Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918
Identifieur interne : 000A94 ( Pmc/Corpus ); précédent : 000A93; suivant : 000A95Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918
Auteurs : Jun Shen ; Jianpeng Ma ; Qinghua WangSource :
- PLoS ONE [ 1932-6203 ] ; 2009.
Abstract
The Pandemic (H1N1) 2009 is spreading to numerous countries and causing many human deaths. Although the symptoms in humans are mild at present, fears are that further mutations in the virus could lead to a potentially more dangerous outbreak in subsequent months. As the primary immunity-eliciting antigen, hemagglutinin (HA) is the major agent for host-driven antigenic drift in A(H3N2) virus. However, whether and how the evolution of HA is influenced by existing immunity is poorly understood for A(H1N1). Here, by analyzing hundreds of A(H1N1) HA sequences since 1918, we show the first evidence that host selections are indeed present in A(H1N1) HAs. Among a subgroup of human A(H1N1) HAs between 1918∼2008, we found strong diversifying (positive) selection at HA1 156 and 190. We also analyzed the evolutionary trends at HA1 190 and 225 that are critical determinants for receptor-binding specificity of A(H1N1) HA. Different A(H1N1) viruses appeared to favor one of these two sites in host-driven antigenic drift: epidemic A(H1N1) HAs favor HA1 190 while the 1918 pandemic and swine HAs favor HA1 225. Thus, our results highlight the urgency to understand the interplay between antigenic drift and receptor binding in HA evolution, and provide molecular signatures for monitoring future antigenically drifted 2009 pandemic and seasonal A(H1N1) influenza viruses.
Url:
DOI: 10.1371/journal.pone.0007789
PubMed: 19924230
PubMed Central: 2773012
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PMC:2773012Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918</title><author><name sortKey="Shen, Jun" sort="Shen, Jun" uniqKey="Shen J" first="Jun" last="Shen">Jun Shen</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Bioengineering, Rice University, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Ma, Jianpeng" sort="Ma, Jianpeng" uniqKey="Ma J" first="Jianpeng" last="Ma">Jianpeng Ma</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Bioengineering, Rice University, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><addr-line>Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Wang, Qinghua" sort="Wang, Qinghua" uniqKey="Wang Q" first="Qinghua" last="Wang">Qinghua Wang</name><affiliation><nlm:aff id="aff2"><addr-line>Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19924230</idno><idno type="pmc">2773012</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773012</idno><idno type="RBID">PMC:2773012</idno><idno type="doi">10.1371/journal.pone.0007789</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000A94</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A94</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918</title><author><name sortKey="Shen, Jun" sort="Shen, Jun" uniqKey="Shen J" first="Jun" last="Shen">Jun Shen</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Bioengineering, Rice University, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Ma, Jianpeng" sort="Ma, Jianpeng" uniqKey="Ma J" first="Jianpeng" last="Ma">Jianpeng Ma</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Bioengineering, Rice University, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><addr-line>Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Wang, Qinghua" sort="Wang, Qinghua" uniqKey="Wang Q" first="Qinghua" last="Wang">Qinghua Wang</name><affiliation><nlm:aff id="aff2"><addr-line>Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The Pandemic (H1N1) 2009 is spreading to numerous countries and causing many human deaths. Although the symptoms in humans are mild at present, fears are that further mutations in the virus could lead to a potentially more dangerous outbreak in subsequent months. As the primary immunity-eliciting antigen, hemagglutinin (HA) is the major agent for host-driven antigenic drift in A(H3N2) virus. However, whether and how the evolution of HA is influenced by existing immunity is poorly understood for A(H1N1). Here, by analyzing hundreds of A(H1N1) HA sequences since 1918, we show the first evidence that host selections are indeed present in A(H1N1) HAs. Among a subgroup of human A(H1N1) HAs between 1918∼2008, we found strong diversifying (positive) selection at HA<sub>1</sub> 156 and 190. We also analyzed the evolutionary trends at HA<sub>1</sub> 190 and 225 that are critical determinants for receptor-binding specificity of A(H1N1) HA. Different A(H1N1) viruses appeared to favor one of these two sites in host-driven antigenic drift: epidemic A(H1N1) HAs favor HA<sub>1</sub> 190 while the 1918 pandemic and swine HAs favor HA<sub>1</sub> 225. Thus, our results highlight the urgency to understand the interplay between antigenic drift and receptor binding in HA evolution, and provide molecular signatures for monitoring future antigenically drifted 2009 pandemic and seasonal A(H1N1) influenza viruses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wang, Tt" uniqKey="Wang T">TT Wang</name></author><author><name sortKey="Palese, P" uniqKey="Palese P">P Palese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Neumann, G" uniqKey="Neumann G">G Neumann</name></author><author><name sortKey="Noda, T" uniqKey="Noda T">T Noda</name></author><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peiris, Js" uniqKey="Peiris J">JS Peiris</name></author><author><name sortKey="Poon, Ll" uniqKey="Poon L">LL Poon</name></author><author><name sortKey="Guan, Y" 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<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">19924230</article-id><article-id pub-id-type="pmc">2773012</article-id><article-id pub-id-type="publisher-id">09-PONE-RA-12140R1</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0007789</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Virology</subject><subject>Virology/Emerging Viral Diseases</subject><subject>Virology/Virus Evolution and Symbiosis</subject></subj-group></article-categories><title-group><article-title>Evolutionary Trends of A(H1N1) Influenza Virus Hemagglutinin Since 1918</article-title><alt-title alt-title-type="running-head">Evolution of A(H1N1) HA</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Shen</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ma</surname><given-names>Jianpeng</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Qinghua</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Bioengineering, Rice University, Houston, Texas, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Martin</surname><given-names>Darren P.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">Institute of Infectious Disease and Molecular Medicine, South Africa</aff><author-notes><corresp id="cor1">* E-mail: <email>E-mail: qinghuaw@bcm.tmc.edu</email> (QW); <email>jpma@bcm.tmc.edu</email> (JM)</corresp><fn fn-type="con"><p>Conceived and designed the experiments: JM QW. Performed the experiments: JS QW. Analyzed the data: JM QW. Contributed reagents/materials/analysis tools: JM QW. Wrote the paper: JS JM QW.</p></fn></author-notes><pub-date pub-type="collection"><year>2009</year></pub-date><pub-date pub-type="epub"><day>17</day><month>11</month><year>2009</year></pub-date><volume>4</volume><issue>11</issue><elocation-id>e7789</elocation-id><history><date date-type="received"><day>7</day><month>8</month><year>2009</year></date><date date-type="accepted"><day>15</day><month>10</month><year>2009</year></date></history><permissions><copyright-statement>Shen et al.</copyright-statement><copyright-year>2009</copyright-year><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p></license></permissions><abstract><p>The Pandemic (H1N1) 2009 is spreading to numerous countries and causing many human deaths. Although the symptoms in humans are mild at present, fears are that further mutations in the virus could lead to a potentially more dangerous outbreak in subsequent months. As the primary immunity-eliciting antigen, hemagglutinin (HA) is the major agent for host-driven antigenic drift in A(H3N2) virus. However, whether and how the evolution of HA is influenced by existing immunity is poorly understood for A(H1N1). Here, by analyzing hundreds of A(H1N1) HA sequences since 1918, we show the first evidence that host selections are indeed present in A(H1N1) HAs. Among a subgroup of human A(H1N1) HAs between 1918∼2008, we found strong diversifying (positive) selection at HA<sub>1</sub> 156 and 190. We also analyzed the evolutionary trends at HA<sub>1</sub> 190 and 225 that are critical determinants for receptor-binding specificity of A(H1N1) HA. Different A(H1N1) viruses appeared to favor one of these two sites in host-driven antigenic drift: epidemic A(H1N1) HAs favor HA<sub>1</sub> 190 while the 1918 pandemic and swine HAs favor HA<sub>1</sub> 225. Thus, our results highlight the urgency to understand the interplay between antigenic drift and receptor binding in HA evolution, and provide molecular signatures for monitoring future antigenically drifted 2009 pandemic and seasonal A(H1N1) influenza viruses.</p></abstract><counts><page-count count="10"></page-count></counts></article-meta></front><body><sec id="s1"><title>Introduction</title><p>Since April 2009, a global outbreak caused by the swine-origin 2009 A(H1N1) influenza virus has spread to numerous countries <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Peiris1" ref-type="bibr">[3]</xref>, <xref rid="pone.0007789-Dawood1" ref-type="bibr">[4]</xref>, <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Solovyov1" ref-type="bibr">[6]</xref>, <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>, <xref rid="pone.0007789-Munster1" ref-type="bibr">[9]</xref>, <xref rid="pone.0007789-Maines1" ref-type="bibr">[10]</xref>, which warranted the declaration of “Pandemic (H1N1) 2009” by the World Health Organization on June 11, 2009. As of September 6, there had been over 277,607 infected individuals and at least 3,205 confirmed human deaths worldwide.</p><p>The Pandemic (H1N1) 2009 is not the first human pandemic caused by A(H1N1) influenza virus. During 1918∼1919, the “Spanish” A(H1N1) influenza virus swept across the globe, infected ∼25% of the entire population and claimed at least 50 million human lives worldwide <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>. In subsequent years, A(H1N1) influenza virus continued to circulate among humans and caused a number of severe outbreaks between 1920s and 1950s <xref rid="pone.0007789-Logan1" ref-type="bibr">[12]</xref>, <xref rid="pone.0007789-Collins1" ref-type="bibr">[13]</xref>, <xref rid="pone.0007789-RasmussenAF1" ref-type="bibr">[14]</xref>, <xref rid="pone.0007789-Sartwell1" ref-type="bibr">[15]</xref>, <xref rid="pone.0007789-Salk1" ref-type="bibr">[16]</xref>, <xref rid="pone.0007789-Kilbourne1" ref-type="bibr">[17]</xref>, <xref rid="pone.0007789-Isaacs1" ref-type="bibr">[18]</xref>, <xref rid="pone.0007789-Viboud1" ref-type="bibr">[19]</xref>, <xref rid="pone.0007789-Viboud2" ref-type="bibr">[20]</xref>, in particular the A(H1N1) epidemic in 1950∼1951 with mortality exceeding those of the 1957 “Asian” and 1968 “Hong Kong” pandemics <xref rid="pone.0007789-Isaacs1" ref-type="bibr">[18]</xref>, <xref rid="pone.0007789-Viboud1" ref-type="bibr">[19]</xref>, <xref rid="pone.0007789-Viboud2" ref-type="bibr">[20]</xref>. In 1957, A(H1N1) influenza virus disappeared, replaced by a reassorted A(H2N2) influenza virus <xref rid="pone.0007789-Scholtissek1" ref-type="bibr">[21]</xref>. However, the A(H1N1) influenza virus reappeared in 1977, with a close genetic and antigenic similarity to those A(H1N1) viruses isolated in 1950 <xref rid="pone.0007789-Nakajima1" ref-type="bibr">[22]</xref>, <xref rid="pone.0007789-Kendal1" ref-type="bibr">[23]</xref>, <xref rid="pone.0007789-Scholtissek2" ref-type="bibr">[24]</xref>, and has co-circulated with A(H3N2) and type B influenza virus to cause seasonal human epidemics ever since.</p><p>The same 1918 pandemic A(H1N1) influenza virus was also spread to swine during 1918∼1919, and became the so-called “classical” swine influenza <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>, <xref rid="pone.0007789-Taubenberger1" ref-type="bibr">[25]</xref>, <xref rid="pone.0007789-Shope1" ref-type="bibr">[26]</xref>, <xref rid="pone.0007789-Morens1" ref-type="bibr">[27]</xref>, first isolated in North American in 1930 <xref rid="pone.0007789-Shope1" ref-type="bibr">[26]</xref> and in Europe in 1976 <xref rid="pone.0007789-Brown1" ref-type="bibr">[28]</xref>, <xref rid="pone.0007789-Olsen1" ref-type="bibr">[29]</xref>. In 1979, a novel lineage of avian-like A(H1N1) influenza virus, believed to have derived from closely related Eurasia avian influenza viruses, emerged in swine in Europe <xref rid="pone.0007789-Pensaert1" ref-type="bibr">[30]</xref> and replaced the classical swine A(H1N1) virus in this region <xref rid="pone.0007789-Brown2" ref-type="bibr">[31]</xref>, <xref rid="pone.0007789-Donatelli1" ref-type="bibr">[32]</xref>, <xref rid="pone.0007789-Reid2" ref-type="bibr">[33]</xref>. These two classes of swine A(H1N1) viruses displayed different evolutionary trajectories <xref rid="pone.0007789-Dunham1" ref-type="bibr">[34]</xref>. In1998, a new triple-reassortant A(H3N2) virus, derived from North American avian, classical swine A(H1N1) and human A(H3N2) viruses, caused outbreaks in North American swine <xref rid="pone.0007789-Brown3" ref-type="bibr">[35]</xref>, <xref rid="pone.0007789-Webby1" ref-type="bibr">[36]</xref>. Mixing of the triple-reassortant H3N2 with established swine lineages gave rise to H1N1 and H1N2 reassortant swine viruses <xref rid="pone.0007789-Newman1" ref-type="bibr">[37]</xref>, <xref rid="pone.0007789-Shinde1" ref-type="bibr">[38]</xref>. Since 2007, human infection caused by A(H1N1) swine virus has become a health concern in the United States <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>.</p><p>The 2009 A(H1N1) influenza virus has its origin as a reassortant from a Eurasian avian-like swine A(H1N1) virus and a triple-reassortant virus circulating in North American swine <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Peiris1" ref-type="bibr">[3]</xref>, <xref rid="pone.0007789-Dawood1" ref-type="bibr">[4]</xref>, <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Solovyov1" ref-type="bibr">[6]</xref>, <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>. As such, the 2009 A(H1N1) virus contains NA and M from Eurasian avian-like swine A(H1N1) virus, and the remaining genes from the triple-reassortant virus - PB2 and PA (avian virus), PB1 (human A(H3N2)), and HA, NP and NS (classical swine A(H1N1)) <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Peiris1" ref-type="bibr">[3]</xref>, <xref rid="pone.0007789-Dawood1" ref-type="bibr">[4]</xref>, <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Solovyov1" ref-type="bibr">[6]</xref>, <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>. In a sense, we are continuingly living in a pandemic that started in 1918 <xref rid="pone.0007789-Morens1" ref-type="bibr">[27]</xref>. Thus, it is not surprising for the similarly mild first waves of the 1918 and 2009 pandemics. Notably, the second wave of the “Spanish” influenza in the fall of 1918 became much more lethal, peaked within one month of the initial introductions in many communities <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>. This makes influenza virologists and healthcare officials fear that further mutations in the 2009 A(H1N1) virus could also lead to a potentially more dangerous second wave in subsequent months. Thus, in-depth studies on the 1918 pandemic strains as well as their post-pandemic decedents should provide critical new insights into the evolution of A(H1N1) in general, and the pandemic potential of the 2009 A(H1N1) in particular.</p><p>HA is one of the two major glycoproteins on the surface of influenza virus. It is the primary antigen that elicits host immune response, and is also responsible for binding to sialic-acid receptors and for mediating viral entry into host cells <xref rid="pone.0007789-Skehel1" ref-type="bibr">[39]</xref>. The hallmarks of highly pathogenic influenza viruses among human population include easy human-to-human transmission as a result of high affinity of HA for human-like α(2,6) receptors, and significant difference in sequence and antigenicity of HA with existing seasonal and vaccine strains <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Skehel1" ref-type="bibr">[39]</xref>. It has been demonstrated on 1918 A(H1N1) HA that HA<sub>1</sub> D190 and D225 are key determinants for effective binding to human-like α(2,6) receptors and consequently high infectivity of the virus among human population <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>, <xref rid="pone.0007789-Tumpey1" ref-type="bibr">[40]</xref>, <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>, <xref rid="pone.0007789-Stevens1" ref-type="bibr">[42]</xref>. A single mutation D225G reduced the binding affinity for α(2,6) receptors <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>, <xref rid="pone.0007789-Stevens1" ref-type="bibr">[42]</xref> and the infectivity of the virus <xref rid="pone.0007789-Tumpey1" ref-type="bibr">[40]</xref>, while a double variant D190E/D225G rendered the HA non-binding to α(2,6) receptors <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>, <xref rid="pone.0007789-Stevens1" ref-type="bibr">[42]</xref> and the virus non-infectious <xref rid="pone.0007789-Tumpey1" ref-type="bibr">[40]</xref>.</p><p>In A(H3N2) virus, HA is the major agent for host-driven antigenic drift <xref rid="pone.0007789-Bush1" ref-type="bibr">[43]</xref>, <xref rid="pone.0007789-Bush2" ref-type="bibr">[44]</xref>. However, it is unclear whether or not and, if yes, how human immunity imposes selection on A(H1N1) HA. In order to address this critical issue, we undertook a systematic computational analysis of the evolution of H1 HA in the region of HA<sub>1</sub>, which is the primary target for host immunity selection <xref rid="pone.0007789-Bush1" ref-type="bibr">[43]</xref>.</p><p>Recent years have witnessed an explosive expansion of available computational methods for phylogenetic analysis of selective pressure, including a variety of methods that look for different types of positive selection such as diversifying selection, toggling selection and directional selection <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref>, <xref rid="pone.0007789-Yang2" ref-type="bibr">[46]</xref>, <xref rid="pone.0007789-Delport1" ref-type="bibr">[47]</xref>, <xref rid="pone.0007789-Seoighe1" ref-type="bibr">[48]</xref>, <xref rid="pone.0007789-KosakovskyPond1" ref-type="bibr">[49]</xref>, <xref rid="pone.0007789-Anisimova1" ref-type="bibr">[50]</xref>, <xref rid="pone.0007789-Delport2" ref-type="bibr">[51]</xref>, <xref rid="pone.0007789-Lemey1" ref-type="bibr">[52]</xref>, <xref rid="pone.0007789-Yang3" ref-type="bibr">[53]</xref>, <xref rid="pone.0007789-Yang4" ref-type="bibr">[54]</xref> implemented in software packages such as HyPhy <xref rid="pone.0007789-Pond1" ref-type="bibr">[55]</xref>, MrBayes <xref rid="pone.0007789-Ronquist1" ref-type="bibr">[56]</xref>, <xref rid="pone.0007789-Huelsenbeck1" ref-type="bibr">[57]</xref> and PAML <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref>. Here we used PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref> for calculation of heterogeneous selection pressure at each codon and HyPhy <xref rid="pone.0007789-Pond1" ref-type="bibr">[55]</xref> for directional selection in 335 non-egg-adapted and 32 egg-adapted human A(H1N1) HA sequences. These sequences were from A(H1N1) viruses isolated all around the globe between 1918∼2009. In addition, we also analyzed 42 classical swine A(H1N1) HA sequences for their close relationship to the 2009 A(H1N1) HA.</p><p>In PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref>, a number of models are available: the branch models allow the ω ratio to vary among branches in the phylogenetic tree and can be used to detect positive selection on particular branches <xref rid="pone.0007789-Yang2" ref-type="bibr">[46]</xref>, <xref rid="pone.0007789-Yang5" ref-type="bibr">[58]</xref>; the site models allow the ω ratio to vary among sites and can be used to detect positive selection at particular sites <xref rid="pone.0007789-Nielsen1" ref-type="bibr">[59]</xref>, <xref rid="pone.0007789-Yang6" ref-type="bibr">[60]</xref>; the branch-site models allow the ω ratio to vary both among sites and among branches <xref rid="pone.0007789-Yang7" ref-type="bibr">[61]</xref> and can be used to detect positive selection that affects only a few sites in a few branches.</p><p>In this analysis, a large dataset composed of over 300 sequences was used to ensure sufficient representative sequences for the total time span of 91 years, which made it impractical for the use of branch-site models in our calculations. However, by separating the sequences into distinct subgroups based on their phylogenetic relationship and applying the site models in PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref>, we successfully detected the branch and the specific sites therein that were under host-driven positive selection. Our study revealed differential evolutionary trends of A(H1N1) HA since 1918, which provided molecular signatures for monitoring future antigenically drifted 2009 pandemic and seasonal A(H1N1) influenza viruses.</p></sec><sec id="s2"><title>Results and Discussion</title><sec id="s2a"><title>Phylogenetic Analysis of Human A(H1N1) HA Sequences Since 1918</title><p>It is known that egg-adapted influenza viruses tend to have non-natural host-associated modifications at certain sites of HA sequences <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>. To eliminate the effects of such modifications in our analysis, we selected only 333 HA sequences of A(H1N1) viruses between 1918∼2009 (as of July 10, 2009) with a well-documented record that they had never been passaged in chicken eggs at any stage. Furthermore, intragenic recombination may give rise to false positives in subsequent detection of positively selected codons <xref rid="pone.0007789-Anisimova2" ref-type="bibr">[65]</xref>, thus the Recombination Detection Program (RDP3) <xref rid="pone.0007789-Heath1" ref-type="bibr">[66]</xref> was used to make sure that all HA sequences used in this study were free of recombination, agreeing with previous observations that intragenic recombination is rare for HA <xref rid="pone.0007789-Nelson1" ref-type="bibr">[67]</xref>. The nucleotide sequences of 333 A(H1N1) HAs in the region of HA<sub>1</sub> including the signal peptide, were analyzed by the ClustalW method <xref rid="pone.0007789-Larkin1" ref-type="bibr">[68]</xref>. The phylogeny tree suggested that these HA sequences belong to two major groups: the majority of HA sequences from 1918 to 2008 formed group I, and those of the 2009 A(H1N1) together with a strain isolated in 2007 formed group II (<xref ref-type="supplementary-material" rid="pone.0007789.s001">Fig. S1</xref>). The separation of the 2009 A(H1N1) HAs from HAs of established human A(H1N1) viruses between 1918∼2008, including the 1918 pandemic and the seasonal A(H1N1) viruses, was consistent with the proposed swine origin of HAs in these viruses <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Peiris1" ref-type="bibr">[3]</xref>, <xref rid="pone.0007789-Dawood1" ref-type="bibr">[4]</xref>, <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Solovyov1" ref-type="bibr">[6]</xref>, <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>. The low sequence identity (∼73%) between the 2009 A(H1N1) HA with seasonal and vaccine A(H1N1) HAs might explain why people were in general immunologically naïve to the former <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>, <xref rid="pone.0007789-1" ref-type="bibr">[69]</xref>. In fact, there did not exist cross-reactivity between the 2009 and seasonal A(H1N1) viruses <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>, nor did the vaccination with recent (2005∼2009) annual vaccines provide immune protection against the 2009 A(H1N1) virus <xref rid="pone.0007789-1" ref-type="bibr">[69]</xref>.</p></sec><sec id="s2b"><title>Evidence for Host-Driven Antigenic Drift in Human A(H1N1) HAs</title><p>In order to understand whether host-driven antigenic drift is imposed on the evolution of HA<sub>1</sub> of A(H1N1) virus, we used likelihood ratio tests (LRT) in the software package PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref> to identify the presence or absence of <italic>positive selection</italic>. In this context, positive selection referred to a significant excess of amino-acid altering (non-synonymous) substitutions over silent (synonymous) substitutions in nucleotide sequences. Large LRT values (or small <italic>p</italic>-values) between alternative models and null models, such as M2a vs. M1a, M8 vs. M7, or M8 vs. M8a, led to the rejection of the null models.</p><p>Since HA sequences of group I was further divided into five subgroups (<xref ref-type="supplementary-material" rid="pone.0007789.s001">Fig. S1</xref>), the PAML calculation was carried out on each of these five subgroups and on group II (<xref ref-type="table" rid="pone-0007789-t001">Table 1</xref>). For group I-<italic>i</italic> that included three 1918 pandemic A(H1N1) HAs, in order to increase the sample size, we also included two partial sequences, A/London/1/1918 and A/London/1/1919 <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>. Except for the subgroup I-<italic>v</italic>, all other subgroups of group I had very low LRT values and large <italic>p</italic>-values (<xref ref-type="table" rid="pone-0007789-t001">Table 1</xref>, <xref ref-type="table" rid="pone-0007789-t002">2</xref>), indicating predominantly neutral or purifying selection. These results were consistent with the overall low prevalence of A(H1N1) virus during the period of 1979∼2006 <xref rid="pone.0007789-Finkelman1" ref-type="bibr">[70]</xref>, and agreed well with a previous study that focused on 1995∼2005 A(H1N1) isolates where no positive selection was detected <xref rid="pone.0007789-Wolf1" ref-type="bibr">[71]</xref>. In sharp contrast, group I-<italic>v</italic> 2006∼2008 had ω>10 and LRT>60, which provided strong evidence for positive selection (<xref ref-type="table" rid="pone-0007789-t001">Table 1</xref>, <xref ref-type="table" rid="pone-0007789-t002">2</xref>) and agreed with the necessity to update the A(H1N1) vaccine strain using A/Brisbane/59/07 for the 2008∼2009 season. Group II including 73 HAs of 2009 A(H1N1) and one of 2007 A(H1N1) also had a very low LRT rate ratio (<xref ref-type="table" rid="pone-0007789-t001">Table 1</xref>, <xref ref-type="table" rid="pone-0007789-t002">2</xref>). Given the largely nonexistence of human immunity against the 2009 A(H1N1), the lack of positive selection among group II was expected. However, with more mild infections rapidly propagating among human population in the first wave, the gradually established human immunity might drive positive selection in future isolates of 2009 A(H1N1) strains.</p><table-wrap id="pone-0007789-t001" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t001</object-id><label>Table 1</label><caption><title>The values of log-likelihood (l), <italic>d</italic><sub>N</sub>/<italic>d</italic><sub>S</sub>, and parameter estimates in CODEML analysis of human A(H1N1) Has.</title></caption><alternatives><graphic id="pone-0007789-t001-1" xlink:href="pone.0007789.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Model</td><td align="left" rowspan="1" colspan="1">l</td><td align="left" rowspan="1" colspan="1"><italic>d</italic><sub>N</sub>/<italic>d</italic><sub>S</sub></td><td align="left" rowspan="1" colspan="1">Parameters estimates</td></tr></thead><tbody><tr><td colspan="4" align="left" rowspan="1"><bold>I-</bold><bold><italic>i</italic></bold><bold> 1918∼1919 (5 strains)</bold><xref ref-type="table-fn" rid="nt101">1</xref></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−806.78</td><td align="left" rowspan="1" colspan="1">0.516</td><td align="left" rowspan="1" colspan="1">ω = 0.516</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−805.91</td><td align="left" rowspan="1" colspan="1">0.323</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.677 (<italic>p</italic><sub>1</sub> = 0.323), ω<sub>0</sub> = 0 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−804.19</td><td align="left" rowspan="1" colspan="1">0.564</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.963, <italic>p</italic><sub>1</sub> = 0 (<italic>p</italic><sub>2</sub> = 0.037), ω<sub>0</sub> = 0 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 15.421</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−805.92</td><td align="left" rowspan="1" colspan="1">0.300</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.005, <italic>q</italic> = 0.012</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−805.91</td><td align="left" rowspan="1" colspan="1">0.323</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.846 (<italic>p</italic><sub>1</sub> = 0.154), <italic>p</italic> = 0.005, <italic>q</italic> = 0.020, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−804.19</td><td align="left" rowspan="1" colspan="1">0.561</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.963 (<italic>p</italic><sub>1</sub> = 0.037), <italic>p</italic> = 0.005, <italic>q</italic> = 7.228, ω<sub>s</sub> = 15.242</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>I-</bold><bold><italic>ii</italic></bold><bold> 1979∼2000 (45 strains)<sup>2</sup></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−2489.23</td><td align="left" rowspan="1" colspan="1">0.223</td><td align="left" rowspan="1" colspan="1">ω = 0.223</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−2486.25</td><td align="left" rowspan="1" colspan="1">0.242</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.855 (<italic>p</italic><sub>1</sub> = 0.145), ω<sub>0</sub> = 0.113 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−2486.25</td><td align="left" rowspan="1" colspan="1">0.242</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.855, <italic>p</italic><sub>1</sub> = 0.056 (<italic>p</italic><sub>2</sub> = 0.089), ω<sub>0</sub> = 0.113 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−2485.63</td><td align="left" rowspan="1" colspan="1">0.232</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.327, <italic>q</italic> = 1.074</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−2485.63</td><td align="left" rowspan="1" colspan="1">0.232</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 1 (<italic>p</italic><sub>1</sub> = 0), <italic>p</italic> = 0.327, <italic>q</italic> = 1.074, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−2485.63</td><td align="left" rowspan="1" colspan="1">0.232</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 1 (<italic>p</italic><sub>1</sub> = 0), <italic>p</italic> = 0.327, <italic>q</italic> = 1.074, ω<sub>s</sub> = 1</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>I-</bold><bold><italic>iii</italic></bold><bold> 2000∼2001 (22 strains)<sup>2</sup></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−1686.21</td><td align="left" rowspan="1" colspan="1">0.279</td><td align="left" rowspan="1" colspan="1">ω = 0.279</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−1684.58</td><td align="left" rowspan="1" colspan="1">0.261</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.793 (<italic>p</italic><sub>1</sub> = 0.207), ω<sub>0</sub> = 0.068 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−1683.09</td><td align="left" rowspan="1" colspan="1">0.287</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.994, <italic>p</italic><sub>1</sub> = 0 (<italic>p</italic><sub>2</sub> = 0.006), ω<sub>0</sub> = 0.225 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 10.636</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−1684.52</td><td align="left" rowspan="1" colspan="1">0.265</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.046, <italic>q</italic> = 0.127</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−1684.58</td><td align="left" rowspan="1" colspan="1">0.261</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.793 (<italic>p</italic><sub>1</sub> = 0.207), <italic>p</italic> = 7.211, <italic>q</italic> = 98.93, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−1683.10</td><td align="left" rowspan="1" colspan="1">0.287</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.994 (<italic>p</italic><sub>1</sub> = 0.006), <italic>p</italic> = 28.774, <italic>q</italic> = 99, ω<sub>s</sub> = 10.638</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>I-</bold><bold><italic>iv</italic></bold><bold> 2001∼2007 (89 strains)<sup>2</sup></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−2720.83</td><td align="left" rowspan="1" colspan="1">0.187</td><td align="left" rowspan="1" colspan="1">ω = 0.187</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−2709.20</td><td align="left" rowspan="1" colspan="1">0.181</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.883 (<italic>p</italic><sub>1</sub> = 0.117), ω<sub>0</sub> = 0.072 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−2708.27</td><td align="left" rowspan="1" colspan="1">0.187</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.906, <italic>p</italic><sub>1</sub> = 0.076 (<italic>p</italic><sub>2</sub> = 0.018), ω<sub>0</sub> = 0.085 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 1.915</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−2708.99</td><td align="left" rowspan="1" colspan="1">0.183</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.137, <italic>q</italic> = 0.612</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−2709.40</td><td align="left" rowspan="1" colspan="1">0.180</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.885 (<italic>p</italic><sub>1</sub> = 0.115), <italic>p</italic> = 7.871, <italic>q</italic> = 98.995, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−2708.82</td><td align="left" rowspan="1" colspan="1">0.186</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.973 (<italic>p</italic><sub>1</sub> = 0.027), <italic>p</italic> = 0.375, <italic>q</italic> = 2.298, ω<sub>s</sub> = 1.936</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>I-</bold><bold><italic>v</italic></bold><bold> 2006∼2008 (100 strains)<sup>2</sup></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−3871.33</td><td align="left" rowspan="1" colspan="1">0.303</td><td align="left" rowspan="1" colspan="1">ω = 0.303</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−3813.28</td><td align="left" rowspan="1" colspan="1">0.241</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.828 (<italic>p</italic><sub>1</sub> = 0.172), ω<sub>0</sub> = 0.082 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−3782.07</td><td align="left" rowspan="1" colspan="1">0.313</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.807, <italic>p</italic><sub>1</sub> = 0.188 (<italic>p</italic><sub>2</sub> = 0.005), ω<sub>0</sub> = 0.083 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 11.142</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−3814.21</td><td align="left" rowspan="1" colspan="1">0.246</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.139, <italic>q</italic> = 0.427</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−3812.40</td><td align="left" rowspan="1" colspan="1">0.231</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.862 (<italic>p</italic><sub>1</sub> = 0.138), <italic>p</italic> = 0.497, <italic>q</italic> = 3.969, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−3781.55</td><td align="left" rowspan="1" colspan="1">0.305</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.994 (<italic>p</italic><sub>1</sub> = 0.006), <italic>p</italic> = 0.180, <italic>q</italic> = 0.546, ω<sub>s</sub> = 10.554</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>II 2007∼2009 (74 strains)<sup>2</sup></bold></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−2374.98</td><td align="left" rowspan="1" colspan="1">0.277</td><td align="left" rowspan="1" colspan="1">ω = 0.277</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−2373.20</td><td align="left" rowspan="1" colspan="1">0.282</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.922 (<italic>p</italic><sub>1</sub> = 0.078), ω<sub>0</sub> = 0.222 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−2372.81</td><td align="left" rowspan="1" colspan="1">0.282</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.922, <italic>p</italic><sub>1</sub> = 0.035 (<italic>p</italic><sub>2</sub> = 0.042), ω<sub>0</sub> = 0.222 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−2373.21</td><td align="left" rowspan="1" colspan="1">0.281</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 1.218, <italic>q</italic> = 3.079</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−2374.03</td><td align="left" rowspan="1" colspan="1">0.282</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.945 (<italic>p</italic><sub>1</sub> = 0.055), <italic>p</italic> = 3.243, <italic>q</italic> = 10.201, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−2372.81</td><td align="left" rowspan="1" colspan="1">0.282</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.946 (<italic>p</italic><sub>1</sub> = 0.054), <italic>p</italic> = 3.158, <italic>q</italic> = 9.900, ω<sub>s</sub> = 1</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt101"><label>1</label><p>Due to the inclusion of two partial sequences of A/London/1/1918 and A/London/1/1919 in this subgroup, the analysis was performed on a total of 187 amino-acid residues that covered the antigenic and receptor-binding sites in the region of HA<sub>1</sub> (51∼237) <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>. <sup>2</sup> The analysis was performed on the first 340 residues of HA<sub>1</sub> including the signal peptide.</p></fn></table-wrap-foot></table-wrap><table-wrap id="pone-0007789-t002" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t002</object-id><label>Table 2</label><caption><title>LRT tests for HA<sub>1</sub> sequences of human A(H1N1) influenza viruses.</title></caption><alternatives><graphic id="pone-0007789-t002-2" xlink:href="pone.0007789.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">LRT (M2a − M1a) (2Δl) (<italic>p</italic>-values)<xref ref-type="table-fn" rid="nt102">1</xref></td><td align="left" rowspan="1" colspan="1">LRT (M8 − M7) (2Δl) (<italic>p</italic>-values)<xref ref-type="table-fn" rid="nt102">1</xref></td><td align="left" rowspan="1" colspan="1">LRT (M8 − M8a) (2Δl) (<italic>p</italic>-values)<sup>2</sup></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">I-<italic>i</italic> 1918∼1919 (5 strains)</td><td align="left" rowspan="1" colspan="1">3.44 (0.1791)</td><td align="left" rowspan="1" colspan="1">3.46 (0.1773)</td><td align="left" rowspan="1" colspan="1">3.44 (0.0318)</td></tr><tr><td align="left" rowspan="1" colspan="1">I-<italic>ii</italic> 1979∼2000 (45 strains)</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">I-<italic>iii</italic> 2000∼2001 (22 strains)</td><td align="left" rowspan="1" colspan="1">2.98 (0.2254)</td><td align="left" rowspan="1" colspan="1">2.84 (0.2417)</td><td align="left" rowspan="1" colspan="1">2.96 (0.0427)</td></tr><tr><td align="left" rowspan="1" colspan="1">I-<italic>iv</italic> 2001∼2007 (89 strains)</td><td align="left" rowspan="1" colspan="1">1.86 (0.3946)</td><td align="left" rowspan="1" colspan="1">0.34 (0.8437)</td><td align="left" rowspan="1" colspan="1">1.16 (0.1407)</td></tr><tr><td align="left" rowspan="1" colspan="1">I-<italic>v</italic> 2006∼2008 (100 strains)</td><td align="left" rowspan="1" colspan="1">62.42 (0.0000)</td><td align="left" rowspan="1" colspan="1">65.32 (0.0000)</td><td align="left" rowspan="1" colspan="1">61.70 (0.0000)</td></tr><tr><td align="left" rowspan="1" colspan="1">II 2007∼2009 (74 strains)</td><td align="left" rowspan="1" colspan="1">0.78 (0.6771)</td><td align="left" rowspan="1" colspan="1">0.80 (0.6703)</td><td align="left" rowspan="1" colspan="1">2.44 (0.0591)</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt102"><label>1</label><p>We used the degree of freedom of 2 for these LRT tests that is expected to be too conservative. <sup>2</sup> The <italic>p</italic>-values were calculated from χ<sup>2</sup> distribution using degree of freedom of 1 that was then divided by a factor of 2 for the mixture distribution, as suggested by the author of PAML 4.0.</p></fn></table-wrap-foot></table-wrap></sec><sec id="s2c"><title>Identification of Positively Selected Codons in Human A(H1N1) HAs</title><p>In order to understand how H1 HA sequences were positively selected by human existing immunity, the CODEML <xref rid="pone.0007789-Yang8" ref-type="bibr">[72]</xref> program in PAML 4.0 was used on subgroup I-<italic>v</italic> in which about 0.6% codons were found to be under positive selection (<xref ref-type="table" rid="pone-0007789-t001">Table 1</xref>, <xref ref-type="table" rid="pone-0007789-t002">2</xref>). Both M2a and M8 models identified HA<sub>1</sub> 156 and 190 with greater than 95% posterior probabilities to be under positive selection (<xref ref-type="table" rid="pone-0007789-t003">Table 3</xref>). In previous studies, the antigenic structure of H1 HA (A/PuertoRico/8/1934) had been determined to include five distinct antigenic sites on the globular domain: Sa, Sb, Ca1, Ca2 and Cb <xref rid="pone.0007789-Caton1" ref-type="bibr">[73]</xref>, <xref rid="pone.0007789-Gerhard1" ref-type="bibr">[74]</xref> (<xref ref-type="fig" rid="pone-0007789-g001">Fig. 1a</xref>). Both of these positively selected codons were located on the site Sb (<xref ref-type="fig" rid="pone-0007789-g001">Fig. 1b</xref>). The focus of positive selection on the Sb antigenic site was consistent with a cross-reactivity analysis of various epidemic H1N1 strains using monoclonal antibodies that it was under much higher pressure for mutations <xref rid="pone.0007789-Gerhard1" ref-type="bibr">[74]</xref>.</p><fig id="pone-0007789-g001" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.g001</object-id><label>Figure 1</label><caption><title>Antigenic structure and positive selection of A(H1N1) HA.</title><p><bold>a</bold>) Antigenic structure of A/PR/8/34 (H1N1) HA (PDB accession code 1RU7 <xref rid="pone.0007789-Gamblin1" ref-type="bibr">[78]</xref>). Five antigenic sites were identified by using a large number of monoclonal antibodies <xref rid="pone.0007789-Caton1" ref-type="bibr">[73]</xref>, <xref rid="pone.0007789-Gerhard1" ref-type="bibr">[74]</xref>: Sa (cyan), Sb (red), Ca1 (yellow), Ca2 (green), Cb (blue), using H3 HA numbering. The receptor-binding site (RBS) was labeled for reference. <bold>b</bold>) Codons on A(H1N1) HA that were identified to be under various selection in PAML and HyPhy analysis.</p></caption><graphic xlink:href="pone.0007789.g001"></graphic></fig><table-wrap id="pone-0007789-t003" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t003</object-id><label>Table 3</label><caption><title>Codons under positive selection in HA<sub>1</sub> of human A(H1N1) influenza viruses.</title></caption><alternatives><graphic id="pone-0007789-t003-3" xlink:href="pone.0007789.t003"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td colspan="2" align="left" rowspan="1"></td><td align="left" rowspan="1" colspan="1">Positively selected sites<xref ref-type="table-fn" rid="nt103">1</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>I-</bold><bold><italic>v</italic></bold><bold> 2006∼2008 (100 strains)</bold></td><td align="left" rowspan="1" colspan="1">M2a</td><td align="left" rowspan="1" colspan="1">156 (97.5%), 190 (100%)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8</td><td align="left" rowspan="1" colspan="1">156 (99.7%), 190 (100%)</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt103"><label>1</label><p>Positively selected sites from PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref> using Bayes Empirical Bayes analysis <xref rid="pone.0007789-Yang8" ref-type="bibr">[72]</xref>. Only codons with greater than 95% posterior probabilities to be under positive selection were listed with the corresponding posterior probabilities shown in parentheses.</p></fn></table-wrap-foot></table-wrap><p>HA<sub>1</sub> 138, 186, 190, 194, 225, 226 and 228 had been previously shown to affect receptor binding to H1 HA <xref rid="pone.0007789-Rogers1" ref-type="bibr">[75]</xref>, <xref rid="pone.0007789-Matrosovich1" ref-type="bibr">[76]</xref>. Among them, two residues, HA<sub>1</sub> 190 and 225, play predominant roles in determining the receptor-binding specificity of H1 HA: D190/D225 for α(2,6) receptors in humans, D190/G225 for α(2,6) and α(2,3) receptors in swine, and E190/G225 for α(2,3) receptors in avian <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>, <xref rid="pone.0007789-Skehel1" ref-type="bibr">[39]</xref>, <xref rid="pone.0007789-Tumpey1" ref-type="bibr">[40]</xref>, <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>, <xref rid="pone.0007789-Stevens1" ref-type="bibr">[42]</xref>, <xref rid="pone.0007789-Matrosovich1" ref-type="bibr">[76]</xref>. Although changes at these two sites had been previously reported to cause antigenic drift in A(H1N1) epidemic strains <xref rid="pone.0007789-Nobusawa1" ref-type="bibr">[77]</xref>, it was a somewhat common belief that key determinants of receptor-binding specificity are in general not subject to selection. Thus, the strong positive selection at HA<sub>1</sub> 190 within subgroup I-<italic>v</italic> is quite unexpected.</p></sec><sec id="s2d"><title>Positive Selection of Egg-Adapted Human A(H1N1) HAs during 1933∼1979</title><p>To compensate for the lack of non-egg-adapted human A(H1N1) HAs for the period of 1933∼1978, we separately collected a total of 32 different egg-adapted A(H1N1) HA sequences between 1933∼1979 that were free of sequence ambiguity (<xref ref-type="supplementary-material" rid="pone.0007789.s002">Fig. S2</xref>). These sequences as a group were analyzed by PAML 4.0, as well as two subgroups that covered the periods of 1947∼1957 (12 sequences) and 1948∼1979 (17 sequences) (<xref ref-type="table" rid="pone-0007789-t004">Table 4</xref>, <xref ref-type="table" rid="pone-0007789-t005">5</xref>), keeping in mind of the egg-adapted mutations at HA<sub>1</sub> 138, 144, 163, 189, 190, 225, and 226 <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>. The two subgroups 1947∼1957 and 1948∼1979 represented A(H1N1) viruses circulating in the 1950s and in the 1970s upon its reemergence in 1977, respectively. Given the close genetic and antigenic similarity of the reappeared A(H1N1) influenza virus in 1977 with the A(H1N1) viruses isolated in 1950 <xref rid="pone.0007789-Nakajima1" ref-type="bibr">[22]</xref>, <xref rid="pone.0007789-Kendal1" ref-type="bibr">[23]</xref>, <xref rid="pone.0007789-Scholtissek2" ref-type="bibr">[24]</xref>, it was of particular interest to investigate whether different evolutionary trends were adopted by the 1947∼1957 and 1948∼1979 subgroups.</p><table-wrap id="pone-0007789-t004" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t004</object-id><label>Table 4</label><caption><title>The values of log-likelihood (l), <italic>d</italic><sub>N</sub>/<italic>d</italic><sub>S</sub>, and parameter estimates in CODEML analysis of egg-adapted human A(H1N1) HAs between 1933-1979.</title></caption><alternatives><graphic id="pone-0007789-t004-4" xlink:href="pone.0007789.t004"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Model</td><td align="left" rowspan="1" colspan="1">l</td><td align="left" rowspan="1" colspan="1"><italic>d</italic><sub>N</sub>/<italic>d</italic><sub>S</sub></td><td align="left" rowspan="1" colspan="1">Parameters estimates</td></tr></thead><tbody><tr><td colspan="4" align="left" rowspan="1"><bold>1933∼1979 (32 strains)</bold><xref ref-type="table-fn" rid="nt104">1</xref></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−3336.01</td><td align="left" rowspan="1" colspan="1">0.411</td><td align="left" rowspan="1" colspan="1">ω = 0.411</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−3283.75</td><td align="left" rowspan="1" colspan="1">0.336</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.705 (<italic>p</italic><sub>1</sub> = 0.295), ω<sub>0</sub> = 0.057 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−3275.24</td><td align="left" rowspan="1" colspan="1">0.454</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.721, <italic>p</italic><sub>1</sub> = 0.234 (<italic>p</italic><sub>2</sub> = 0.046), ω<sub>0</sub> = 0.079 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 3.571</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−3285.56</td><td align="left" rowspan="1" colspan="1">0.345</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.068, <italic>q</italic> = 0.129</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−3283.78</td><td align="left" rowspan="1" colspan="1">0.336</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.705 (<italic>p</italic><sub>1</sub> = 0.295), <italic>p</italic> = 6.100, <italic>q</italic> = 99, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−3275.41</td><td align="left" rowspan="1" colspan="1">0.452</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.942 (<italic>p</italic><sub>1</sub> = 0.058), <italic>p</italic> = 0.206, <italic>q</italic> = 0.534, ω<sub>s</sub> = 3.283</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>1947∼1957 (12 strains)</bold><xref ref-type="table-fn" rid="nt104">1</xref></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−2068.01</td><td align="left" rowspan="1" colspan="1">0.435</td><td align="left" rowspan="1" colspan="1">ω = 0.435</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−2056.27</td><td align="left" rowspan="1" colspan="1">0.337</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.689 (<italic>p</italic><sub>1</sub> = 0.311), ω<sub>0</sub> = 0.038 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−2046.27</td><td align="left" rowspan="1" colspan="1">0.501</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.967, <italic>p</italic><sub>1</sub> = 0 (<italic>p</italic><sub>2</sub> = 0.033), ω<sub>0</sub> = 0.256 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 7.651</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−2056.44</td><td align="left" rowspan="1" colspan="1">0.324</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.012, <italic>q</italic> = 0.023</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−2056.28</td><td align="left" rowspan="1" colspan="1">0.337</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.688 (<italic>p</italic><sub>1</sub> = 0.312), <italic>p</italic> = 3.886, <italic>q</italic> = 99, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−2046.29</td><td align="left" rowspan="1" colspan="1">0.501</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.967 (<italic>p</italic><sub>1</sub> = 0.033), <italic>p</italic> = 34.141, <italic>q</italic> = 99, ω<sub>s</sub> = 7.667</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold>1948∼1979 (17 strains)</bold><xref ref-type="table-fn" rid="nt104">1</xref></td></tr><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−1759.58</td><td align="left" rowspan="1" colspan="1">0.385</td><td align="left" rowspan="1" colspan="1">ω = 0.385</td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−1751.46</td><td align="left" rowspan="1" colspan="1">0.260</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.740 (<italic>p</italic><sub>1</sub> = 0.260), ω<sub>0</sub> = 0 (ω<sub>1</sub> = 1)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−1747.17</td><td align="left" rowspan="1" colspan="1">0.408</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.794, <italic>p</italic><sub>1</sub> = 0.168 (<italic>p</italic><sub>2</sub> = 0.039), ω<sub>0</sub> = 0 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 6.226</td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−1751.61</td><td align="left" rowspan="1" colspan="1">0.300</td><td align="left" rowspan="1" colspan="1"><italic>p</italic> = 0.005, <italic>q</italic> = 0.012</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−1751.46</td><td align="left" rowspan="1" colspan="1">0.260</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.740 (<italic>p</italic><sub>1</sub> = 0.260), <italic>p</italic> = 0.005, <italic>q</italic> = 2.350, ω<sub>s</sub> = 1</td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω>1)</td><td align="left" rowspan="1" colspan="1">−1747.19</td><td align="left" rowspan="1" colspan="1">0.411</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.969 (<italic>p</italic><sub>1</sub> = 0.031), <italic>p</italic> = 0.006, <italic>q</italic> = 0.025, ω<sub>s</sub> = 6.964</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt104"><label>1</label><p>The analysis was performed on the first 337 residues of HA<sub>1</sub> including the signal peptide.</p></fn></table-wrap-foot></table-wrap><table-wrap id="pone-0007789-t005" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t005</object-id><label>Table 5</label><caption><title>LRT tests and codons under positive selection for HA<sub>1</sub> sequences of egg-adapted human A(H1N1) influenza viruses between 1933-1979.</title></caption><alternatives><graphic id="pone-0007789-t005-5" xlink:href="pone.0007789.t005"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td colspan="3" align="left" rowspan="1"></td><td align="left" rowspan="1" colspan="1">LRT (2Δl) (<italic>p</italic>-values)</td><td align="left" rowspan="1" colspan="1">Positively selected sites<xref ref-type="table-fn" rid="nt105">1</xref></td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>1933∼1979 (32 strains)</bold></td><td align="left" rowspan="1" colspan="1">M2a</td><td align="left" rowspan="1" colspan="1">M2a-M1a</td><td align="left" rowspan="1" colspan="1">17.02 (0.0002)</td><td align="left" rowspan="1" colspan="1"><bold>77 (95.8%)</bold>, 225 (98.8%)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8</td><td align="left" rowspan="1" colspan="1">M8-M7</td><td align="left" rowspan="1" colspan="1">20.30 (0.0000)</td><td align="left" rowspan="1" colspan="1"><bold>77 (98.7%)</bold>, 225 (99.6%), <bold>227 (97.7%)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8-M8a</td><td align="left" rowspan="1" colspan="1">16.74 (0.0000)</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>1947∼1957 (12 strains)</bold></td><td align="left" rowspan="1" colspan="1">M2a</td><td align="left" rowspan="1" colspan="1">M2a-M1a</td><td align="left" rowspan="1" colspan="1">20.0 (0.0000)</td><td align="left" rowspan="1" colspan="1"><bold>143 (99.3%), 264 (99.6%)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8</td><td align="left" rowspan="1" colspan="1">M8-M7</td><td align="left" rowspan="1" colspan="1">20.30 (0.0000)</td><td align="left" rowspan="1" colspan="1"><bold>143 (99.6%), 166 (95.1%), 264 (99.7%)</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8-M8a</td><td align="left" rowspan="1" colspan="1">19.98 (0.0000)</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>1948∼1979 (17 strains)</bold></td><td align="left" rowspan="1" colspan="1">M2a</td><td align="left" rowspan="1" colspan="1">M2a-M1a</td><td align="left" rowspan="1" colspan="1">8.58 (0.0137)</td><td align="left" rowspan="1" colspan="1">225 (99.1%)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8</td><td align="left" rowspan="1" colspan="1">M8-M7</td><td align="left" rowspan="1" colspan="1">8.84 (0.0120)</td><td align="left" rowspan="1" colspan="1">225 (99.8%)</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">M8-M8a</td><td align="left" rowspan="1" colspan="1">8.54 (0.0017)</td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt105"><label>1</label><p>Positively selected sites from PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref> using Bayes Empirical Bayes analysis <xref rid="pone.0007789-Yang8" ref-type="bibr">[72]</xref>. Only codons with greater than 95% posterior probabilities to be under positive selection were listed with the corresponding posterior probabilities shown in parentheses. Highlighted in bold were codons that were not associated with egg-adapted substitutions <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>.</p></fn></table-wrap-foot></table-wrap><p>For both the entire group 1933∼1979 and the subgroup 1947∼1957, comparisons of M2a-M1a, M8-M7, or M8-M8a yielded large LRT values and very small <italic>p</italic>-values, suggesting the presence of positive selection at about 5% and 3% codons, respectively (<xref ref-type="table" rid="pone-0007789-t004">Table 4</xref>, <xref ref-type="table" rid="pone-0007789-t005">5</xref>). However, it is noteworthy that the subgroup 1948∼1979 had much smaller LRT values, suggesting that the positive pressure of the entire group 1933∼1979 be mostly from the contribution of the subgroup 1947∼1957.</p><p>We further employed the CODEML in PAML 4.0 to analyze the positively selected codons in each group. The results were shown in <xref ref-type="table" rid="pone-0007789-t005">Table 5</xref> where highlighted in bold were the codons not known to be possible egg-adapted mutations (HA<sub>1</sub> 138, 144, 163, 189, 190, 225, and 226) <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>. For the entire group 1933∼1979, HA<sub>1</sub> 77, 225 and 227 were found to be under positive selection with greater than 95% posterior probability in model M8 (<xref ref-type="fig" rid="pone-0007789-g001">Fig. 1b</xref>). They were located in the antigenic sites Cb (HA<sub>1</sub> 77) and Ca2 (HA<sub>1</sub> 225 and 227), respectively (<xref ref-type="fig" rid="pone-0007789-g001">Fig. 1b</xref>). In addition, for the subgroup 1948∼1979, HA<sub>1</sub> 225 was found to be under positive selection with greater than 99% posterior probability in both models M2a and M8. However, given the fact that these HAs were from egg-adapted A(H1N1) viruses in which HA<sub>1</sub> 225 was one of the most frequently changed site <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>, and the predominant residue at this site (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>), G225, was commonly found in swine and avian A(H1N1) HAs, it was possible that the changes at HA<sub>1</sub> 225 was due to positive selection imposed by adaptation in eggs. At posterior probability of 90%, HA<sub>1</sub> 138 and 189 were positively selected as well, however, both sites were involved in egg-adapted substitutions <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>. In sharp contrast, however, HA<sub>1</sub> 143, 166 and 264 in the subgroup 1947∼1957 were found to be under positive selection (<xref ref-type="table" rid="pone-0007789-t005">Table 5</xref>), none of which was among the previously identified egg-adapted mutations. Antigenically, these codons were located in the antigenic sites Ca2, Sa and Cb, respectively (<xref ref-type="fig" rid="pone-0007789-g001">Fig. 1b</xref>). For their relatively distant location from the receptor-binding site, HA<sub>1</sub> 143, 166 and 264 are probably mutations driven by existing human immunity for antibody escape.</p><table-wrap id="pone-0007789-t006" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t006</object-id><label>Table 6</label><caption><title>Codons at HA<sub>1</sub> 190 and 225 in human and swine A(H1N1) influenza viruses.</title></caption><alternatives><graphic id="pone-0007789-t006-6" xlink:href="pone.0007789.t006"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">D190</td><td align="left" rowspan="1" colspan="1">Non-D190</td><td align="left" rowspan="1" colspan="1">D225</td><td align="left" rowspan="1" colspan="1">G225</td><td align="left" rowspan="1" colspan="1">Non-D225/G225</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Human 1979∼2008 Epidemic (575 sequences)</td><td align="left" rowspan="1" colspan="1">477 (83.0%)<xref ref-type="table-fn" rid="nt106">*</xref></td><td align="left" rowspan="1" colspan="1">98 (17.0%)</td><td align="left" rowspan="1" colspan="1">565 (98.2%)</td><td align="left" rowspan="1" colspan="1">2 (0.4%)</td><td align="left" rowspan="1" colspan="1">8 (1.4%)</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1918 Pandemic (5 sequences)</td><td align="left" rowspan="1" colspan="1">5 (100%)</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3 (60%)</td><td align="left" rowspan="1" colspan="1">2 (40%)</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 2009 Pandemic (73 sequences)</td><td align="left" rowspan="1" colspan="1">73 (100%)</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">69 (94.5%)</td><td align="left" rowspan="1" colspan="1">1 (1.4%)</td><td align="left" rowspan="1" colspan="1">3 (4.1%)</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1947∼1957 (12 strains) (egg-adapted)</td><td align="left" rowspan="1" colspan="1">9 (75%)</td><td align="left" rowspan="1" colspan="1">3 (25%)</td><td align="left" rowspan="1" colspan="1">2 (16.7%)</td><td align="left" rowspan="1" colspan="1">10 (83.3%)</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1948∼1979 (17 strains) (egg-adapted)</td><td align="left" rowspan="1" colspan="1">16 (94.1%)</td><td align="left" rowspan="1" colspan="1">1 (5.9%)</td><td align="left" rowspan="1" colspan="1">4 (23.5%)</td><td align="left" rowspan="1" colspan="1">13 (76.5%)</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Swine 1990∼2009 (42 sequences)</td><td align="left" rowspan="1" colspan="1">41 (97.6%)</td><td align="left" rowspan="1" colspan="1">1 (2.4%)</td><td align="left" rowspan="1" colspan="1">28 (66.6%)</td><td align="left" rowspan="1" colspan="1">12 (28.6%)</td><td align="left" rowspan="1" colspan="1">2 (4.8%)</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt106"><label>*</label><p>The number of cases that a particular type of residues occurs at each site. Shown in parenthesis was the occurrence in percentage.</p></fn></table-wrap-foot></table-wrap><p>Thus, there appeared to have different evolutionary patterns for the subgroup 1947∼1957 circulating in the 1950s and the subgroup 1948∼1979 circulating mostly in the 1970s. The former subgroup was subjected to positive selection pressure at HA<sub>1</sub> 143, 166 and 264 (<xref ref-type="table" rid="pone-0007789-t005">Table 5</xref>), and had a much larger variability at HA<sub>1</sub> 190, with 25% being non-D190 (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). In marked contrast, the latter subgroup was probably not under host-driven positive selection in humans and had highly conserved HA<sub>1</sub> 190 (94.1% being D190).</p></sec><sec id="s2e"><title>Evolution of Swine A(H1N1) HAs during 1990∼2009</title><p>Given the swine origin of the 2009 pandemic A(H1N1) HA, we also analyzed 42 non-redundant, non-ambiguous swine A(H1N1) HA sequences during 1990∼2009 available from GISAID/Epifludb (<xref ref-type="table" rid="pone-0007789-t007">Table 7</xref>, <xref ref-type="supplementary-material" rid="pone.0007789.s003">Fig. S3</xref>). The reason that we focused on this period was mainly for the antigenic stasis of swine A(H1N1) until 1998 <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref> since the introduction of the 1918 “Spanish” A(H1N1) virus into swine <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Peiris1" ref-type="bibr">[3]</xref>, <xref rid="pone.0007789-Dawood1" ref-type="bibr">[4]</xref>, <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Solovyov1" ref-type="bibr">[6]</xref>, <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>. Overall, the alternative models M2a and M8 fitted the data only marginally better than the null models M1a, M7 and M8a, respectively (<xref ref-type="table" rid="pone-0007789-t007">Table 7</xref>). Thus, it seemed that swine A(H1N1) HAs during 1990∼2009 were not subjected to strong host-driven positive selection.</p><table-wrap id="pone-0007789-t007" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t007</object-id><label>Table 7</label><caption><title>The values of log-likelihood (l), <italic>d</italic><sub>N</sub>/<italic>d</italic><sub>S</sub>, and parameter estimates in CODEML analysis of swine A(H1N1) HAs between 1990–2009.</title></caption><alternatives><graphic id="pone-0007789-t007-7" xlink:href="pone.0007789.t007"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Model</td><td align="left" rowspan="1" colspan="1">l</td><td align="left" rowspan="1" colspan="1"><italic>d</italic><sub>N</sub>/<italic>d</italic><sub>S</sub></td><td align="left" rowspan="1" colspan="1">Parameters estimates</td><td align="left" rowspan="1" colspan="1">LRT (2Δl) (<italic>p</italic>-values)</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">M0 (one-ratio)</td><td align="left" rowspan="1" colspan="1">−6021.08</td><td align="left" rowspan="1" colspan="1">0.158</td><td align="left" rowspan="1" colspan="1">ω = 0.158</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">M1a (nearly neutral)</td><td align="left" rowspan="1" colspan="1">−5949.30</td><td align="left" rowspan="1" colspan="1">0.217</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.864 (<italic>p</italic><sub>1</sub> = 0.136), ω<sub>0</sub> = 0.094 (ω<sub>1</sub> = 1)</td><td align="left" rowspan="1" colspan="1">LRT (M2a-M1a) = 1.24 (0.5379)</td></tr><tr><td align="left" rowspan="1" colspan="1">M2a (positive selection)</td><td align="left" rowspan="1" colspan="1">−5948.68</td><td align="left" rowspan="1" colspan="1">0.224</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.864, <italic>p</italic><sub>1</sub> = 0.134 (<italic>p</italic><sub>2</sub> = 0.002), ω<sub>0</sub> = 0.095 (ω<sub>1</sub> = 1), ω<sub>2</sub> = 3.682</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">M7 (beta)</td><td align="left" rowspan="1" colspan="1">−5925.79</td><td align="left" rowspan="1" colspan="1">0.174</td><td align="left" rowspan="1" colspan="1"><italic>P</italic> = 0.381, <italic>q</italic> = 1.768</td><td align="left" rowspan="1" colspan="1">LRT (M8-M7) = 6.78 (0.0337) LRT (M8-M8a) = 3.40 (0.0326)</td></tr><tr><td align="left" rowspan="1" colspan="1">M8a (beta&ω = 1)</td><td align="left" rowspan="1" colspan="1">−5924.10</td><td align="left" rowspan="1" colspan="1">0.171</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.970 (<italic>p</italic><sub>1</sub> = 0.030), <italic>p</italic> = 0.460, <italic>q</italic> = 2.617, ω<sub>s</sub> = 1</td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">M8 (beta&ω)</td><td align="left" rowspan="1" colspan="1">−5922.40</td><td align="left" rowspan="1" colspan="1">0.177</td><td align="left" rowspan="1" colspan="1"><italic>p</italic><sub>0</sub> = 0.995 (<italic>p</italic><sub>1</sub> = 0.005), <italic>p</italic> = 0.413, <italic>q</italic> = 2.052, ω<sub>s</sub> = 2.546</td><td align="left" rowspan="1" colspan="1"></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt107"><label></label><p>The analysis was performed on the first 338 residues of HA<sub>1</sub> including the signal peptide.</p></fn></table-wrap-foot></table-wrap></sec><sec id="s2f"><title>Directional Evolution of Human A(H1N1) HAs</title><p>In order to test whether directional evolution of protein sequences existed in the evolution of human A(H1N1) HAs, we employed a maximum likelihood method developed by Kosakovsky Pond and colleagues <xref rid="pone.0007789-KosakovskyPond1" ref-type="bibr">[49]</xref>. In each subgroup, we used the oldest HA sequence as the root. In agreement with CODEML analysis reported in previous sections, among all non-egg adapted human A(H1N1) HAs, directional evolution was only identified in the subgroup I-<italic>v</italic>, at sites HA<sub>1</sub> 143, 156, 158, 190, 193 and 197 (<xref ref-type="table" rid="pone-0007789-t008">Table 8</xref>, <xref ref-type="table" rid="pone-0007789-t009">9</xref>). HA<sub>1</sub> 143 belonged to the antigenic site Ca2 of A(H1N1) HA, whilst all other sites were located in the antigenic site Sb (<xref ref-type="fig" rid="pone-0007789-g001">Fig. 1b</xref>). Among these sites, HA<sub>1</sub> 156, 190 and 193 were identified by CODEML in PAML 4.0 to be under positive selection with 99.7%, 100%, and 80.9% posterior probability in model M8, respectively (<xref ref-type="table" rid="pone-0007789-t003">Table 3</xref>). In previous structural studies, residue HA<sub>1</sub> 190 in 1934 human A(H1N1) HA and HA<sub>1</sub> 190 and 193 in 1930 swine A(H1N1) HA were found to directly interact with bound human-like α(2,6)-receptors <xref rid="pone.0007789-Gamblin1" ref-type="bibr">[78]</xref>. Thus, it remains to be investigated the impacts of directional evolution at HA<sub>1</sub> 190 and 193 on receptor binding and antigenic drift.</p><table-wrap id="pone-0007789-t008" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t008</object-id><label>Table 8</label><caption><title>Directional selection analysis on human A(H1N1) Has.</title></caption><alternatives><graphic id="pone-0007789-t008-8" xlink:href="pone.0007789.t008"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Tree L</td><td align="left" rowspan="1" colspan="1">Residue</td><td align="left" rowspan="1" colspan="1"><italic>P</italic>-Value</td><td align="left" rowspan="1" colspan="1">Bias</td><td align="left" rowspan="1" colspan="1">Proportion (%)</td><td align="left" rowspan="1" colspan="1">No. of Sites</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Human I-<italic>v</italic> (100 sequences)</td><td align="left" rowspan="1" colspan="1">0.474</td><td align="left" rowspan="1" colspan="1">T</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">32.995</td><td align="left" rowspan="1" colspan="1">5.4</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">R</td><td align="left" rowspan="1" colspan="1">0.0002</td><td align="left" rowspan="1" colspan="1">12.583</td><td align="left" rowspan="1" colspan="1">11.8</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">V</td><td align="left" rowspan="1" colspan="1">0.0004</td><td align="left" rowspan="1" colspan="1">34.478</td><td align="left" rowspan="1" colspan="1">4.0</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">K</td><td align="left" rowspan="1" colspan="1">0.0023</td><td align="left" rowspan="1" colspan="1">29.301</td><td align="left" rowspan="1" colspan="1">7.2</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1933∼1979 (32 strains) (egg-adapted)</td><td align="left" rowspan="1" colspan="1">0.613</td><td align="left" rowspan="1" colspan="1">D</td><td align="left" rowspan="1" colspan="1">0.0000</td><td align="left" rowspan="1" colspan="1">78.148</td><td align="left" rowspan="1" colspan="1">3.4</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1948∼1979 (17 strains) (egg-adapted)</td><td align="left" rowspan="1" colspan="1">0.091</td><td align="left" rowspan="1" colspan="1">D</td><td align="left" rowspan="1" colspan="1">0.0007</td><td align="left" rowspan="1" colspan="1">133.611</td><td align="left" rowspan="1" colspan="1">5.1</td><td align="left" rowspan="1" colspan="1">1</td></tr></tbody></table></alternatives></table-wrap><table-wrap id="pone-0007789-t009" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0007789.t009</object-id><label>Table 9</label><caption><title>Sites found to be under directional selection in human A(H1N1) Has.</title></caption><alternatives><graphic id="pone-0007789-t009-9" xlink:href="pone.0007789.t009"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Sites</td><td align="left" rowspan="1" colspan="1">Composition</td><td align="left" rowspan="1" colspan="1">Root</td><td align="left" rowspan="1" colspan="1">Preferred</td><td align="left" rowspan="1" colspan="1">Inferred Substitutions</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Human I-<italic>v</italic> (100 sequences)</td><td align="left" rowspan="1" colspan="1">143</td><td align="left" rowspan="1" colspan="1">V<sub>99</sub>T<sub>1</sub></td><td align="left" rowspan="1" colspan="1">V</td><td align="left" rowspan="1" colspan="1">V</td><td align="left" rowspan="1" colspan="1">T→<sub>1</sub>V</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">156</td><td align="left" rowspan="1" colspan="1">G<sub>90</sub>R<sub>9</sub>E<sub>1</sub></td><td align="left" rowspan="1" colspan="1">R</td><td align="left" rowspan="1" colspan="1">R</td><td align="left" rowspan="1" colspan="1">G→<sub>1</sub>E, G→<sub>7</sub>R</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">158</td><td align="left" rowspan="1" colspan="1">N<sub>96</sub>K<sub>4</sub></td><td align="left" rowspan="1" colspan="1">N</td><td align="left" rowspan="1" colspan="1">K</td><td align="left" rowspan="1" colspan="1">N→<sub>4</sub>K</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">190</td><td align="left" rowspan="1" colspan="1">D<sub>67</sub>N<sub>25</sub>V<sub>8</sub></td><td align="left" rowspan="1" colspan="1">D</td><td align="left" rowspan="1" colspan="1">V</td><td align="left" rowspan="1" colspan="1">D→<sub>16</sub>N, D→<sub>4</sub>V</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">193</td><td align="left" rowspan="1" colspan="1">A<sub>52</sub>T<sub>48</sub></td><td align="left" rowspan="1" colspan="1">A</td><td align="left" rowspan="1" colspan="1">T</td><td align="left" rowspan="1" colspan="1">A→<sub>6</sub>T</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">197</td><td align="left" rowspan="1" colspan="1">T<sub>82</sub>K<sub>18</sub></td><td align="left" rowspan="1" colspan="1">T</td><td align="left" rowspan="1" colspan="1">T</td><td align="left" rowspan="1" colspan="1">K→<sub>2</sub>T</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1933∼1979 (32 strains) (egg-adapted)</td><td align="left" rowspan="1" colspan="1">225</td><td align="left" rowspan="1" colspan="1">G<sub>23</sub>D<sub>9</sub></td><td align="left" rowspan="1" colspan="1">D</td><td align="left" rowspan="1" colspan="1">D</td><td align="left" rowspan="1" colspan="1">D→<sub>1</sub>G, G→<sub>6</sub>D</td></tr><tr><td align="left" rowspan="1" colspan="1">Human 1948∼1979 (17 strains) (egg-adapted)</td><td align="left" rowspan="1" colspan="1">225</td><td align="left" rowspan="1" colspan="1">G<sub>13</sub>D<sub>4</sub></td><td align="left" rowspan="1" colspan="1">G</td><td align="left" rowspan="1" colspan="1">D</td><td align="left" rowspan="1" colspan="1">G→<sub>4</sub>D</td></tr></tbody></table></alternatives></table-wrap><p>We also performed directional evolution study on egg-adapted human A(H1N1) HA sequences, and found that in both the entire group 1933∼1979 and the subgroup 1948∼1979, multiple favored mutations of D225→G and G225→D were detected (<xref ref-type="table" rid="pone-0007789-t008">Table 8</xref>, <xref ref-type="table" rid="pone-0007789-t009">9</xref>). Given its involvement in egg-adaptation, the directional evolution at HA<sub>1</sub> 225 may be the consequence of egg-adaptation. In contrast, no residues in the subgroup 1947∼1957 were identified to be under directional selection.</p></sec><sec id="s2g"><title>Evolution of Human and Swine A(H1N1) HAs at HA<sub>1</sub> 190 and 225</title><p>For their predominant roles in determining receptor-binding specificity of A(H1N1) HA, and the positive selection on HA<sub>1</sub> 190 in the subgroup I-<italic>v</italic>, we further investigated the evolution of HA<sub>1</sub> 190 and 225 in A(H1N1) strains during 1918∼1009. These included 653 non-egg-adapted HAs (five pandemic HAs from 1918∼1919, 575 epidemic HAs from 1979∼2008, and 73 pandemic HAs from 2009), and 42 swine HAs (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). For the 575 epidemic HAs, HA<sub>1</sub> 190 was highly variable (17.0% sequences did not have D190), while HA<sub>1</sub> 225 was more conserved (only 1.8% sequences did not have D225) (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). Among all the deviations (a total of 107 cases) from the ideal D190/D225 combination for human A(H1N1) viruses, two predominant ones were N190/D225 (69.2%) and V190/D225 (19.6%). At present, we don't know the exact effects of these mutations, or in combination with other concurring mutations at or around the receptor-binding site, on binding to human receptors. Further experiments are needed to clarify these issues. However, in previous studies, a single mutation D190N of A(H1N1) HA was shown to result in a lower binding affinity for human-like α(2,6) receptors, and a higher binding affinity for avian-like α(2,3) receptors <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>.</p><p>The five HA sequences retrieved from victims of 1918 “Spanish” A(H1N1) influenza virus shared 98.9% to 99.8% sequence identity <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>. Among them, there were two non-synonymous substitutions of D225G, one in A/New York/1/1918 and the other one in A/London/1/1919 (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). The HAs harboring the mutation D225G had reduced binding affinity for human receptors <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>, <xref rid="pone.0007789-Tumpey1" ref-type="bibr">[40]</xref>, <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>.</p><p>In the 73 HA sequences from the 2009 pandemic A(H1N1), D190 was strictly conserved, while D225 was 94.5% conserved (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). At HA<sub>1</sub> 225, the deviations were 1.1% for G225 and 3.3% for E225. Thus, the complete conservation at HA<sub>1</sub> 190 and the nearly complete conservation at HA<sub>1</sub> 225 were consistent to the importance of these residues in allowing for binding to human-like α(2,6) receptors <xref rid="pone.0007789-Tumpey1" ref-type="bibr">[40]</xref>, <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>, supporting the substantially higher human-to-human transmissibility of the 2009 A(H1N1) virus than seasonal A(H1N1) viruses <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>.</p><p>Therefore, there were two distinct evolutionary trends in host-driven antigenic drift of human A(H1N1) HAs at residues in the receptor-binding site: the 1918 pandemic HAs underwent antigenic drift at HA<sub>1</sub> 225, while the epidemic HAs undertook antigenic drift at HA<sub>1</sub> 190. In the absence of selection, the 2009 A(H1N1) viruses were highly conserved at both HA<sub>1</sub> 190 and 225, which was distinct from those two host-selected evolutionary trends (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). With gradually established immunity among human population, we wondered how the 2009 A(H1N1) virus would undergo antigenic drift in the months to come. Thus, we also looked at the conservation at HA<sub>1</sub> 190 and 225 in 42 swine A(H1N1) HA sequences (<xref ref-type="table" rid="pone-0007789-t006">Table 6</xref>). Surprisingly, among these sequences, D190 was conserved at 97.6%, while D225 and G225 were observed at 66.6% and 28.6%, respectively. The similarly high variability of HA<sub>1</sub> 225 in swine A(H1N1) HAs with that of 1918 pandemic HAs was consistent with the relative antigenic stasis of swine A(H1N1) until 1998 <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref> and agreed well with the suggestion that the introduction of the 2009 pandemic A(H1N1) virus into humans be a single event or multiple events of similar viruses <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, <xref rid="pone.0007789-Peiris1" ref-type="bibr">[3]</xref>, <xref rid="pone.0007789-Dawood1" ref-type="bibr">[4]</xref>, <xref rid="pone.0007789-Fraser1" ref-type="bibr">[5]</xref>, <xref rid="pone.0007789-Solovyov1" ref-type="bibr">[6]</xref>, <xref rid="pone.0007789-Smith1" ref-type="bibr">[7]</xref>, <xref rid="pone.0007789-Garten1" ref-type="bibr">[8]</xref>.</p><p>The deviations from the ideal D190/D225 combination in A(H1N1) HAs might result in reduced binding to human receptors <xref rid="pone.0007789-Reid1" ref-type="bibr">[11]</xref>, <xref rid="pone.0007789-Srinivasan1" ref-type="bibr">[41]</xref>, <xref rid="pone.0007789-Stevens1" ref-type="bibr">[42]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>, <xref rid="pone.0007789-Gambaryan2" ref-type="bibr">[79]</xref>. However, two possibilities, which are not mutually exclusive, may explain the fact that mutations are frequently observed at these two sites: one is that other concurring mutations at or around the receptor-binding site may sufficiently maintain the receptor binding affinity so that the overall binding affinity is largely unaffected; the second is that the gain in evading antibody neutralization far overweighs the reduction in receptor binding. Due to the overlapping locations of the ever-changing antigenic sites and the more-conserved receptor-binding site of HA, there is a constant dilemma of whether or not a residue at the receptor-binding site should change. Although the involvement of residues in antigenic drift that are critical for receptor binding was also observed in HAs of other types and subtypes including influenza B virus HA <xref rid="pone.0007789-Shen1" ref-type="bibr">[80]</xref>, H3 <xref rid="pone.0007789-Bush1" ref-type="bibr">[43]</xref>, <xref rid="pone.0007789-Bush2" ref-type="bibr">[44]</xref>and H5 HA <xref rid="pone.0007789-Bush2" ref-type="bibr">[44]</xref>, <xref rid="pone.0007789-Shi1" ref-type="bibr">[81]</xref>, the interplay between these two opposing forces in HA evolution is still very poorly understood. Although previous studies on A(H3N2) HAs suggested covariation of antigenicity and receptor-binding specificity as a possible mechanism for the antigenic differences observed in viruses propagated in different cells <xref rid="pone.0007789-Daniels1" ref-type="bibr">[82]</xref>, questions such as how residues involved in receptor binding are actively utilized for antigenic drift in influenza evolution in the same hosts need to be urgently addressed in order for us to comprehend the powerful strategies that the virus employs for recurring influenza infections.</p></sec><sec id="s2h"><title>Implications for the 2009 Pandemic</title><p>By analyzing hundreds of A(H1N1) HA sequences between 1918∼2009, our study revealed positive selection in the subgroup I-<italic>v</italic> of A(H1N1) HAs. The positively selected codons were located at HA<sub>1</sub> 156 and 190 in the Sb antigenic site <xref rid="pone.0007789-Wiley1" ref-type="bibr">[83]</xref>. It was surprising that HA<sub>1</sub> 190, which is critical for receptor-binding specificity of A(H1N1) HAs, was also under positive selection. Through further analysis of HA<sub>1</sub> 190, together with HA<sub>1</sub> 225, the other critical determinant for receptor-binding specificity of A(H1N1), we found that the epidemic HAs and the 1918 pandemic and swine HAs favored one of these two sites for antigenic drift. Whether the 2009 pandemic A(H1N1) HA will adopt any of these two trends, or use a novel mechanism that does not involve HA<sub>1</sub> 190 and 225, will unfold in the coming months. If the latter is to be used, the 2009 A(H1N1) viruses may maintain their intrinsic high transmissibility, which, together with mutations in other genes such as NS1 and PB1-F2 with signatures of elevated pathogenicity <xref rid="pone.0007789-Wang1" ref-type="bibr">[1]</xref>, <xref rid="pone.0007789-Neumann1" ref-type="bibr">[2]</xref>, may suffice a new disastrous pandemic in the near future.</p></sec></sec><sec id="s3"><title>Materials and Methods</title><sec id="s3a"><title>Phylogenetic Analysis of A(H1N1) HAs</title><p>We obtained all available HA sequences (over 1,000) of non-egg-adapted A(H1N1) viruses for the period of 1918∼2009 (as of July 10, 2009) from GISAID/Epifludb. We then removed the sequences with one or more ambiguous nucleotide sequences within the HA<sub>1</sub> region and deleted identical sequences. This gave us a dataset of 652 HA sequences that included three 1918 pandemic HAs, 575 epidemic HAs from 1979∼2008 that collectively formed group I, and 73 pandemic HAs from 2009 and one HA from 2007 that belonged to group II. To facilitate the speed of computing, we further removed closely related sequences and obtained a dataset of 333 HA sequences. The program RDP3 (<ext-link ext-link-type="uri" xlink:href="http://darwin.uvigo.es/rdp/rdp.html">http://darwin.uvigo.es/rdp/rdp.html</ext-link>) <xref rid="pone.0007789-Heath1" ref-type="bibr">[66]</xref> was used to make sure that no recombination was present in any of these HA sequences. The ClustalW method <xref rid="pone.0007789-Larkin1" ref-type="bibr">[68]</xref> with the MEGALIGN program of DNASTAR package (<ext-link ext-link-type="uri" xlink:href="http://www.dnastar.com">www.dnastar.com</ext-link>) was used for phylogenetic analysis of H1 HA sequences in the region of HA<sub>1</sub> (<xref ref-type="supplementary-material" rid="pone.0007789.s001">Fig. S1</xref>).</p><p>Due to the historic use of eggs for amplification of influenza viruses before sequencing, there presented a vacuum in sequence for non-egg-adapted A(H1N1) viruses between 1919 and 1979. In order to gain insights into the evolution of A(H1N1) viruses for this period, we separately collected a total of 32 different egg-adapted A(H1N1) HA sequences between 1933∼1979 that were free of sequence ambiguity (<xref ref-type="supplementary-material" rid="pone.0007789.s002">Fig. S2</xref>). These sequences were similarly analyzed while keeping in mind of the possible egg-adapted mutations at HA<sub>1</sub> 138, 144, 163, 189, 190, 225, and 226 <xref rid="pone.0007789-Robertson1" ref-type="bibr">[62]</xref>, <xref rid="pone.0007789-Xu1" ref-type="bibr">[63]</xref>, <xref rid="pone.0007789-Gambaryan1" ref-type="bibr">[64]</xref>.</p><p>In order to compare the evolution of swine A(H1N1) HA sequences, we also retrieved 42 unique swine H1 HA sequences for the period of 1990∼2009 that were free of ambiguous nucleotide sequences (<xref ref-type="supplementary-material" rid="pone.0007789.s003">Fig. S3</xref>). The reason that we focused on 1990∼2009 was that previous studies suggested that swine A(H1N1) viruses be antigenically stable for the period of 1930 to 1990s <xref rid="pone.0007789-Sheerar1" ref-type="bibr">[84]</xref>.</p></sec><sec id="s3b"><title>Analysis of Positive Selection by PAML 4.0</title><p>The site-specific models implemented in the CODEML program in PAML 4.0 <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref> was used to calculate heterogeneous selection pressure at amino-acid positions <xref rid="pone.0007789-Yang1" ref-type="bibr">[45]</xref>, <xref rid="pone.0007789-Yang4" ref-type="bibr">[54]</xref>, <xref rid="pone.0007789-Yang8" ref-type="bibr">[72]</xref>, <xref rid="pone.0007789-Yang9" ref-type="bibr">[85]</xref>. The models used in this study were M0, M1a, M2a, M7 and M8. M1a (nearly neutral), M7 (beta) and M8a (beta and ω = 1) were null models that did not support ω>1. In contrast, the alternative models M2a (positive selection) and M8 (beta and ω), compared to M1a and M7 respectively, each had an additional class that allowed ω>1. Likelihood ratio tests (LRT) comparing M2a versus M1a, M8 versus M7, and M8 versus M8a provided test for the existence of positive selection. In the test, twice the log likelihood difference, 2Δl = 2(l<sub>1</sub>−l<sub>0</sub>), was calculated where l<sub>1</sub>and l<sub>0</sub>were the log likelihoods for the alternative model and null model, respectively. A larger value of LRT over those of χ<sup>2</sup> distribution led to rejection of the null models <xref rid="pone.0007789-Yang8" ref-type="bibr">[72]</xref>. In order to calculate the codon-substitution models for heterogeneous selection pressure at each codon, the Bayes Empirical Bayes (BEB) analysis implemented in CODEML <xref rid="pone.0007789-Yang8" ref-type="bibr">[72]</xref> was used, which has been shown to yield robust results even for small datasets. For all calculations, multiple runs, each with different initial parameter values, were performed to ensure optimization and convergence.</p></sec><sec id="s3c"><title>Directional Evolution of Protein Sequences Using HyPhy</title><p>Each group of A(H1N1) HA sequences aligned by the ClustalW method (<xref ref-type="supplementary-material" rid="pone.0007789.s001">Fig. S1</xref>, <xref ref-type="supplementary-material" rid="pone.0007789.s002">S2</xref>, <xref ref-type="supplementary-material" rid="pone.0007789.s003">S3</xref>) was input to the PhyML program <xref rid="pone.0007789-Guindon1" ref-type="bibr">[86]</xref> to generate an unrooted phylogenetic tree, which was then rooted using the Treeview software <xref rid="pone.0007789-Page1" ref-type="bibr">[87]</xref> by selecting the oldest sequence in each group as the root/ancestor. This rooted phylogenetic tree was used for directional evolution of protein sequences <xref rid="pone.0007789-KosakovskyPond1" ref-type="bibr">[49]</xref> implemented in the HyPhy <xref rid="pone.0007789-Pond1" ref-type="bibr">[55]</xref> software package.</p></sec></sec><sec sec-type="supplementary-material" id="s4"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pone.0007789.s001"><label>Figure S1</label><caption><p>Phylogenetic tree of 333 HA sequences of A (H1N1) influenza viruses isolated between 1918∼2009 without egg-adaptation.</p><p>(41.64 MB TIF)</p></caption><media xlink:href="pone.0007789.s001.tif"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0007789.s002"><label>Figure S2</label><caption><p>Phylogenetic tree of 32 HA sequences of egg-adapted human A(H1N1) influenza viruses isolated between 1933∼1979.</p><p>(1.02 MB TIF)</p></caption><media xlink:href="pone.0007789.s002.tif"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0007789.s003"><label>Figure S3</label><caption><p>Phylogenetic tree of 42 HA sequences of swine A(H1N1) influenza viruses isolated between 1990∼2009.</p><p>(1.39 MB TIF)</p></caption><media xlink:href="pone.0007789.s003.tif"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec></body><back><ack><p>We gratefully thank Dr. Robert Couch for insightful comments on the manuscript, Drs. Alexander Klimov, Xiyan Xu and Rebecca Garten for help with sequence retrieval, Dr. Sergei Kosakovsky Pond for help with the HyPhy software, Mingyang Lu for Figure 1 and Athanasios Dousis for computational help.</p></ack><fn-group><fn fn-type="COI-statement"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="financial-disclosure"><p><bold>Funding: </bold>JM acknowledges support from National Institutes of Health (R01-GM067801), National Science Foundation (MCB-0818353), The Welch Foundation (Q-1512), the Welch Chemistry and Biology Collaborative Grant from John S. Dunn Gulf Coast Consortium for Chemical Genomics and the Faculty Initiatives Fund from Rice University. QW acknowledges support from a Beginning Grant-in-Aid award from American Heart Association (0865186F) and of a grant from THE National Institutes of Health (R01-AI067839). 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