Diversity and distribution of type A influenza viruses: an updated panorama analysis based on protein sequences
Identifieur interne : 000094 ( Main/Exploration ); précédent : 000093; suivant : 000095Diversity and distribution of type A influenza viruses: an updated panorama analysis based on protein sequences
Auteurs : Qingye Zhuang [République populaire de Chine] ; Suchun Wang [République populaire de Chine] ; Shuo Liu [République populaire de Chine] ; Guangyu Hou [République populaire de Chine] ; Jinping Li [République populaire de Chine] ; Wenming Jiang [République populaire de Chine] ; Kaicheng Wang [République populaire de Chine] ; Cheng Peng [République populaire de Chine] ; Dong Liu [République populaire de Chine] ; Aizhen Guo [République populaire de Chine] ; Jiming Chen [République populaire de Chine]Source :
- Virology Journal [ 1743-422X ] ; 2019.
Abstract
Type A influenza viruses (IAVs) cause significant infections in humans and multiple species of animals including pigs, horses, birds, dogs and some marine animals. They are of complicated phylogenetic diversity and distribution, and analysis of their phylogenetic diversity and distribution from a panorama view has not been updated for multiple years.
139,872 protein sequences of IAVs from GenBank were selected, and they were aligned and phylogenetically analyzed using the software tool MEGA 7.0. Lineages and subordinate lineages were classified according to the topology of the phylogenetic trees and the host, temporal and spatial distribution of the viruses, and designated using a novel universal nomenclature system.
Large phylogenetic trees of the two external viral genes (HA and NA) and six internal genes (PB2, PB1, PA, NP, MP and NS) were constructed, and the diversity and the host, temporal and spatial distribution of these genes were calculated and statistically analyzed. Various features regarding the diversity and distribution of IAVs were confirmed, revised or added through this study, as compared with previous reports. Lineages and subordinate lineages were classified and designated for each of the genes based on the updated panorama views.
The panorama views of phylogenetic diversity and distribution of IAVs and their nomenclature system were updated and assumed to be of significance for studies and communication of IAVs.
The online version of this article (10.1186/s12985-019-1188-7) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12985-019-1188-7
PubMed: 31242907
PubMed Central: 6595669
Affiliations:
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uniqKey="Peng C" first="Cheng" last="Peng">Cheng Peng</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.414245.2</institution-id><institution>National Avian Influenza Professional Laboratory,</institution><institution>China Animal Health and Epidemiology Center,</institution></institution-wrap>369 Nanjing Road, Qingdao, 266032 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>369 Nanjing Road, Qingdao</wicri:regionArea><wicri:noRegion>Qingdao</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Dong" sort="Liu, Dong" uniqKey="Liu D" first="Dong" last="Liu">Dong Liu</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Qingdao YeBio Bioengineering Co., Ltd, 369 Nanjing Road, Qingdao, 266032 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Qingdao YeBio Bioengineering Co., Ltd, 369 Nanjing Road, Qingdao</wicri:regionArea><wicri:noRegion>Qingdao</wicri:noRegion></affiliation></author><author><name sortKey="Guo, Aizhen" sort="Guo, Aizhen" uniqKey="Guo A" first="Aizhen" last="Guo">Aizhen Guo</name><affiliation wicri:level="3"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0004 1790 4137</institution-id><institution-id institution-id-type="GRID">grid.35155.37</institution-id><institution>The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine,</institution><institution>Huazhong Agricultural University,</institution></institution-wrap>1 Shizishan Street, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Shizishan Street, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName></affiliation></author><author><name sortKey="Chen, Jiming" sort="Chen, Jiming" uniqKey="Chen J" first="Jiming" last="Chen">Jiming Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.414245.2</institution-id><institution>National Avian Influenza Professional Laboratory,</institution><institution>China Animal Health and Epidemiology Center,</institution></institution-wrap>369 Nanjing Road, Qingdao, 266032 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>369 Nanjing Road, Qingdao</wicri:regionArea><wicri:noRegion>Qingdao</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p id="Par1">Type A influenza viruses (IAVs) cause significant infections in humans and multiple species of animals including pigs, horses, birds, dogs and some marine animals. They are of complicated phylogenetic diversity and distribution, and analysis of their phylogenetic diversity and distribution from a panorama view has not been updated for multiple years.</p></sec><sec><title>Methods</title><p id="Par2">139,872 protein sequences of IAVs from GenBank were selected, and they were aligned and phylogenetically analyzed using the software tool MEGA 7.0. Lineages and subordinate lineages were classified according to the topology of the phylogenetic trees and the host, temporal and spatial distribution of the viruses, and designated using a novel universal nomenclature system.</p></sec><sec><title>Results</title><p id="Par3">Large phylogenetic trees of the two external viral genes (HA and NA) and six internal genes (PB2, PB1, PA, NP, MP and NS) were constructed, and the diversity and the host, temporal and spatial distribution of these genes were calculated and statistically analyzed. Various features regarding the diversity and distribution of IAVs were confirmed, revised or added through this study, as compared with previous reports. Lineages and subordinate lineages were classified and designated for each of the genes based on the updated panorama views.</p></sec><sec><title>Conclusions</title><p id="Par4">The panorama views of phylogenetic diversity and distribution of IAVs and their nomenclature system were updated and assumed to be of significance for studies and communication of IAVs.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12985-019-1188-7) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author><author><name sortKey="Bean, Wj" uniqKey="Bean W">WJ Bean</name></author><author><name sortKey="Gorman, Ot" uniqKey="Gorman O">OT Gorman</name></author><author><name sortKey="Chambers, Tm" uniqKey="Chambers T">TM Chambers</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author><author><name sortKey="Munster, V" uniqKey="Munster V">V Munster</name></author><author><name sortKey="Wallensten, A" uniqKey="Wallensten A">A Wallensten</name></author><author><name sortKey="Bestebroer, Tm" uniqKey="Bestebroer T">TM Bestebroer</name></author><author><name sortKey="Herfst, S" uniqKey="Herfst S">S Herfst</name></author><author><name sortKey="Smith, D" uniqKey="Smith D">D Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tong, S" uniqKey="Tong S">S Tong</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Rivailler, P" uniqKey="Rivailler P">P Rivailler</name></author><author><name sortKey="Conrardy, C" uniqKey="Conrardy C">C Conrardy</name></author><author><name sortKey="Castillo, Da" uniqKey="Castillo D">DA Castillo</name></author><author><name sortKey="Chen, Lm" uniqKey="Chen L">LM Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tong, S" uniqKey="Tong S">S Tong</name></author><author><name sortKey="Zhu, X" uniqKey="Zhu X">X Zhu</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Shi, M" uniqKey="Shi M">M Shi</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Bourgeois, M" uniqKey="Bourgeois M">M Bourgeois</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Pusch, Elizabeth" uniqKey="Pusch E">Elizabeth Pusch</name></author><author><name sortKey="Suarez, David" uniqKey="Suarez D">David Suarez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alonso, Wj" uniqKey="Alonso W">WJ Alonso</name></author><author><name sortKey="Yu, C" uniqKey="Yu C">C Yu</name></author><author><name sortKey="Viboud, C" uniqKey="Viboud C">C Viboud</name></author><author><name sortKey="Richard, Sa" uniqKey="Richard S">SA Richard</name></author><author><name sortKey="Schuck Paim, C" uniqKey="Schuck Paim C">C Schuck-Paim</name></author><author><name sortKey="Simonsen, L" uniqKey="Simonsen L">L Simonsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y Chen</name></author><author><name sortKey="Chen, Yf" uniqKey="Chen Y">YF Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, H" uniqKey="Wu H">H Wu</name></author><author><name sortKey="Peng, X" uniqKey="Peng X">X Peng</name></author><author><name sortKey="Peng, X" uniqKey="Peng X">X Peng</name></author><author><name sortKey="Cheng, L" uniqKey="Cheng L">L Cheng</name></author><author><name sortKey="Lu, X" uniqKey="Lu X">X Lu</name></author><author><name sortKey="Jin, C" uniqKey="Jin C">C Jin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="To, Kelvin Kw" uniqKey="To K">Kelvin KW To</name></author><author><name sortKey="Ng, Kenneth Hl" uniqKey="Ng K">Kenneth HL Ng</name></author><author><name sortKey="Que, Tak Lun" uniqKey="Que T">Tak-Lun Que</name></author><author><name sortKey="Chan, Jacky Mc" uniqKey="Chan J">Jacky MC Chan</name></author><author><name sortKey="Tsang, Kay Yan" uniqKey="Tsang K">Kay-Yan Tsang</name></author><author><name sortKey="Tsang, Alan Kl" uniqKey="Tsang A">Alan KL Tsang</name></author><author><name sortKey="Chen, Honglin" uniqKey="Chen H">Honglin Chen</name></author><author><name sortKey="Yuen, Kwok Yung" uniqKey="Yuen K">Kwok-Yung Yuen</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Uyeki, Timothy M" uniqKey="Uyeki T">Timothy M. 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