The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments
Identifieur interne : 000941 ( Pmc/Checkpoint ); précédent : 000940; suivant : 000942The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments
Auteurs : Monica K. Borucki ; Jonathan E. Allen ; Haiyin Chen-Harris ; Adam Zemla ; Gilda Vanier ; Shalini Mabery ; Clinton Torres ; Pamela Hullinger ; Tom SlezakSource :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.
Url:
DOI: 10.1371/journal.pone.0052752
PubMed: 23308119
PubMed Central: 3538757
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.</p>
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<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Woolhouse, Mej" uniqKey="Woolhouse M">MEJ Woolhouse</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Elena, Sf" uniqKey="Elena S">SF Elena</name>
</author>
<author><name sortKey="Carrasco, P" uniqKey="Carrasco P">P Carrasco</name>
</author>
<author><name sortKey="Daros, J A" uniqKey="Daros J">J-A Daros</name>
</author>
<author><name sortKey="Sanjuan, R" uniqKey="Sanjuan R">R Sanjuan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Domingo, E" uniqKey="Domingo E">E Domingo</name>
</author>
<author><name sortKey="Sheldon, J" uniqKey="Sheldon J">J Sheldon</name>
</author>
<author><name sortKey="Perales, C" uniqKey="Perales C">C Perales</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Borderia, Av" uniqKey="Borderia A">AV Borderia</name>
</author>
<author><name sortKey="Stapleford, Ka" uniqKey="Stapleford K">KA Stapleford</name>
</author>
<author><name sortKey="Vignuzzi, M" uniqKey="Vignuzzi M">M Vignuzzi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Graham, Rl" uniqKey="Graham R">RL Graham</name>
</author>
<author><name sortKey="Baric, Rs" uniqKey="Baric R">RS Baric</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vijgen, L" uniqKey="Vijgen L">L Vijgen</name>
</author>
<author><name sortKey="Keyaerts, E" uniqKey="Keyaerts E">E Keyaerts</name>
</author>
<author><name sortKey="Lemey, P" uniqKey="Lemey P">P Lemey</name>
</author>
<author><name sortKey="Maes, P" uniqKey="Maes P">P Maes</name>
</author>
<author><name sortKey="Van Reeth, K" uniqKey="Van Reeth K">K Van Reeth</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vijgen, L" uniqKey="Vijgen L">L Vijgen</name>
</author>
<author><name sortKey="Keyaerts, E" uniqKey="Keyaerts E">E Keyaerts</name>
</author>
<author><name sortKey="Moes, E" uniqKey="Moes E">E Moes</name>
</author>
<author><name sortKey="Thoelen, I" uniqKey="Thoelen I">I Thoelen</name>
</author>
<author><name sortKey="Wollants, E" uniqKey="Wollants E">E Wollants</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gonzalez, Jm" uniqKey="Gonzalez J">JM González</name>
</author>
<author><name sortKey="Gomez Puertas, P" uniqKey="Gomez Puertas P">P Gomez-Puertas</name>
</author>
<author><name sortKey="Cavanagh, D" uniqKey="Cavanagh D">D Cavanagh</name>
</author>
<author><name sortKey="Gorbalenya, Ae" uniqKey="Gorbalenya A">AE Gorbalenya</name>
</author>
<author><name sortKey="Enjuanes, L" uniqKey="Enjuanes L">L Enjuanes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Han, Mg" uniqKey="Han M">MG Han</name>
</author>
<author><name sortKey="Cheon, D S" uniqKey="Cheon D">D-S Cheon</name>
</author>
<author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name>
</author>
<author><name sortKey="Saif, Lj" uniqKey="Saif L">LJ Saif</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schultze, B" uniqKey="Schultze B">B Schultze</name>
</author>
<author><name sortKey="Herrler, G" uniqKey="Herrler G">G Herrler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, W" uniqKey="Li W">W Li</name>
</author>
<author><name sortKey="Wong, S K" uniqKey="Wong S">S-K Wong</name>
</author>
<author><name sortKey="Li, F" uniqKey="Li F">F Li</name>
</author>
<author><name sortKey="Kuhn, Jh" uniqKey="Kuhn J">JH Kuhn</name>
</author>
<author><name sortKey="Huang, Ic" uniqKey="Huang I">IC Huang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Peng, G" uniqKey="Peng G">G Peng</name>
</author>
<author><name sortKey="Sun, D" uniqKey="Sun D">D Sun</name>
</author>
<author><name sortKey="Rajashankar, Kr" uniqKey="Rajashankar K">KR Rajashankar</name>
</author>
<author><name sortKey="Qian, Z" uniqKey="Qian Z">Z Qian</name>
</author>
<author><name sortKey="Holmes, Kv" uniqKey="Holmes K">KV Holmes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name>
</author>
<author><name sortKey="Hasoksuz, M" uniqKey="Hasoksuz M">M Hasoksuz</name>
</author>
<author><name sortKey="Spiro, D" uniqKey="Spiro D">D Spiro</name>
</author>
<author><name sortKey="Halpin, R" uniqKey="Halpin R">R Halpin</name>
</author>
<author><name sortKey="Wang, S" uniqKey="Wang S">S Wang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chouljenko, Vn" uniqKey="Chouljenko V">VN Chouljenko</name>
</author>
<author><name sortKey="Lin, Xq" uniqKey="Lin X">XQ Lin</name>
</author>
<author><name sortKey="Storz, J" uniqKey="Storz J">J Storz</name>
</author>
<author><name sortKey="Kousoulas, Kg" uniqKey="Kousoulas K">KG Kousoulas</name>
</author>
<author><name sortKey="Gorbalenya, Ae" uniqKey="Gorbalenya A">AE Gorbalenya</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Perlman, S" uniqKey="Perlman S">S Perlman</name>
</author>
<author><name sortKey="Netland, J" uniqKey="Netland J">J Netland</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Devaraj, Sg" uniqKey="Devaraj S">SG Devaraj</name>
</author>
<author><name sortKey="Wang, N" uniqKey="Wang N">N Wang</name>
</author>
<author><name sortKey="Chen, Z" uniqKey="Chen Z">Z Chen</name>
</author>
<author><name sortKey="Chen, Z" uniqKey="Chen Z">Z Chen</name>
</author>
<author><name sortKey="Tseng, M" uniqKey="Tseng M">M Tseng</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sun, L" uniqKey="Sun L">L Sun</name>
</author>
<author><name sortKey="Xing, Y" uniqKey="Xing Y">Y Xing</name>
</author>
<author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
<author><name sortKey="Zheng, Y" uniqKey="Zheng Y">Y Zheng</name>
</author>
<author><name sortKey="Yang, Y" uniqKey="Yang Y">Y Yang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Almeida, Ms" uniqKey="Almeida M">MS Almeida</name>
</author>
<author><name sortKey="Johnson, Ma" uniqKey="Johnson M">MA Johnson</name>
</author>
<author><name sortKey="Herrmann, T" uniqKey="Herrmann T">T Herrmann</name>
</author>
<author><name sortKey="Geralt, M" uniqKey="Geralt M">M Geralt</name>
</author>
<author><name sortKey="Wuthrich, K" uniqKey="Wuthrich K">K Wüthrich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brockway, Sm" uniqKey="Brockway S">SM Brockway</name>
</author>
<author><name sortKey="Lu, Xt" uniqKey="Lu X">XT Lu</name>
</author>
<author><name sortKey="Peters, Tr" uniqKey="Peters T">TR Peters</name>
</author>
<author><name sortKey="Dermody, Ts" uniqKey="Dermody T">TS Dermody</name>
</author>
<author><name sortKey="Denison, Mr" uniqKey="Denison M">MR Denison</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Saif, Lj" uniqKey="Saif L">LJ Saif</name>
</author>
<author><name sortKey="Redman, Dr" uniqKey="Redman D">DR Redman</name>
</author>
<author><name sortKey="Brock, Kv" uniqKey="Brock K">KV Brock</name>
</author>
<author><name sortKey="Kohler, Em" uniqKey="Kohler E">EM Kohler</name>
</author>
<author><name sortKey="Heckert, Ra" uniqKey="Heckert R">RA Heckert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="St Cyr Coats, Ks" uniqKey="St Cyr Coats K">KS St Cyr-Coats</name>
</author>
<author><name sortKey="Storz, J" uniqKey="Storz J">J Storz</name>
</author>
<author><name sortKey="Hussain, Ka" uniqKey="Hussain K">KA Hussain</name>
</author>
<author><name sortKey="Schnorr, Kl" uniqKey="Schnorr K">KL Schnorr</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Parker, Md" uniqKey="Parker M">MD Parker</name>
</author>
<author><name sortKey="Yoo, D" uniqKey="Yoo D">D Yoo</name>
</author>
<author><name sortKey="Cox, Gj" uniqKey="Cox G">GJ Cox</name>
</author>
<author><name sortKey="Babiuk, La" uniqKey="Babiuk L">LA Babiuk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Belouzard, S" uniqKey="Belouzard S">S Belouzard</name>
</author>
<author><name sortKey="Chu, Vc" uniqKey="Chu V">VC Chu</name>
</author>
<author><name sortKey="Whittaker, Gr" uniqKey="Whittaker G">GR Whittaker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zemla, A" uniqKey="Zemla A">A Zemla</name>
</author>
<author><name sortKey="Zhou, Ce" uniqKey="Zhou C">CE Zhou</name>
</author>
<author><name sortKey="Slezak, T" uniqKey="Slezak T">T Slezak</name>
</author>
<author><name sortKey="Kuczmarski, T" uniqKey="Kuczmarski T">T Kuczmarski</name>
</author>
<author><name sortKey="Rama, D" uniqKey="Rama D">D Rama</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zagordi, O" uniqKey="Zagordi O">O Zagordi</name>
</author>
<author><name sortKey="Bhattacharya, A" uniqKey="Bhattacharya A">A Bhattacharya</name>
</author>
<author><name sortKey="Eriksson, N" uniqKey="Eriksson N">N Eriksson</name>
</author>
<author><name sortKey="Beerenwinkel, N" uniqKey="Beerenwinkel N">N Beerenwinkel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zagordi, O" uniqKey="Zagordi O">O Zagordi</name>
</author>
<author><name sortKey="Klein, R" uniqKey="Klein R">R Klein</name>
</author>
<author><name sortKey="Daumer, M" uniqKey="Daumer M">M Daumer</name>
</author>
<author><name sortKey="Beerenwinkel, N" uniqKey="Beerenwinkel N">N Beerenwinkel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wright, Cf" uniqKey="Wright C">CF Wright</name>
</author>
<author><name sortKey="Morelli, Mj" uniqKey="Morelli M">MJ Morelli</name>
</author>
<author><name sortKey="Thebaud, G" uniqKey="Thebaud G">G Thébaud</name>
</author>
<author><name sortKey="Knowles, Nj" uniqKey="Knowles N">NJ Knowles</name>
</author>
<author><name sortKey="Herzyk, P" uniqKey="Herzyk P">P Herzyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hofmann, Ma" uniqKey="Hofmann M">MA Hofmann</name>
</author>
<author><name sortKey="Sethna, Pb" uniqKey="Sethna P">PB Sethna</name>
</author>
<author><name sortKey="Brian, Da" uniqKey="Brian D">DA Brian</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Akaike, T" uniqKey="Akaike T">T Akaike</name>
</author>
<author><name sortKey="Fujii, S" uniqKey="Fujii S">S Fujii</name>
</author>
<author><name sortKey="Kato, A" uniqKey="Kato A">A Kato</name>
</author>
<author><name sortKey="Yoshitake, J" uniqKey="Yoshitake J">J Yoshitake</name>
</author>
<author><name sortKey="Miyamoto, Y" uniqKey="Miyamoto Y">Y Miyamoto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Watanabe, R" uniqKey="Watanabe R">R Watanabe</name>
</author>
<author><name sortKey="Matsuyama, S" uniqKey="Matsuyama S">S Matsuyama</name>
</author>
<author><name sortKey="Shirato, K" uniqKey="Shirato K">K Shirato</name>
</author>
<author><name sortKey="Maejima, M" uniqKey="Maejima M">M Maejima</name>
</author>
<author><name sortKey="Fukushi, S" uniqKey="Fukushi S">S Fukushi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De Haan, Cam" uniqKey="De Haan C">CAM de Haan</name>
</author>
<author><name sortKey="Haijema, Bj" uniqKey="Haijema B">BJ Haijema</name>
</author>
<author><name sortKey="Schellen, P" uniqKey="Schellen P">P Schellen</name>
</author>
<author><name sortKey="Schreur, Pw" uniqKey="Schreur P">PW Schreur</name>
</author>
<author><name sortKey="Te Lintelo, E" uniqKey="Te Lintelo E">E te Lintelo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bernard, Ka" uniqKey="Bernard K">KA Bernard</name>
</author>
<author><name sortKey="Klimstra, Wb" uniqKey="Klimstra W">WB Klimstra</name>
</author>
<author><name sortKey="Johnston, Re" uniqKey="Johnston R">RE Johnston</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De Haan, Cam" uniqKey="De Haan C">CAM de Haan</name>
</author>
<author><name sortKey="Li, Z" uniqKey="Li Z">Z Li</name>
</author>
<author><name sortKey="Te Lintelo, E" uniqKey="Te Lintelo E">E te Lintelo</name>
</author>
<author><name sortKey="Bosch, Bj" uniqKey="Bosch B">BJ Bosch</name>
</author>
<author><name sortKey="Haijema, Bj" uniqKey="Haijema B">BJ Haijema</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Spillmann, D" uniqKey="Spillmann D">D Spillmann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jacques, A" uniqKey="Jacques A">A Jacques</name>
</author>
<author><name sortKey="Bleau, C" uniqKey="Bleau C">C Bleau</name>
</author>
<author><name sortKey="Turbide, C" uniqKey="Turbide C">C Turbide</name>
</author>
<author><name sortKey="Beauchemin, N" uniqKey="Beauchemin N">N Beauchemin</name>
</author>
<author><name sortKey="Lamontagne, L" uniqKey="Lamontagne L">L Lamontagne</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bertram, S" uniqKey="Bertram S">S Bertram</name>
</author>
<author><name sortKey="Glowacka, I" uniqKey="Glowacka I">I Glowacka</name>
</author>
<author><name sortKey="Muller, Ma" uniqKey="Muller M">MA Müller</name>
</author>
<author><name sortKey="Lavender, H" uniqKey="Lavender H">H Lavender</name>
</author>
<author><name sortKey="Gnirss, K" uniqKey="Gnirss K">K Gnirss</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chouljenko, Vn" uniqKey="Chouljenko V">VN Chouljenko</name>
</author>
<author><name sortKey="Kousoulas, Kg" uniqKey="Kousoulas K">KG Kousoulas</name>
</author>
<author><name sortKey="Lin, X" uniqKey="Lin X">X Lin</name>
</author>
<author><name sortKey="Storz, J" uniqKey="Storz J">J Storz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Xm" uniqKey="Zhang X">XM Zhang</name>
</author>
<author><name sortKey="Kousoulas, Kg" uniqKey="Kousoulas K">KG Kousoulas</name>
</author>
<author><name sortKey="Storz, J" uniqKey="Storz J">J Storz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mcroy, Wc" uniqKey="Mcroy W">WC McRoy</name>
</author>
<author><name sortKey="Baric, Rs" uniqKey="Baric R">RS Baric</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stabel, Jr" uniqKey="Stabel J">JR Stabel</name>
</author>
<author><name sortKey="Stabel, Tj" uniqKey="Stabel T">TJ Stabel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cho, Ko" uniqKey="Cho K">KO Cho</name>
</author>
<author><name sortKey="Hasoksuz, M" uniqKey="Hasoksuz M">M Hasoksuz</name>
</author>
<author><name sortKey="Nielsen, Pr" uniqKey="Nielsen P">PR Nielsen</name>
</author>
<author><name sortKey="Chang, Ko" uniqKey="Chang K">KO Chang</name>
</author>
<author><name sortKey="Lathrop, S" uniqKey="Lathrop S">S Lathrop</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name>
</author>
<author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name>
</author>
<author><name sortKey="Peterson, D" uniqKey="Peterson D">D Peterson</name>
</author>
<author><name sortKey="Peterson, N" uniqKey="Peterson N">N Peterson</name>
</author>
<author><name sortKey="Stecher, G" uniqKey="Stecher G">G Stecher</name>
</author>
<author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name>
</author>
</analytic>
</biblStruct>
</listBibl>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23308119</article-id>
<article-id pub-id-type="pmc">3538757</article-id>
<article-id pub-id-type="publisher-id">PONE-D-12-29217</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0052752</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Evolution</subject>
<subject>Genome Sequencing</subject>
</subj-group>
</subj-group>
<subj-group><subject>Microbiology</subject>
<subj-group><subject>Virology</subject>
<subj-group><subject>Viral classification</subject>
<subj-group><subject>RNA viruses</subject>
</subj-group>
</subj-group>
<subj-group><subject>Emerging Viral Diseases</subject>
<subject>Viral Evolution</subject>
<subject>Viral Transmission and Infection</subject>
</subj-group>
</subj-group>
<subj-group><subject>Emerging Infectious Diseases</subject>
<subject>Host-Pathogen Interaction</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Computer Science</subject>
<subj-group><subject>Computing Methods</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments</article-title>
<alt-title alt-title-type="running-head">Role of Quasispecies in Coronavirus Evolution</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Borucki</surname>
<given-names>Monica K.</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Allen</surname>
<given-names>Jonathan E.</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen-Harris</surname>
<given-names>Haiyin</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zemla</surname>
<given-names>Adam</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vanier</surname>
<given-names>Gilda</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mabery</surname>
<given-names>Shalini</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Torres</surname>
<given-names>Clinton</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hullinger</surname>
<given-names>Pamela</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Slezak</surname>
<given-names>Tom</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
</contrib>
</contrib-group>
<aff id="aff1"><addr-line>Lawrence Livermore National Laboratory, Livermore, California, United States of America</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Coffey</surname>
<given-names>Lark L.</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Blood Systems Research Institute, United States of America</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>borucki2@llnl.gov</email>
</corresp>
<fn fn-type="COI-statement"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con"><p>Conceived and designed the experiments: MKB JEA TS. Performed the experiments: GV SM AZ CT. Analyzed the data: MKB JEA HC. Contributed reagents/materials/analysis tools: PH TS. Wrote the paper: MKB HC JEA.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>7</day>
<month>1</month>
<year>2013</year>
</pub-date>
<volume>8</volume>
<issue>1</issue>
<elocation-id>e52752</elocation-id>
<history><date date-type="received"><day>25</day>
<month>9</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>21</day>
<month>11</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-year>2013</copyright-year>
<license xlink:href="https://creativecommons.org/publicdomain/zero/1.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.</license-p>
</license>
</permissions>
<abstract><p>The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.</p>
</abstract>
<funding-group><funding-statement>Funding was provided by Lawrence Livermore National Laboratory internal funding (LDRD 10-LW-020) and a grant from the Defense Threat Reduction Agency, Transformational Medical Technologies Initiative. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Allen, Jonathan E" sort="Allen, Jonathan E" uniqKey="Allen J" first="Jonathan E." last="Allen">Jonathan E. Allen</name>
<name sortKey="Borucki, Monica K" sort="Borucki, Monica K" uniqKey="Borucki M" first="Monica K." last="Borucki">Monica K. Borucki</name>
<name sortKey="Chen Harris, Haiyin" sort="Chen Harris, Haiyin" uniqKey="Chen Harris H" first="Haiyin" last="Chen-Harris">Haiyin Chen-Harris</name>
<name sortKey="Hullinger, Pamela" sort="Hullinger, Pamela" uniqKey="Hullinger P" first="Pamela" last="Hullinger">Pamela Hullinger</name>
<name sortKey="Mabery, Shalini" sort="Mabery, Shalini" uniqKey="Mabery S" first="Shalini" last="Mabery">Shalini Mabery</name>
<name sortKey="Slezak, Tom" sort="Slezak, Tom" uniqKey="Slezak T" first="Tom" last="Slezak">Tom Slezak</name>
<name sortKey="Torres, Clinton" sort="Torres, Clinton" uniqKey="Torres C" first="Clinton" last="Torres">Clinton Torres</name>
<name sortKey="Vanier, Gilda" sort="Vanier, Gilda" uniqKey="Vanier G" first="Gilda" last="Vanier">Gilda Vanier</name>
<name sortKey="Zemla, Adam" sort="Zemla, Adam" uniqKey="Zemla A" first="Adam" last="Zemla">Adam Zemla</name>
</noCountry>
</tree>
</affiliations>
</record>
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