathobiology</named-content><named-content content-type="organisation-division">Faculty of Veterinary Medicine</named-content><institution>Utrecht University</institution><city>Utrecht</city><country country="NL">The Netherlands</country></aff><aff id="tbed13000-aff-0002"><label><sup>2</sup></label><named-content content-type="organisation-division">Department of Infection Biology</named-content><institution>University of Liverpool, Leahurst Campus</institution><city>Liverpool</city><named-content content-type="country-part">Cheshire</named-content><country country="GB">UK</country></aff><aff id="tbed13000-aff-0003"><label><sup>3</sup></label><named-content content-type="organisation-division">Department of Veterinary Medical Sciences</named-content><institution>University of Bologna</institution><city>Ozzano dell'Emilia</city><named-content content-type="country-part">BO</named-content><country country="IT">Italy</country></aff><aff id="tbed13000-aff-0004"><label><sup>4</sup></label><named-content content-type="organisation-division">Department of Animal Medicine, Production and Health</named-content><institution>University of Padua</institution><city>Legnaro</city><named-content content-type="country-part">PD</named-content><country country="IT">Italy</country></aff><author-notes><corresp id="correspondenceTo"><label>*</label><bold>Correspondence</bold><break></break>Andrea Laconi, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.<break></break>Emails: <email>a.laconi@uu.nl</email>; <email>a.laconi85@gmail.com</email><break></break></corresp></author-notes><pub-date pub-type="epub"><day>20</day><month>9</month><year>2018</year></pub-date><pub-date pub-type="ppub"><month>1</month><year>2019</year></pub-date><volume>66</volume><issue>1</issue><issue-id pub-id-type="doi">10.1111/tbed.2019.66.issue-1</issue-id><fpage>207</fpage><lpage>216</lpage><history><date date-type="received"><day>07</day><month>2</month><year>2018</year></date><date date-type="rev-recd"><day>16</day><month>7</month><year>2018</year></date><date date-type="accepted"><day>12</day><month>8</month><year>2018</year></date></history><permissions><pmc-comment> Copyright © 2019 Blackwell Verlag GmbH </pmc-comment>
<copyright-statement content-type="article-copyright">© 2018 Blackwell Verlag GmbH</copyright-statement><license><license-p>This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="file:TBED-66-207.pdf"></self-uri><abstract id="tbed13000-abs-0001"><title>Abstract</title><p>Infectious Bronchitis virus (<styled-content style="fixed-case" toggle="no">IBV</styled-content>) genotype Q1 was detected for the first time in China in 1996, and then spread worldwide. The first report of Q1 genotype in Italy occurred in 2011 and a deep molecular investigation of a Q1 isolated in Italy in 2013 has led to speculation regarding the origin of this genotype. Phylogenetic analysis of the <italic>S1</italic> sequence of a Q1 Italian strain revealed a close relationship with sequences of the 624I strains circulating in Italy in the early 1990s and this led to the idea that 624I was an ancestor of the Q1 genotype. Despite the fact that most heterogeneity of <styled-content style="fixed-case" toggle="no">IBV</styled-content>s occurs in the <italic>S1</italic> gene, the sequence analysis of this gene alone was not sufficient to confirm or deny this hypothesis. In the present study, an Italian 624I (gammaCoV/AvCov/Ck/Italy/<styled-content style="fixed-case" toggle="no">IP</styled-content>14425/96) was fully sequenced for the first time and compared to all available complete Q1 genome sequences. This analysis confirmed the genetic correlation between GammaCoV/AvCov/Ck/Italy/<styled-content style="fixed-case" toggle="no">IP</styled-content>14425/96 and Q1 strains, suggesting a common origin between 624I and Q1 genotypes.</p></abstract><counts><fig-count count="4"></fig-count><table-count count="2"></table-count><page-count count="10"></page-count><word-count count="5391"></word-count></counts><custom-meta-group><custom-meta><meta-name>source-schema-version-number</meta-name><meta-value>2.0</meta-value></custom-meta><custom-meta><meta-name>cover-date</meta-name><meta-value>January 2019</meta-value></custom-meta><custom-meta><meta-name>details-of-publishers-convertor</meta-name><meta-value>Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.0 mode:remove_FC converted:15.04.2020</meta-value></custom-meta></custom-meta-group></article-meta><notes><p content-type="self-citation"><mixed-citation publication-type="journal" id="tbed13000-cit-1001"><string-name><surname>Laconi</surname><given-names>A</given-names></string-name>, <string-name><surname>Listorti</surname><given-names>V</given-names></string-name>, <string-name><surname>Franzo</surname><given-names>G</given-names></string-name>, et al. <article-title>Molecular characterization of whole genome sequence of infectious bronchitis virus 624I genotype confirms the close relationship with Q1 genotype</article-title>. <source xml:lang="en">Transbound Emerg Dis</source>. <year>2019</year>;<volume>66</volume>:<fpage>207</fpage>–<lpage>216</lpage>. <pub-id pub-id-type="doi">10.1111/tbed.13000</pub-id><pub-id pub-id-type="pmid">30126059</pub-id></mixed-citation></p></notes></front><body id="tbed13000-body-0001"><sec id="tbed13000-sec-0001"><label>1</label><title>INTRODUCTION</title><p>Infectious bronchitis (IB) is an avian disease distributed worldwide that represents one of the most persistent health problems of the commercial poultry industry (Cook, Jackwood, & Jones, <xref rid="tbed13000-bib-0011" ref-type="ref">2012</xref>; de Wit, Cook, & van der Heijden, <xref rid="tbed13000-bib-0039" ref-type="ref">2011</xref>). It is caused by a Gammacoronavirus called Infectious Bronchitis Virus (IBV) and has a positive sense single‐stranded 27.6 kb RNA genome (Jackwood & De Wit, <xref rid="tbed13000-bib-0017" ref-type="ref">2013</xref>). The IBV genome can evolve rapidly by mutation and recombination events, resulting in the emergence of new IBV variants which sometimes confer minimal or negligible cross‐protection (de Wit et al., <xref rid="tbed13000-bib-0039" ref-type="ref">2011</xref>). A majority of such variants cause a transitory problem, which then disappear or remain confined into a specific geographical region. However, a few variants can persist and spread to new areas where they continue to cause disease (Jackwood, <xref rid="tbed13000-bib-0016" ref-type="ref">2012</xref>; de Wit et al., <xref rid="tbed13000-bib-0039" ref-type="ref">2011</xref>).</p><p>Recently, genotypes of Asian origin have spread to cause worldwide disease and major economic losses (de Wit et al., <xref rid="tbed13000-bib-0039" ref-type="ref">2011</xref>). IBV Q1 is one such genotype. It was first detected in China in 1996 (Yu et al., <xref rid="tbed13000-bib-0042" ref-type="ref">2001</xref>) and then reported in Asia, Middle East, Europe, and South America (Ababneh, Dalab, Alsaad, & Al‐Zghoul, <xref rid="tbed13000-bib-0001" ref-type="ref">2012</xref>; Huang, Lee, Cheng, & Wang, <xref rid="tbed13000-bib-0015" ref-type="ref">2004</xref>; Jackwood, <xref rid="tbed13000-bib-0016" ref-type="ref">2012</xref>; Marandino et al., <xref rid="tbed13000-bib-0027" ref-type="ref">2015</xref>; Rimondi et al., <xref rid="tbed13000-bib-0034" ref-type="ref">2009</xref>). In Italy, the Q1 genotype was reported for the first time in 2011 after causing an outbreak of disease associated with respiratory signs, increased mortality, kidney lesions, and proventriculitis (Toffan et al., <xref rid="tbed13000-bib-0037" ref-type="ref">2013</xref>). Since then, the genotype has been continuously detected in Italy (Massi et al., <xref rid="tbed13000-bib-0031" ref-type="ref">2015</xref>). Phylogenetic analysis performed using full or partial <italic>S1</italic> sequences showed a high identity (>99%) with Chinese Q1 isolates (Franzo et al., <xref rid="tbed13000-bib-0012" ref-type="ref">2015</xref>; Massi et al., <xref rid="tbed13000-bib-0031" ref-type="ref">2015</xref>; Toffan et al., <xref rid="tbed13000-bib-0037" ref-type="ref">2013</xref>). At a similar period, a high identity (94.1%) between those strains and strains belonging to the 624I genotype was observed (Franzo et al., <xref rid="tbed13000-bib-0012" ref-type="ref">2015</xref>; Massi et al., <xref rid="tbed13000-bib-0031" ref-type="ref">2015</xref>), such that the recently proposed new IBV nomenclature based on the <italic>S1</italic> sequence placed them in the same lineage (GI‐16) (Valastro et al., <xref rid="tbed13000-bib-0038" ref-type="ref">2016</xref>).</p><p>IBV 624I had been reported for the first time in Italy in 1993 (Capua, Gough, Mancini, Casaccia, & Weiss, <xref rid="tbed13000-bib-0007" ref-type="ref">1994</xref>; Capua et al., <xref rid="tbed13000-bib-0009" ref-type="ref">1999</xref>), producing disease associated with kidney lesions and drop in egg production in breeders and layers (Capua, Grasso, Ferdinandi, Weiss, & Casaccia, <xref rid="tbed13000-bib-0008" ref-type="ref">1996</xref>). This genotype continued to be detected in Italy until 2004 and then reappeared from 2010 when it was again detected in a few broiler farms affected by respiratory disease located in different areas of Italy. In the following years, the number of detections increased (Massi, <xref rid="tbed13000-bib-0030" ref-type="ref">2013</xref>) but since 2013 the 624I genotype has not been further detected (Massi et al., <xref rid="tbed13000-bib-0031" ref-type="ref">2015</xref>).</p><p>A recent retrospective study carried out on 123 IBV strains isolated in Italy between 1963 and 1989 revealed that 624I genotype had not only circulated long before its first reporting in 1993, but that in fact it has been one of the major IBV genotypes circulating in the Country at that time (Taddei et al., <xref rid="tbed13000-bib-0036" ref-type="ref">2012</xref>). Evidence of the presence of this genotype has also been found in Slovenia, where several 624I strains were isolated between 1991 and 1999 (Krapez, Slavec, Barlic‐Maganja, & Rojs, <xref rid="tbed13000-bib-0021" ref-type="ref">2010</xref>), in Poland and South Africa (Capua et al., <xref rid="tbed13000-bib-0009" ref-type="ref">1999</xref>) and eventually in Russia where 624I genotype was reported in 2002 (Bochkov, Batchenko, Shcherbakova, Borisov, & Drygin, <xref rid="tbed13000-bib-0006" ref-type="ref">2006</xref>).</p><p>The high identity observed between Q1 and 624I genotypes raises questions regarding their possible related origins. IBV 624I has been hypothesized to be an ancestor of the Q1 genotype (Franzo et al., <xref rid="tbed13000-bib-0012" ref-type="ref">2015</xref>; Massi, <xref rid="tbed13000-bib-0030" ref-type="ref">2013</xref>), but unfortunately the unavailability of any 624I full genome sequence did not allow such final conclusions to be drawn.</p><p>In the present study, an IBV 624I was fully sequenced and phylogenetic analysis was performed both using a dataset based on available IBV full‐length genome sequences and, due to the larger number of published sequences, a dataset based on full <italic>S1</italic> gene. In addition, recombination analysis was carried out using the complete IBV 624I and Q1 strains.</p></sec><sec id="tbed13000-sec-0002"><label>2</label><title>MATERIALS AND METHODS</title><sec id="tbed13000-sec-0003"><label>2.1</label><title>Virus</title><p>IBV 624I strain was isolated in 1996 during a disease outbreak in chicken farms located in Northern Italy. The virus was isolated in specific pathogen‐free (SPF) chicken eggs and the 3th passage was propagated in SPF chicken embryo tracheal organ cultures (TOC). After isolation, the virus underwent serological analysis, resulting as belonging to the 624I serotype. In this study, this virus is named gammaCoV/AvCov/Ck/Italy/IP14425/96.</p></sec><sec id="tbed13000-sec-0004"><label>2.2</label><title>RNA extraction, RT‐PCR, and sequencing</title><p>The RNA was extracted from the supernatant of infected TOC using Qiamp viral RNA mini kit (Qiagen, Hilden, Germany) following the manufacture's protocol. Viral RNA was firstly retro‐transcribed using Super Script III enzyme (Invitrogen, Carlsbad, CA, USA), then amplified using Ranger enzyme (Bioline, London, UK) according to the manufacturer's instructions<bold>.</bold> Retrotranscription, amplification, and sequencing were carried out using primers previously designed for IBV full genome sequencing (Franzo et al., <xref rid="tbed13000-bib-0012" ref-type="ref">2015</xref>; Listorti et al., <xref rid="tbed13000-bib-0026" ref-type="ref">2017</xref>). Where primers did not work due to sequence differences, new primers were designed based on the newly determined sequences flanking those genome regions (Table <xref rid="tbed13000-tbl-0001" ref-type="table">1</xref>). Sequencing was performed by Source BioScience (Nottingham, UK). Each genome fragment was sequenced twice. Where gammaCoV/AvCov/Ck/Italy/IP14425/96a sequence differed from those of Q1 strains, the locations were sequenced again, starting with a new retrotranscription of the region.</p><table-wrap id="tbed13000-tbl-0001" xml:lang="en" orientation="portrait" position="float"><label>Table 1</label><caption><p>Primers used for reverse transcription, PCR and sequencing</p></caption><table frame="hsides" rules="groups"><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><thead valign="top"><tr style="border-bottom:solid 1px #000000"><th align="left" valign="top" rowspan="1" colspan="1">RT</th><th align="left" valign="top" rowspan="1" colspan="1">Sequence 5′‐3′</th><th align="left" valign="top" rowspan="1" colspan="1">Sequencing</th><th align="left" valign="top" rowspan="1" colspan="1">Sequences 5′‐3′</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">2.06neg</td><td align="left" rowspan="1" colspan="1">tttagtaaaaagaccacc</td><td align="left" rowspan="1" colspan="1">0.67+</td><td align="left" rowspan="1" colspan="1">cctaaggattacgctgatgcttttgc</td></tr><tr><td align="left" rowspan="1" colspan="1">4.26neg</td><td align="left" rowspan="1" colspan="1">catacttttgcgcatc</td><td align="left" rowspan="1" colspan="1">1.26+</td><td align="left" rowspan="1" colspan="1">ttcgcaggaacttgtcttgcaagc</td></tr><tr><td align="left" rowspan="1" colspan="1">6.18neg</td><td align="left" rowspan="1" colspan="1">agaaaacctacaccag</td><td align="left" rowspan="1" colspan="1">2.52+</td><td align="left" rowspan="1" colspan="1">tagaggaatgtcacagcttggtgc</td></tr><tr><td align="left" rowspan="1" colspan="1">8.18neg</td><td align="left" rowspan="1" colspan="1">gtaaagaatgtactaaac</td><td align="left" rowspan="1" colspan="1">3.04+</td><td align="left" rowspan="1" colspan="1">tacaccaatgtcacagcttggtgc</td></tr><tr><td align="left" rowspan="1" colspan="1">10.10neg</td><td align="left" rowspan="1" colspan="1">cacagttgtgtgcactaactcaaag</td><td align="left" rowspan="1" colspan="1">3.10+</td><td align="left" rowspan="1" colspan="1">ctctcgatgttgtgaatttaccatctgg</td></tr><tr><td align="left" rowspan="1" colspan="1">12.10neg</td><td align="left" rowspan="1" colspan="1">ctccataagaatcctg</td><td align="left" rowspan="1" colspan="1">IB4.6+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">gtacggatgaagtaatagaagcttc</td></tr><tr><td align="left" rowspan="1" colspan="1">14.13neg</td><td align="left" rowspan="1" colspan="1">taaaacttggttgttcc</td><td align="left" rowspan="1" colspan="1">4.80+</td><td align="left" rowspan="1" colspan="1">tgattgtgatgttgtgaatttaccatctgg</td></tr><tr><td align="left" rowspan="1" colspan="1">16.10neg</td><td align="left" rowspan="1" colspan="1">ttcacataaagcatcaac</td><td align="left" rowspan="1" colspan="1">IB5.15neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">catcagtatcaggtgttaacttataag</td></tr><tr><td align="left" rowspan="1" colspan="1">QX18.10neg</td><td align="left" rowspan="1" colspan="1">catagaagaagaatggcatagctttc</td><td align="left" rowspan="1" colspan="1">5.32+</td><td align="left" rowspan="1" colspan="1">ctattagtcttagggcaatatggg</td></tr><tr><td align="left" rowspan="1" colspan="1">19.73neg</td><td align="left" rowspan="1" colspan="1">caaaatgcattactcgc</td><td align="left" rowspan="1" colspan="1">IB5.70+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">gtgtggtttatttacacaagtaatccag</td></tr><tr><td align="left" rowspan="1" colspan="1">22.51neg</td><td align="left" rowspan="1" colspan="1">catatcttctttttgacc</td><td align="left" rowspan="1" colspan="1">6.53+</td><td align="left" rowspan="1" colspan="1">gttaaacctacagcatatgcttacc</td></tr><tr><td align="left" rowspan="1" colspan="1">24.08neg</td><td align="left" rowspan="1" colspan="1">tttgaatcattaaacagac</td><td align="left" rowspan="1" colspan="1">IB6.7neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ctaatcgttctgaaagtgcctgatcaag</td></tr><tr><td align="left" rowspan="1" colspan="1">26.24neg</td><td align="left" rowspan="1" colspan="1">ccaagatacatttccag</td><td align="left" rowspan="1" colspan="1">IB7.15+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ctttataacaagatctggtgctaaac</td></tr><tr><td align="left" rowspan="1" colspan="1">27.89neg</td><td align="left" rowspan="1" colspan="1">Ttgctctaactctatac</td><td align="left" rowspan="1" colspan="1">7.17+</td><td align="left" rowspan="1" colspan="1">aatgctcctccggtagtatggaag</td></tr><tr><td align="left" rowspan="1" colspan="1">Dta‐Adaptneg<xref ref-type="fn" rid="tbed13000-note-0003">b</xref></td><td align="left" rowspan="1" colspan="1">gcatctcgaggcttgtggcttttttttttttttttttttta</td><td align="left" rowspan="1" colspan="1">IB8.2neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">caacccaaactagcattattgtaaacac</td></tr><tr><td align="left" rowspan="1" colspan="1">Dtc‐Adaptneg<xref ref-type="fn" rid="tbed13000-note-0003">b</xref></td><td align="left" rowspan="1" colspan="1">gcatctcgaggcttgtggctttttttttttttttttttttc</td><td align="left" rowspan="1" colspan="1">8.60+</td><td align="left" rowspan="1" colspan="1">gtatgatggcaacgagtttgttgg</td></tr><tr><td align="left" rowspan="1" colspan="1">Dtg‐Adaptneg<xref ref-type="fn" rid="tbed13000-note-0003">b</xref></td><td align="left" rowspan="1" colspan="1">gcatctcgaggcttgtggctttttttttttttttttttttg</td><td align="left" rowspan="1" colspan="1">IB8.61neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">taccaacaaactcgttgccatc</td></tr><tr><td align="left" rowspan="1" colspan="1">PCR</td><td align="left" rowspan="1" colspan="1">Sequence 5′‐3′</td><td align="left" rowspan="1" colspan="1">9.26+</td><td align="left" rowspan="1" colspan="1">cctgtcactatgcgttctaatggtac</td></tr><tr><td align="left" rowspan="1" colspan="1">0.06+</td><td align="left" rowspan="1" colspan="1">gcgctagatttccaacttaacaaaacg</td><td align="left" rowspan="1" colspan="1">10.60+</td><td align="left" rowspan="1" colspan="1">ggtaaatccacctaaaactgtgtggg</td></tr><tr><td align="left" rowspan="1" colspan="1">2.03neg</td><td align="left" rowspan="1" colspan="1">gacttgcgaaacaagatgccaaatgcc</td><td align="left" rowspan="1" colspan="1">11.13+</td><td align="left" rowspan="1" colspan="1">gaagttagatagcatggagagacg</td></tr><tr><td align="left" rowspan="1" colspan="1">1.92+</td><td align="left" rowspan="1" colspan="1">tggaggcttgcatatggaaaagtgcg</td><td align="left" rowspan="1" colspan="1">12.64+</td><td align="left" rowspan="1" colspan="1">gacttaaagtcagaagtaacagctg</td></tr><tr><td align="left" rowspan="1" colspan="1">4.20neg</td><td align="left" rowspan="1" colspan="1">ggtataaagaggatttctttatcctcaagatcatg</td><td align="left" rowspan="1" colspan="1">13.18+</td><td align="left" rowspan="1" colspan="1">gatctcctcaagtatgattatactgagg</td></tr><tr><td align="left" rowspan="1" colspan="1">4,10+</td><td align="left" rowspan="1" colspan="1">cggaggatggtgttaaataccgc</td><td align="left" rowspan="1" colspan="1">QX13.90+</td><td align="left" rowspan="1" colspan="1">gaggtgacgtctaaatattttgaatg</td></tr><tr><td align="left" rowspan="1" colspan="1">6.08neg</td><td align="left" rowspan="1" colspan="1">caaataatattagaaagaccaaataaagccaattcc</td><td align="left" rowspan="1" colspan="1">14.69+</td><td align="left" rowspan="1" colspan="1">caaggtcttgtagcagatatttctgg</td></tr><tr><td align="left" rowspan="1" colspan="1">5.90+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">gactatggtaaagactcatttgacg</td><td align="left" rowspan="1" colspan="1">15.25+</td><td align="left" rowspan="1" colspan="1">aagtgttgctatgaccatgtcatgc</td></tr><tr><td align="left" rowspan="1" colspan="1">8.05neg</td><td align="left" rowspan="1" colspan="1">cctggtttagtatactcacatacactacc</td><td align="left" rowspan="1" colspan="1">IB15.60+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ggtgcagcttggtgattttacctttg</td></tr><tr><td align="left" rowspan="1" colspan="1">7.97+</td><td align="left" rowspan="1" colspan="1">cctaatggtgttaggcttatagttcc</td><td align="left" rowspan="1" colspan="1">IB16.40neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ctataaccttgaaacactgacgtg</td></tr><tr><td align="left" rowspan="1" colspan="1">10.10neg</td><td align="left" rowspan="1" colspan="1">gtactaaagactacaggatcataccattg</td><td align="left" rowspan="1" colspan="1">QX16.80neg</td><td align="left" rowspan="1" colspan="1">gaatcagctgtaacacagaatataac</td></tr><tr><td align="left" rowspan="1" colspan="1">10.02+</td><td align="left" rowspan="1" colspan="1">cagttattattggagtttgtgctgaag</td><td align="left" rowspan="1" colspan="1">16.62+</td><td align="left" rowspan="1" colspan="1">catgaaagtggctcagcctacaac</td></tr><tr><td align="left" rowspan="1" colspan="1">12.08neg</td><td align="left" rowspan="1" colspan="1">gaatcctgatccggagttggacttggc</td><td align="left" rowspan="1" colspan="1">17.18+</td><td align="left" rowspan="1" colspan="1">caacatgttttataacacgtgatgaggc</td></tr><tr><td align="left" rowspan="1" colspan="1">12.01+</td><td align="left" rowspan="1" colspan="1">gtggcagcaggtaatcaacctttagg</td><td align="left" rowspan="1" colspan="1">18.02neg</td><td align="left" rowspan="1" colspan="1">ctgcttgacattgggtactactggattc</td></tr><tr><td align="left" rowspan="1" colspan="1">14.12neg</td><td align="left" rowspan="1" colspan="1">ataaaacttggttgttccaataactacagg</td><td align="left" rowspan="1" colspan="1">18.18+</td><td align="left" rowspan="1" colspan="1">taacctacctggttgtaatggtgg</td></tr><tr><td align="left" rowspan="1" colspan="1">14.05+</td><td align="left" rowspan="1" colspan="1">gtgtctatcctttctactatgactaataggc</td><td align="left" rowspan="1" colspan="1">18.71+</td><td align="left" rowspan="1" colspan="1">gaagagaaatattcgcacactgcc</td></tr><tr><td align="left" rowspan="1" colspan="1">16.09neg</td><td align="left" rowspan="1" colspan="1">cacataaagcatcaacagctgcatgag</td><td align="left" rowspan="1" colspan="1">19.67neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">gtattgacagagttgtgtatactttggc</td></tr><tr><td align="left" rowspan="1" colspan="1">QX15.06+</td><td align="left" rowspan="1" colspan="1">gatgattgcactcgcatagtacctc</td><td align="left" rowspan="1" colspan="1">19.46+</td><td align="left" rowspan="1" colspan="1">gtaacagtgtcaattgattaccatagc</td></tr><tr><td align="left" rowspan="1" colspan="1">QX18.10neg</td><td align="left" rowspan="1" colspan="1">catagaagaagaatggcatagctttc</td><td align="left" rowspan="1" colspan="1">19.97+</td><td align="left" rowspan="1" colspan="1">gatagccaataatggcaatgatgacg</td></tr><tr><td align="left" rowspan="1" colspan="1">17.62+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">tactcaggcttatgcttgttggaagc</td><td align="left" rowspan="1" colspan="1">IB20.40+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">cattgtttatagtgtctcttttgtttgcac</td></tr><tr><td align="left" rowspan="1" colspan="1">19.67neg</td><td align="left" rowspan="1" colspan="1">gtattgacagagttgtgtatactttgcc</td><td align="left" rowspan="1" colspan="1">IB21.70neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">gtcacaaattgcccttatgtaagttatgg</td></tr><tr><td align="left" rowspan="1" colspan="1">19.46+</td><td align="left" rowspan="1" colspan="1">gtaacagtgtcaattgattaccatagc</td><td align="left" rowspan="1" colspan="1">IB21.95+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ccagcagtttgtagtttctggtgg</td></tr><tr><td align="left" rowspan="1" colspan="1">22.26neg</td><td align="left" rowspan="1" colspan="1">tccatacgcgtttgtatgtactcatctg</td><td align="left" rowspan="1" colspan="1">IB23.60neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">cacgtgcagtgatgtagtaactacc</td></tr><tr><td align="left" rowspan="1" colspan="1">IB21.95+</td><td align="left" rowspan="1" colspan="1">ccagcagtttgtagtttctggtgg</td><td align="left" rowspan="1" colspan="1">QX24.20neg</td><td align="left" rowspan="1" colspan="1">ctacttacactgtttcaattgttttctc</td></tr><tr><td align="left" rowspan="1" colspan="1">IB24.07neg</td><td align="left" rowspan="1" colspan="1">gaatcattaaacagactttttaggtctg</td><td align="left" rowspan="1" colspan="1">IB24.70+<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">gtactcttggtactgaacaagcag</td></tr><tr><td align="left" rowspan="1" colspan="1">23.99+</td><td align="left" rowspan="1" colspan="1">cattatgcctctaatgagtaagtgtgg</td><td align="left" rowspan="1" colspan="1">IB25.60neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ctcttgaaaagagagcatgaaacaaagagg</td></tr><tr><td align="left" rowspan="1" colspan="1">26.24neg<xref ref-type="fn" rid="tbed13000-note-0004">a</xref></td><td align="left" rowspan="1" colspan="1">ccaagatacatttccag</td><td align="left" rowspan="1" colspan="1">QX27.20<xref ref-type="fn" rid="tbed13000-note-0003">a,b</xref></td><td align="left" rowspan="1" colspan="1">cctacatgtctatcgccaggg</td></tr><tr><td align="left" rowspan="1" colspan="1">26.02+</td><td align="left" rowspan="1" colspan="1">gaaaagcgcgaatttatctgagagaagg</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">27.83neg</td><td align="left" rowspan="1" colspan="1">catagccaattaaacttaacttaaactaaaatttagctc</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">26.49+</td><td align="left" rowspan="1" colspan="1">gatagccaagatggtatagtgtggg</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">Adapt neg<xref ref-type="fn" rid="tbed13000-note-0003">b</xref></td><td align="left" rowspan="1" colspan="1">gcatctcgagggttgtggc</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot id="tbed13000-ntgp-0001"><title><italic>Notes</italic></title><fn id="tbed13000-note-0001"><p>Primer names generally indicate approximate binding positions in the 624I genome.</p></fn><fn id="tbed13000-note-0002"><p>Coding and anticoding sense primers are labelled + and neg, respectively.</p></fn><fn id="tbed13000-note-0003"><p><sup>a</sup>Indicates primers designed for the 624I IBV strain sequencing based on the newly determined flanking sequences. <sup>b</sup>Indicates primers used for the retrotranscription, amplification, and sequencing of the 3′END of the genome.</p></fn></table-wrap-foot><permissions><copyright-holder>John Wiley & Sons, Ltd</copyright-holder><license><license-p>This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.</license-p></license></permissions></table-wrap></sec><sec id="tbed13000-sec-0005"><label>2.3</label><title>RT‐PCR of the 3′ END of genome</title><p>3′ end of the genome was determined using a 3′RACE protocol previously described (Laconi et al., <xref rid="tbed13000-bib-0023" ref-type="ref">2016</xref>). Briefly, RT was performed with a primer containing 20 Ts followed by an adaptor sequence at its 5′ terminus. This was amplified by PCR using two primers, one within the end of the genome and one matching the adaptor (Table <xref rid="tbed13000-tbl-0001" ref-type="table">1</xref>). These PCR products were sequenced towards the polyA tail.</p></sec><sec id="tbed13000-sec-0006"><label>2.4</label><title>Sequences analysis and comparison</title><p>Chromatograms were analysed using the program Chromas (<ext-link ext-link-type="uri" xlink:href="http://technelysium.com.au/wp/chromas/">http://technelysium.com.au/wp/chromas/</ext-link>) and sequences aligned using BioEdit (<ext-link ext-link-type="uri" xlink:href="http://www.mbio.ncsu.edu/bioedit/bioedit.html">http://www.mbio.ncsu.edu/bioedit/bioedit.html</ext-link>) against the genome of IBV strains gammaCoV/Ck/Italy/I2022/13 (KP780179) and CK/CH/LDL/97I (JX195177). Open Reading Frame (ORF) prediction was carried out using ORFfinder program (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/orffinder/">https://www.ncbi.nlm.nih.gov/orffinder/</ext-link>).</p></sec><sec id="tbed13000-sec-0007"><label>2.5</label><title>Complete genome sequences analysis</title><p>A dataset containing 313 complete genome sequences (nt) of IBV was downloaded from ViPr, an open source bioinformatics database and analysis resource for virology research. To minimize the computational load, cd‐hit‐est test of the CD‐HIT Suite (Li & Godzik, <xref rid="tbed13000-bib-0024" ref-type="ref">2006</xref>) was used to cluster sequences that shared over 98% identity and a prototype sequence within each cluster was selected. After clustering, 187 representative sequences remained. Sequences were aligned using ClustaW and phylogenetic analysis was carried out with MEGA7 software (Kumar, Stecher, & Tamura, <xref rid="tbed13000-bib-0022" ref-type="ref">2016</xref>) using Maximum Likelihood method with Tamura‐Nei substitution model and 1,000 bootstrap replicates to assess the robustness of the branches.</p></sec><sec id="tbed13000-sec-0008"><label>2.6</label><title>S1 gene sequences analysis</title><p>A dataset containing all available complete or nearly complete <italic>S1</italic> gene sequences (at least 1,000 bp) was downloaded from ViPr. After clustering, 320 sequences remained. The sequences were aligned using ClustalW method, and a phylogenetic tree was constructed using the Maximum Likelihood method with Kimura 2 parameter substitution model and 1,000 bootstrap replicates to assign confidence level to the branches in MEGA 7 software. Based on these results, a subset of sequences clustering with gammaCoV/AvCov/Ck/Italy/IP14425/96 was selected and expanded to its original number of taxa. Sequences belonging to this dataset were aligned with ClustalW method, and a phylogenetic tree was reconstructed using the parameters previously described.</p></sec><sec id="tbed13000-sec-0009"><label>2.7</label><title>Recombination event analysis</title><p>Presence of past recombination events for strain gammaCoV/AvCov/Ck/Italy/IP14425/96 was evaluated using RDP4 software (<ext-link ext-link-type="uri" xlink:href="http://web.cbio.uct.ac.za/~darren/rdp.html)(Martin">http://web.cbio.uct.ac.za/~darren/rdp.html)(Martin</ext-link>; Martin, Murrell, Khoosal, & Muhire, <xref rid="tbed13000-bib-0029" ref-type="ref">2017</xref>). Occurrence of possible recombination events was also evaluated for the available Q1 full genome sequences: gammaCoV/Ck/Italy/I2022/13 (KP780179), an Italian isolate from 2013 and CK/CH/LDL/97I (JX195177), a Chinese isolate from 1997. The Kimura 2 parameter substitution model with a window size of 200 nucleotides and a step size of 20 nucleotides was used to calculate the pairwise percentage of identity between gammaCoV/AvCov/Ck/Italy/IP14425/96, the Q1 strains and 13 complete genome sequences of relevant strains, selected on the previous phylogenetic analysis. Phylogenetic analysis was performed for those genome portions where a sharp change in percentage of identity strongly suggested recombination events using a dataset including all the sequences available for the given regions.</p></sec></sec><sec id="tbed13000-sec-0010"><label>3</label><title>RESULTS</title><sec id="tbed13000-sec-0011"><label>3.1</label><title>Genome organization of strain gammaCoV/AvCov/Ck/Italy/IP14425/96</title><p>A consensus sequence of 27.573 bp was obtained (minimum coverage 2X), with the 5′ UTR incomplete by approximately 100 nt. The ORF analysis predicted 13 ORFs and revealed the following genome organization: 5′UTR‐1a‐1b‐S‐3a‐3b‐E‐M‐4b‐4c‐5a‐5b‐N‐6b‐3′UTR (Table <xref rid="tbed13000-tbl-0002" ref-type="table">2</xref>). The same genome organization was observed for viruses gammaCoV/Ck/Italy/I2022/13, CK/CH/LDL/97I and UY/09/CA/01, all belonging to the Q1 genotype (Table <xref rid="tbed13000-tbl-0002" ref-type="table">2</xref>).</p><table-wrap id="tbed13000-tbl-0002" xml:lang="en" orientation="portrait" position="float"><label>Table 2</label><caption><p>Genomic organization of 624I and Q1 strains</p></caption><table frame="hsides" rules="groups"><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><col style="border-right:solid 1px #000000" span="1"></col><thead valign="top"><tr style="border-bottom:solid 1px #000000"><th align="left" rowspan="2" valign="top" colspan="1">Gene</th><th align="left" colspan="4" style="border-bottom:solid 1px #000000" valign="top" rowspan="1">Genome position</th></tr><tr style="border-bottom:solid 1px #000000"><th align="left" valign="top" rowspan="1" colspan="1">gammaCoV/AvCoV/Ck/Italy/P14425/96</th><th align="left" valign="top" rowspan="1" colspan="1">gammaCoV/Ck/Italy/I2022/13</th><th align="left" valign="top" rowspan="1" colspan="1">CK/CH/LDL/97I</th><th align="left" valign="top" rowspan="1" colspan="1">UY/09/CA/01</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">1a</td><td align="char" char="." rowspan="1" colspan="1">433‐12288</td><td align="char" char="." rowspan="1" colspan="1">432‐12290</td><td align="char" char="." rowspan="1" colspan="1">433‐12291</td><td align="char" char="." rowspan="1" colspan="1">432‐12254</td></tr><tr><td align="left" rowspan="1" colspan="1">1ab</td><td align="char" char="." rowspan="1" colspan="1">12363‐20321</td><td align="char" char="." rowspan="1" colspan="1">12365‐20323</td><td align="char" char="." rowspan="1" colspan="1">12366‐20324</td><td align="char" char="." rowspan="1" colspan="1">12329‐20287</td></tr><tr><td align="left" rowspan="1" colspan="1">S</td><td align="char" char="." rowspan="1" colspan="1">20272‐23772</td><td align="char" char="." rowspan="1" colspan="1">20274‐23774</td><td align="char" char="." rowspan="1" colspan="1">20275‐23775</td><td align="char" char="." rowspan="1" colspan="1">20238‐23711</td></tr><tr><td align="left" rowspan="1" colspan="1">3a</td><td align="char" char="." rowspan="1" colspan="1">23772‐23945</td><td align="char" char="." rowspan="1" colspan="1">23774‐23947</td><td align="char" char="." rowspan="1" colspan="1">23775‐23948</td><td align="char" char="." rowspan="1" colspan="1">23738‐23911</td></tr><tr><td align="left" rowspan="1" colspan="1">3b</td><td align="char" char="." rowspan="1" colspan="1">23945‐24136</td><td align="char" char="." rowspan="1" colspan="1">23947‐24141</td><td align="char" char="." rowspan="1" colspan="1">23938‐24142</td><td align="char" char="." rowspan="1" colspan="1">23911‐24105</td></tr><tr><td align="left" rowspan="1" colspan="1">E</td><td align="char" char="." rowspan="1" colspan="1">24117‐24404</td><td align="char" char="." rowspan="1" colspan="1">24122‐24430</td><td align="char" char="." rowspan="1" colspan="1">24123‐24431</td><td align="char" char="." rowspan="1" colspan="1">24086‐24394</td></tr><tr><td align="left" rowspan="1" colspan="1">M</td><td align="char" char="." rowspan="1" colspan="1">24394‐25074</td><td align="char" char="." rowspan="1" colspan="1">24423‐25103</td><td align="char" char="." rowspan="1" colspan="1">24424‐25104</td><td align="char" char="." rowspan="1" colspan="1">24387‐25067</td></tr><tr><td align="left" rowspan="1" colspan="1">4b</td><td align="char" char="." rowspan="1" colspan="1">25075‐25359</td><td align="char" char="." rowspan="1" colspan="1">25104‐25388</td><td align="char" char="." rowspan="1" colspan="1">25105‐25377</td><td align="char" char="." rowspan="1" colspan="1">25068‐25352</td></tr><tr><td align="left" rowspan="1" colspan="1">4c</td><td align="char" char="." rowspan="1" colspan="1">25280‐25450</td><td align="char" char="." rowspan="1" colspan="1">25309‐25470</td><td align="char" char="." rowspan="1" colspan="1">25310‐25387</td><td align="char" char="." rowspan="1" colspan="1">25273‐25434</td></tr><tr><td align="left" rowspan="1" colspan="1">5a</td><td align="char" char="." rowspan="1" colspan="1">25434‐25631</td><td align="char" char="." rowspan="1" colspan="1">25454‐25651</td><td align="char" char="." rowspan="1" colspan="1">25466‐25663</td><td align="char" char="." rowspan="1" colspan="1">25418‐25614</td></tr><tr><td align="left" rowspan="1" colspan="1">5b</td><td align="char" char="." rowspan="1" colspan="1">25628‐25876</td><td align="char" char="." rowspan="1" colspan="1">25648‐25896</td><td align="char" char="." rowspan="1" colspan="1">25660‐25908</td><td align="char" char="." rowspan="1" colspan="1">25612‐25860</td></tr><tr><td align="left" rowspan="1" colspan="1">N</td><td align="char" char="." rowspan="1" colspan="1">25819‐27045</td><td align="char" char="." rowspan="1" colspan="1">25839‐27068</td><td align="char" char="." rowspan="1" colspan="1">25851‐27080</td><td align="char" char="." rowspan="1" colspan="1">25803‐27032</td></tr><tr><td align="left" rowspan="1" colspan="1">6b</td><td align="char" char="." rowspan="1" colspan="1">27054‐27278</td><td align="char" char="." rowspan="1" colspan="1">27058‐27222</td><td align="char" char="." rowspan="1" colspan="1">27089‐27403</td><td align="char" char="." rowspan="1" colspan="1">27041‐27265</td></tr></tbody></table><table-wrap-foot id="tbed13000-ntgp-0002"><title><italic>Notes</italic></title><fn id="tbed13000-note-0004"><p>Strains belonging to the two genotypes show the same genome organization.</p></fn><fn id="tbed13000-note-0005"><p>Accessory genes <italic>4b</italic>,<italic> 4c</italic>, and <italic>6b</italic> have been identified in the genome of all the four viruses.</p></fn></table-wrap-foot><permissions><copyright-holder>John Wiley & Sons, Ltd</copyright-holder><license><license-p>This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.</license-p></license></permissions></table-wrap></sec><sec id="tbed13000-sec-0012"><label>3.2</label><title>Accession number</title><p>Sequence of the IBV strain gammaCoV/AvCov/Ck/Italy/IP14425/96 was submitted to the GenBank database and the following accession number was assigned: MG021194.</p></sec><sec id="tbed13000-sec-0013"><label>3.3</label><title>Phylogenetic analysis of full genomes of IBV strains</title><p>The phylogenetic analysis of the 187 representative full IBV genome sequences demonstrated that gammaCoV/AvCov/Ck/Italy/IP14425/96 clustered together with Q1 strains gammaCoV/Ck/Italy/I2022/13, CK/CH/LDL/97I and UY/09/CA/01, occupying a basal position in the specific cluster (Figure <xref rid="tbed13000-fig-0001" ref-type="fig">1</xref>). In the same clade, the Uruguayan strain UY/11/CA/18 (MF421320), was also present, previously ascribed to the SAI genotype (Lineage G‐11) (Figure <xref rid="tbed13000-fig-0001" ref-type="fig">1</xref>) (Marandino et al., <xref rid="tbed13000-bib-0027" ref-type="ref">2015</xref>).</p><fig fig-type="Figure" xml:lang="en" id="tbed13000-fig-0001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Phylogenetic tree based on Maximum Likelihood method with Tamura‐Nei substitution model constructed using 187 representative complete <styled-content style="fixed-case" toggle="no">IBV</styled-content> and <styled-content style="fixed-case" toggle="no">TC</styled-content>oV genomes. For easiness of representation, the upper part of the phylogenetic tree was compressed and the strains considered in the present study marked in red [Colour figure can be viewed at <ext-link ext-link-type="uri" xlink:href="http://wileyonlinelibrary.com">http://wileyonlinelibrary.com</ext-link>]</p></caption><graphic id="nlm-graphic-1" xlink:href="TBED-66-207-g001"></graphic></fig><p>GammaCoV/AvCov/Ck/Italy/IP14425/96 624I strain showed the highest sequence identity with the Italian Q1 strain gammaCoV/Ck/Italy/I2022/13 (<italic>p</italic>‐distance 0.054), while the percentage of identity slightly decreased when the virus was compared to the Chinese (<italic>p</italic>‐distance 0.058) and the Uruguayan (<italic>p</italic>‐distance 0.062) Q1 strains.</p></sec><sec id="tbed13000-sec-0014"><label>3.4</label><title>Phylogenetic analysis of full <italic>S1</italic> sequences</title><p>Phylogenetic analysis using a dataset characterized by 320 representative full <italic>S1</italic> sequences showed that gammaCoV/AvCov/Ck/Italy/IP14425/96 clustered together with strains previously identified as 624/I genotype isolated in Italy in the late ‘80s and early ‘90s and strains belonging to Q1 genotype, isolated in Italy, in China, in Taiwan, and South America (Figure <xref rid="tbed13000-fig-0002" ref-type="fig">2</xref>a). The highest sequence identity was observed with strain 624I/94/JQ901492.1 (<italic>p</italic>‐distance = 0.036) while the identity was lower when compared to Q1 strains (data not shown).</p><fig fig-type="Figure" xml:lang="en" id="tbed13000-fig-0002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>(a) Phylogenetic tree based on Maximum Likelihood method with Kimura‐2 model constructed using 320 <italic>S1</italic> gene complete sequences. For easiness of representation, strain reported in the present study and closely related strains, are marked in red. (b) Expanded phylogenetic tree based on Maximum Likelihood method with Kimura‐2 model constructed using <italic>S1</italic> complete sequences closely related to gammaCoV/AvCov/Ck/Italy/<styled-content style="fixed-case" toggle="no">IP</styled-content>14425/96 [Colour figure can be viewed at <ext-link ext-link-type="uri" xlink:href="http://wileyonlinelibrary.com">http://wileyonlinelibrary.com</ext-link>]</p></caption><graphic id="nlm-graphic-3" xlink:href="TBED-66-207-g002"></graphic></fig><p>The subtree obtained with the expanded dataset shows three clades, of which one contained all 624/I strains and occupied a basal position with respect to the others. In the remaining two clades, Q1 Italian, Chinese and some of the Taiwanese strains, cluster together, while the remaining Q1 Taiwan strains and all South American Q1 strains form a distinctive phylogenetic group (Figure <xref rid="tbed13000-fig-0002" ref-type="fig">2</xref>b).</p></sec><sec id="tbed13000-sec-0015"><label>3.5</label><title>Recombination analysis</title><p>Recombination analysis was performed to assess the possible recombinant nature of the 624I strain gammaCoV/AvCov/Ck/Italy/IP14425/96 and of the Q1 strains gammaCoV/Ck/Italy/I2022/13 and CK/CH/LDL/97I.</p><p>Possible recombination events were identified in the <italic>1a</italic> gene sequence of the strain CK/CH/LDL/97I with a H120 vaccine strain (FJ888351) (Figure <xref rid="tbed13000-fig-0003" ref-type="fig">3</xref>a). Neither gammaCoV/Ck/Italy/I2022/13 nor gammaCoV/AvCov/Ck/Italy/IP14425/96 Q1 strains showed a similar recombination event in the <italic>1a</italic> gene (Figures <xref rid="tbed13000-fig-0003" ref-type="fig">3</xref>b,c).</p><fig fig-type="Figure" xml:lang="en" id="tbed13000-fig-0003" orientation="portrait" position="float"><label>Figure 3</label><caption><p><styled-content style="fixed-case" toggle="no">RDP</styled-content> screenshots displaying the possible recombination events associated with <styled-content style="fixed-case" toggle="no">CK</styled-content>/<styled-content style="fixed-case" toggle="no">CH</styled-content>/<styled-content style="fixed-case" toggle="no">LDL</styled-content>/97I (a), gammaCoV/Ck/Italy/I2022/13 (b), and gammaCoV/AvCov/Ck/Italy/P14425/96 (c) Each panel displays the pairwise identities among the possible recombinant and its putative parents. Crossover sites indicating sharp changes in pairwise identity are pointed out by arrows. (a) Comparisons among the putative recombinant <styled-content style="fixed-case" toggle="no">CK</styled-content>/<styled-content style="fixed-case" toggle="no">CH</styled-content>/<styled-content style="fixed-case" toggle="no">LDL</styled-content>/97I show sharp changes in the pairwise identity within the <italic>1a</italic> gene, H120 vaccine strain <styled-content style="fixed-case" toggle="no">FJ</styled-content>888351 has been identified as putative parental strains for that genomic region. (b) Comparison among the putative recombinant gammaCoV/Ck/Italy/I2022/13 shows sharp changes in the pairwise identity within the <italic>1a</italic> gene; strain gammaCoV/AvCov/Ck/Italy/P14425I/96 has been identified as major parental strain for that region. (c) Comparison among the putative recombinant gammaCoV/AvCov/Ck/Italy/P14425/96 shows sharp changes in the pairwise identity within the <italic>1a</italic> gene; strain gammaCoV/Ck/Italy/I2022/13 has been identified as major parental strain for that genomic region [Colour figure can be viewed at <ext-link ext-link-type="uri" xlink:href="http://wileyonlinelibrary.com">http://wileyonlinelibrary.com</ext-link>]</p></caption><graphic id="nlm-graphic-5" xlink:href="TBED-66-207-g003"></graphic></fig><p>A phylogenetic analysis was performed considering only the <italic>1a</italic> gene, revealing that CK/CH/LDL/97I clustered with H120 and Mass strains, while gammaCoV/AvCov/Ck/Italy/IP14425/96 and gammaCoV/Ck/Italy/I2022/13 form a distinctive clade together with a QX‐like Italian strain (ITA/90254/2005 ‐ FN430414) (Figure <xref rid="tbed13000-fig-0004" ref-type="fig">4</xref>).</p><fig fig-type="Figure" xml:lang="en" id="tbed13000-fig-0004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Phylogenetic tree based on Maximum Likelihood method with Tamura‐Nei substitution constructed model using 187 representative <styled-content style="fixed-case" toggle="no">IBV</styled-content> and <styled-content style="fixed-case" toggle="no">TC</styled-content>oV <italic>1a</italic> genes. For easiness of representation, the upper part of the phylogenetic tree was compressed and the strains considered in the present study marked in red [Colour figure can be viewed at <ext-link ext-link-type="uri" xlink:href="http://wileyonlinelibrary.com">http://wileyonlinelibrary.com</ext-link>]</p></caption><graphic id="nlm-graphic-7" xlink:href="TBED-66-207-g004"></graphic></fig></sec></sec><sec id="tbed13000-sec-0016"><label>4</label><title>DISCUSSION</title><p>The genome of the IBV strain gammaCoV/AvCov/Ck/Italy/IP14425/96 isolated in Italy in 1996 was fully sequenced and this represents the first report of a full genome sequencing of a virus belonging to the 624I genotype. The isolate shows a genome organization slightly different when compared to the genome organization of most IBVs previously reported (5′UTR‐1a‐1b‐S‐3a‐3b‐E‐M‐5a‐5b‐N‐3′UTR) (Cavanagh, <xref rid="tbed13000-bib-0010" ref-type="ref">2005</xref>), since ORF analysis showed the presence of accessory genes <italic>4b</italic>,<italic> 4c</italic>, and <italic>6b</italic> already reported for TCoV and other IBVs (Abolnik, <xref rid="tbed13000-bib-0002" ref-type="ref">2015</xref>; Hewson, Ignjatovic, Browning, Devlin, & Noormohammadi, <xref rid="tbed13000-bib-0014" ref-type="ref">2011</xref>). It is not clear whether the scarcity of reports of presence of the accessory genes <italic>4b</italic>,<italic> 4c</italic>, and <italic>6b</italic> in IBVs is due to their absence in some genomes; or whether it depends on algorithms and software used by other authors for those ORF's detections. A recent ORF analysis of the genome of the Q1 strain gammaCoV/Ck/Italy/I2022/13, (Marandino et al., <xref rid="tbed13000-bib-0028" ref-type="ref">2017</xref>) did not support the presence of ORF <italic>6b</italic> in contrast to the results presented here. On the contrary, a recent study confirmed the expression of the 4b protein after M41 IBV infection in vitro (Bentley, Keep, Armesto, & Britton, <xref rid="tbed13000-bib-0004" ref-type="ref">2013</xref>). IBV accessory genes <italic>3a</italic>,<italic> 3b</italic>,<italic> 5a</italic>, and <italic>5b</italic> are known to be not necessary for viral replication, but several studies demonstrated their involvement in the pathogenicity of the virus (van Beurden et al., <xref rid="tbed13000-bib-0005" ref-type="ref">2017</xref>; Kint, Dickhout et al., <xref rid="tbed13000-bib-0018" ref-type="ref">2015</xref>; Kint, Fernandez‐Gutierrez et al., <xref rid="tbed13000-bib-0019" ref-type="ref">2015</xref>, <xref rid="tbed13000-bib-0020" ref-type="ref">2016</xref>). A similar function might be hypothesized also for genes <italic>4b</italic>,<italic> 4c</italic>, and <italic>6b</italic>, especially in the light that the <italic>4b</italic> homologous gene in the MERS‐CoV has been reported as an antagonist of type I interferon response (Yang et al., <xref rid="tbed13000-bib-0040" ref-type="ref">2013</xref>) and that the <italic>6b</italic> homologue in SARS‐CoV was shown to be able to induce apoptosis (Ye, Wong, Li, & Xie, <xref rid="tbed13000-bib-0041" ref-type="ref">2008</xref>). More studies need to be done to improve the knowledge on these three accessory genes, in particular whether they are peculiar of certain genotypes and whether their expression influences the pathogenicity or the tropism of the virus.</p><p>Phylogenetic analyses performed using two different datasets, one built with IBV complete genome sequences and one built with IBV complete or nearly complete <italic>S1</italic> gene sequences, showed that 624I and Q1 genotypes clustered together. Our findings, strongly suggest a common origin between the two genotypes. The basal location of the 624I strain in both the phylogenetic trees, coupled with the epidemiological data available, suggests that this genotype might have played a role in the emergence of Chinese Q1. This model requires long‐distance intercontinental dispersion of the 624I genotype and this possibility is supported by its ability to circulate for extended periods within the same country (Taddei et al., <xref rid="tbed13000-bib-0036" ref-type="ref">2012</xref>) and beyond a geographical area (Capua et al., <xref rid="tbed13000-bib-0009" ref-type="ref">1999</xref>; Krapez et al., <xref rid="tbed13000-bib-0021" ref-type="ref">2010</xref>). Unfortunately, there is no comprehensive model explaining the intercontinental dispersal of the 624I genotype. Some hypothesis can be proposed, such as migratory birds, illegal trading and poultry movement. Albeit speculative, these hypotheses seem to be supported by the detection of 624I genotype in Russia, which represents an intermediate position between Europe and the Far East (Bochkov et al., <xref rid="tbed13000-bib-0006" ref-type="ref">2006</xref>). Further investigations are needed since, despite the IBV worldwide dissemination has been observed and accepted for other genotypes (Franzo et al., <xref rid="tbed13000-bib-0013" ref-type="ref">2017</xref>), the mechanism behind this evidence is not fully understood.</p><p>The recombination analysis showed that the Chinese strain CK/CH/LDL/97I underwent recombination with a H120 vaccine strain, which has been previously demonstrated to be involved in recombination events leading to reversion to virulence and the emerge of new genotypes in China (Zhang et al., <xref rid="tbed13000-bib-0043" ref-type="ref">2010</xref>). The identification of such a recombination event within the <italic>1a</italic> gene might explain the relatively high genetic diversity between 624I strain gammaCoV/AvCov/Ck/Italy/IP14425/96 and Q1 Chinese strain CK/CH/LDL/97I, two viruses isolated only one year apart.</p><p>The absence of such recombination in the genome of Q1 Italian strain gammaCoV/Ck/Italy/I2022/13 suggests that not all Q1 strains emerged as a result of a recombination event with a H120 strain. The absence of a recombination event in the <italic>1a</italic> gene of Q1 Italian strain gammaCoV/Ck/Italy/I2022/13 might indicate that Chinese and Italian Q1 strains are the result of independent evolutions from the 624I genotype. However, the huge differences in field conditions and therefore genetic pressures between the two countries, together with the phylogenetic results based on <italic>S1</italic> gene sequences in which Q1 Italian strains cluster together with Chinese and Taiwanese strains, make this hypothesis highly unlikely.</p><p>Taken as a whole, the data presented in this study suggest the 624I genotype to be the ancestor of Q1.</p></sec></body><back><ref-list content-type="cited-references" id="tbed13000-bibl-0001"><title>REFERENCES></title><ref id="tbed13000-bib-0001"><mixed-citation publication-type="journal" id="tbed13000-cit-0001"><string-name><surname>Ababneh</surname>, <given-names>M.</given-names></string-name>, <string-name><surname>Dalab</surname>, <given-names>A. 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