Mixed Infection and the Genesis of Influenza Virus Diversity▿
Identifieur interne : 000371 ( Pmc/Corpus ); précédent : 000370; suivant : 000372Mixed Infection and the Genesis of Influenza Virus Diversity▿
Auteurs : Elodie Ghedin ; Adam Fitch ; Alex Boyne ; Sara Griesemer ; Jay Depasse ; Jayati Bera ; Xu Zhang ; Rebecca A. Halpin ; Marita Smit ; Lance Jennings ; Kirsten St. George ; Edward C. Holmes ; David J. SpiroSource :
- Journal of Virology [ 0022-538X ] ; 2009.
Abstract
The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve to one capable of human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes coinfect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection with influenza virus is therefore central to understanding the emergence of pandemic, antigenic, and drug-resistant strains. To better understand the potential for such events, we explored patterns of intrahost genetic diversity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences sampled from individual influenza patients we reveal a high level of mixed infection, including diverse lineages of the same influenza virus subtype, drug-resistant and -sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza virus types (A and B). These results reveal that individuals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents.
Url:
DOI: 10.1128/JVI.00773-09
PubMed: 19553313
PubMed Central: 2738154
Links to Exploration step
PMC:2738154Le document en format XML
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<idno type="eISSN">1098-5514</idno>
<imprint><date when="2009">2009</date>
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<front><div type="abstract" xml:lang="en"><p>The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve to one capable of human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes coinfect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection with influenza virus is therefore central to understanding the emergence of pandemic, antigenic, and drug-resistant strains. To better understand the potential for such events, we explored patterns of intrahost genetic diversity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences sampled from individual influenza patients we reveal a high level of mixed infection, including diverse lineages of the same influenza virus subtype, drug-resistant and -sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza virus types (A and B). These results reveal that individuals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Virol</journal-id>
<journal-id journal-id-type="publisher-id">jvi</journal-id>
<journal-title>Journal of Virology</journal-title>
<issn pub-type="ppub">0022-538X</issn>
<issn pub-type="epub">1098-5514</issn>
<publisher><publisher-name>American Society for Microbiology (ASM)</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">19553313</article-id>
<article-id pub-id-type="pmc">2738154</article-id>
<article-id pub-id-type="publisher-id">0773-09</article-id>
<article-id pub-id-type="doi">10.1128/JVI.00773-09</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Genetic Diversity and Evolution</subject>
</subj-group>
</article-categories>
<title-group><article-title>Mixed Infection and the Genesis of Influenza Virus Diversity<xref ref-type="fn" rid="fn1">▿</xref>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ghedin</surname>
<given-names>Elodie</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fitch</surname>
<given-names>Adam</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Boyne</surname>
<given-names>Alex</given-names>
</name>
<xref ref-type="aff" rid="aff1">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Griesemer</surname>
<given-names>Sara</given-names>
</name>
<xref ref-type="aff" rid="aff1">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>DePasse</surname>
<given-names>Jay</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bera</surname>
<given-names>Jayati</given-names>
</name>
<xref ref-type="aff" rid="aff1">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zhang</surname>
<given-names>Xu</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Halpin</surname>
<given-names>Rebecca A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Smit</surname>
<given-names>Marita</given-names>
</name>
<xref ref-type="aff" rid="aff1">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jennings</surname>
<given-names>Lance</given-names>
</name>
<xref ref-type="aff" rid="aff1">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>St. George</surname>
<given-names>Kirsten</given-names>
</name>
<xref ref-type="aff" rid="aff1">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Holmes</surname>
<given-names>Edward C.</given-names>
</name>
<xref ref-type="aff" rid="aff1">5</xref>
<xref ref-type="aff" rid="aff1">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Spiro</surname>
<given-names>David J.</given-names>
</name>
<xref ref-type="aff" rid="aff1">2</xref>
</contrib>
</contrib-group>
<aff id="aff1">University of Pittsburgh School of Medicine, Departments of Medicine and Computational Biology, Pittsburgh, Pennsylvania 15261,<label>1</label>
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850,<label>2</label>
Wadsworth Center, New York State Department of Health, Albany, New York 12201,<label>3</label>
Canterbury Health Laboratories, Christchurch, New Zealand,<label>4</label>
The Pennsylvania State University, University Park, Pennsylvania 16802,<label>5</label>
Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892<label>6</label>
</aff>
<author-notes><fn id="cor1"><label>*</label>
<p>Corresponding author. Mailing address: Division of Infectious Diseases, University of Pittsburgh School of Medicine, 3550 Terrace Street, Room 830, Pittsburgh, PA 15261. Phone: (412) 383-5850. Fax: (412) 383-5851. E-mail: <email>elg21@pitt.edu</email>
</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>9</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>24</day>
<month>6</month>
<year>2009</year>
</pub-date>
<volume>83</volume>
<issue>17</issue>
<fpage>8832</fpage>
<lpage>8841</lpage>
<history><date date-type="received"><day>16</day>
<month>4</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>16</day>
<month>6</month>
<year>2009</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2009, American Society for Microbiology</copyright-statement>
<copyright-year>2009</copyright-year>
</permissions>
<self-uri xlink:title="pdf" xlink:href="zjv01709008832.pdf"></self-uri>
<abstract><p>The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve to one capable of human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes coinfect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection with influenza virus is therefore central to understanding the emergence of pandemic, antigenic, and drug-resistant strains. To better understand the potential for such events, we explored patterns of intrahost genetic diversity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences sampled from individual influenza patients we reveal a high level of mixed infection, including diverse lineages of the same influenza virus subtype, drug-resistant and -sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza virus types (A and B). These results reveal that individuals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents.</p>
</abstract>
</article-meta>
</front>
<floats-wrap><fig position="float" id="f1"><label>FIG. 1.</label>
<caption><p>Maximum-likelihood phylogenetic trees for M (a), PB1 (b), PA (c), and NP (d) segment clones from sample NZ094 compared to a representative sample of viruses circulating in the years 2004 and 2005. Clones from sample NZ094 are shown in red and italics, while consensus segment assemblies from whole-genome sequencing of the isolate are shown in light blue. Viruses associated with adamantane resistance are shaded. All branches are drawn to a scale of nucleotide substitutions per site, and the tree is midpoint rooted for purposes of clarity only. Bootstrap support values are shown for the node distinguishing the adamantane-resistant viruses. Only small (often nonoverlapping) subcloned regions were available for the PA segment, and so no bootstrap analysis could be undertaken in this case.</p>
</caption>
<graphic xlink:href="zjv0170922660001"></graphic>
</fig>
<fig position="float" id="f2"><label>FIG. 2.</label>
<caption><p>Maximum-likelihood phylogenetic trees for the HA (a), PB2 (b), NA (c), and NS (d) segment clones from sample NZ094 compared to a representative sample of viruses circulating in the years 2004 and 2005. Clones from sample NZ094 are shown in red and italics, while consensus segment assemblies from whole-genome sequencing of the isolate are shown in light blue. Viruses associated with adamantane resistance are shaded in all cases. All branches are drawn to a scale of nucleotide substitutions per site, and the tree is midpoint rooted for purposes of clarity only. Bootstrap support values are shown for the node distinguishing the adamantane-resistant and -sensitive lineages. A grouping of adamantane-resistant viruses was only weakly supported in the NA gene (51% bootstrap support), and there was insufficient phylogenetic resolution in the NS gene to reveal any higher-order groupings.</p>
</caption>
<graphic xlink:href="zjv0170922660002"></graphic>
</fig>
<fig position="float" id="f3"><label>FIG. 3.</label>
<caption><p>Color-coded representation of protein residues for translated pyrosequencing reads of the HA1, M, and NA segments of isolate NZ094. This representation shows the alignment of specific residues that differ from the N-lineage isolates A/Canterbury/20/2005 (GenBank accession numbers CY008340, CY008341, and CY008342), A/Canterbury/220/2005, (CY008380, CY008381, and CY008382), and A/Canterbury/237/2005 (CY008412, CY008413, and CY008414). These N-lineage isolates are highlighted by the gray box at the top of the figure. Protein residues from consensus assemblies from whole-genome sequencing of isolate NZ094 are represented above the pyrosequencing read data. The HA1 residues are numbered relative to the HA1 domain, not from the first methionine of the HA coding sequence. Color coding: light blue, N, asparagine; dark blue, F, phenylalanine; royal blue, R, arginine; turquoise, K, lysine; red, D, aspartic acid; pink, S, serine.</p>
</caption>
<graphic xlink:href="zjv0170922660003"></graphic>
</fig>
<fig position="float" id="f4"><label>FIG. 4.</label>
<caption><p>Maximum-likelihood phylogenetic tree for HA segment clones from sample WW537 in comparison with those circulating during the same time period (1997-1998 northern hemisphere season) in New York State. Clones from sample WW537 are shown in red and italics. The two antigenically distinct lineages of HA are highlighted, and bootstrap support values are shown for key nodes. All horizontal branches are drawn to a scale of nucleotide substitutions per site, and the tree is midpoint rooted for purposes of clarity only.</p>
</caption>
<graphic xlink:href="zjv0170922660004"></graphic>
</fig>
<fig position="float" id="f5"><label>FIG. 5.</label>
<caption><p>Alignment of nonconserved HA1 residues of the HA across all eight clones from sample WW537. Numbering of the residues is given both from the first methionine of the coding sequence (CDS) and from the first residue of the HA1 domain (HA1 numbering). Gray letters at the top of each column correspond to residues of epitopic sites where antibodies have been shown to bind. L, leucine; S, serine; K, lysine; E, glutamic acid; Q, glutamine; T, threonine; N, asparagine; G, glycine; R, arginine; V, valine; A, alanine; I, isoleucine; D, aspartic acid.</p>
</caption>
<graphic xlink:href="zjv0170922660005"></graphic>
</fig>
<table-wrap position="float" id="t1"><label>TABLE 1.</label>
<caption><p>Influenza A virus segment clones from patients NZ094 and WW537 and GenBank accession numbers</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Organism</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Segment</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Blinded no.</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Clone name</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">GenBank accession no.</th>
</tr>
</thead>
<tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">Influenza A virus Canterbury/200/2004 (H3N2)</td>
<td colspan="1" rowspan="1" align="left" valign="top">1 (PB2)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.1a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S1C004</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039886">CY039886</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.1b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S1C008</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039887">CY039887</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.1c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S1C002</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039888">CY039888</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.1d</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S1C003</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039889">CY039889</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.1e</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S1C005</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039890">CY039890</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.1f</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S1C006</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039891">CY039891</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">2 (PB1)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.2a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S2C026</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039892">CY039892</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.2b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S2C006</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039939">CY039939</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.2c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S2C018</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039940">CY039940</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.2d</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S2C021</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039941">CY039941</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.2e</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S2C024</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039942">CY039942</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.2f</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S2C028</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039943">CY039943</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">3 (PA)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C101</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039944">CY039944</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C102</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039945">CY039945</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C104</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039946">CY039946</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3d</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C201</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039947">CY039947</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3e</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C205</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039948">CY039948</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3f</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C302</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039949">CY039949</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3g</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C303</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039950">CY039950</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3h</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C401</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039951">CY039951</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3i</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C405</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039952">CY039952</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3j</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C406</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039953">CY039953</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3k</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C503</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039954">CY039954</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3l</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C504</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039955">CY039955</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3m</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C602</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039956">CY039956</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3n</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C603</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039957">CY039957</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3o</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C604</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039958">CY039958</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.3p</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S3C605</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039959">CY039959</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">4 (HA)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4Cx06</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039960">CY039960</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4Cx04</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039961">CY039961</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4Cx03</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039962">CY039962</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4d</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4Cx02</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039963">CY039963</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4e</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4Cx01</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039964">CY039964</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4f</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4C007</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039965">CY039965</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.4g</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S4C006</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039966">CY039966</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">5 (NP)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.5a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S5C002</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039967">CY039967</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.5b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S5C005</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039968">CY039968</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.5c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S5C001</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039969">CY039969</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.5d</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S5C004</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039970">CY039970</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">6 (NA)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.6a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S6C001</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039971">CY039971</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.6b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S6C003</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039972">CY039972</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.6c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S6C005</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039973">CY039973</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">7 (M)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S7C001</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039974">CY039974</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7b</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S7C005</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039975">CY039975</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7c</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S7C004</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039976">CY039976</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7d</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S7C007</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039977">CY039977</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7e</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P11S7C008</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039978">CY039978</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7f</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S7C002</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039979">CY039979</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7g</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S7C004</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039980">CY039980</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7h</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S7C006</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039981">CY039981</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7i</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S7C005</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039982">CY039982</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.7j</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S7C007</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039983">CY039983</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">8 (NS)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NZ-00094.8a</td>
<td colspan="1" rowspan="1" align="left" valign="top">NZ094P32S8C001</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039984">CY039984</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">Influenza A virus New York/537/1998 (H3N2)</td>
<td colspan="1" rowspan="1" align="left" valign="top">4 (HA)</td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4a</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4C34</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039878">CY039878</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4b</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4C8</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039879">CY039879</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4c</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4Cr1</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039880">CY039880</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4d</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4Cr5</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039938">CY039938</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4e</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4Cr7</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039882">CY039882</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4f</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4Cr8</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039883">CY039883</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4g</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4C36</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039884">CY039884</ext-link>
</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">NIGSP-NYS-00537.4h</td>
<td colspan="1" rowspan="1" align="left" valign="top">WW537H3N2S4C6</td>
<td colspan="1" rowspan="1" align="left" valign="top"><ext-link ext-link-type="gen" xlink:href="CY039885">CY039885</ext-link>
</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap position="float" id="t2"><label>TABLE 2.</label>
<caption><p>Amino acid replacements characterizing the adamantane-resistant N-lineage that were found in cloned segments from patient NZ094</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Protein</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Amino acid replacement in N-lineage</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">NZ094</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Clones (Sanger)<xref ref-type="table-fn" rid="t2fn1"><italic>a</italic>
</xref>
</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Reads (pyrosequencing)<xref ref-type="table-fn" rid="t2fn2"><italic>b</italic>
</xref>
</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">% of reads</th>
</tr>
</thead>
<tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">PB1</td>
<td colspan="1" rowspan="1" align="left" valign="top">V113A</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/6</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">PA</td>
<td colspan="1" rowspan="1" align="left" valign="top">E101G</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/4</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">S208T</td>
<td colspan="1" rowspan="1" align="center" valign="top">ND<xref ref-type="table-fn" rid="t2fn3"><italic>c</italic>
</xref>
</td>
<td colspan="1" rowspan="1" align="center" valign="top">ND</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">K256Q</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/4</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">D382E</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">5/9</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">I421V</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">5/9</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">Y437H</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">6/10</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">I602V</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/3</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">NP</td>
<td colspan="1" rowspan="1" align="left" valign="top">A280V</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">2/4</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">I312V</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">2/4</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">S377G</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">2/4</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">M1</td>
<td colspan="1" rowspan="1" align="left" valign="top">K174R</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/9</td>
<td colspan="1" rowspan="1" align="center" valign="top">22/48</td>
<td colspan="1" rowspan="1" align="char" char="." valign="top">46</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">V219I</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/9</td>
<td colspan="1" rowspan="1" align="center" valign="top">ND</td>
<td colspan="1" rowspan="1" align="char" char="." valign="top"></td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">M2</td>
<td colspan="1" rowspan="1" align="left" valign="top">S31N</td>
<td colspan="1" rowspan="1" align="center" valign="top">+</td>
<td colspan="1" rowspan="1" align="center" valign="top">1/9</td>
<td colspan="1" rowspan="1" align="center" valign="top">24/51</td>
<td colspan="1" rowspan="1" align="char" char="." valign="top">47</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">HA1<xref ref-type="table-fn" rid="t2fn4"><italic>d</italic>
</xref>
</td>
<td colspan="1" rowspan="1" align="left" valign="top">S193F</td>
<td colspan="1" rowspan="1" align="center" valign="top">−</td>
<td colspan="1" rowspan="1" align="center" valign="top">0/7</td>
<td colspan="1" rowspan="1" align="center" valign="top">0/65</td>
<td colspan="1" rowspan="1" align="char" char="." valign="top">0</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top"></td>
<td colspan="1" rowspan="1" align="left" valign="top">D225N</td>
<td colspan="1" rowspan="1" align="center" valign="top">−</td>
<td colspan="1" rowspan="1" align="center" valign="top">0/7</td>
<td colspan="1" rowspan="1" align="center" valign="top">0/65</td>
<td colspan="1" rowspan="1" align="char" char="." valign="top">0</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">NA</td>
<td colspan="1" rowspan="1" align="left" valign="top">D93N</td>
<td colspan="1" rowspan="1" align="center" valign="top">−</td>
<td colspan="1" rowspan="1" align="center" valign="top">0/3</td>
<td colspan="1" rowspan="1" align="center" valign="top">0/283</td>
<td colspan="1" rowspan="1" align="char" char="." valign="top">0</td>
</tr>
</tbody>
</table>
<table-wrap-foot><fn id="t2fn1"><label>a</label>
<p>Ratio of clones sequenced that possess amino acid replacement.</p>
</fn>
<fn id="t2fn2"><label>b</label>
<p>Ratio of pyrosequence reads that possess amino acid replacement.</p>
</fn>
<fn id="t2fn3"><label>c</label>
<p>ND, not determined.</p>
</fn>
<fn id="t2fn4"><label>d</label>
<p>The residue positions for HA1 are given in HA1 numbering.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap position="float" id="t3"><label>TABLE 3.</label>
<caption><p>Influenza A and B viral RNA copy numbers from isolate WW347, as determined using quantitative real-time RT-PCR</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="2" align="center" valign="middle">Sample</th>
<th colspan="2" rowspan="1" align="center" valign="bottom">Viral RNA copy no./reaction mixture<xref ref-type="table-fn" rid="t3fn1"><italic>a</italic>
</xref>
<hr></hr>
</th>
</tr>
<tr><th colspan="1" rowspan="1" align="center" valign="bottom">Influenza A virus</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Influenza B virus</th>
</tr>
</thead>
<tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">WW347 first pass</td>
<td colspan="1" rowspan="1" align="center" valign="top">6.82E+07</td>
<td colspan="1" rowspan="1" align="center" valign="top">9.24E+05</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">WW347 culture</td>
<td colspan="1" rowspan="1" align="center" valign="top">3.99E+08</td>
<td colspan="1" rowspan="1" align="center" valign="top">7.07E+07</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">No-template control</td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">Amplification control<xref ref-type="table-fn" rid="t3fn2"><italic>b</italic>
</xref>
</td>
<td colspan="1" rowspan="1" align="center" valign="top">2.20E+01</td>
<td colspan="1" rowspan="1" align="center" valign="top">1.00E+02</td>
</tr>
</tbody>
</table>
<table-wrap-foot><fn id="t3fn1"><label>a</label>
<p>Values represent RNA extracted from a first-pass culture of a nasopharyngeal specimen and subsequent cell culture.</p>
</fn>
<fn id="t3fn2"><label>b</label>
<p>The amplification control for influenza A virus was diluted RNA, extracted from an amplified New York A/H1N1 (2006) strain. The amplification control for influenza B virus was diluted RNA, extracted from an amplified New York B (2006) strain. Positive controls were usually prepared at a relatively low concentration.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<table-wrap position="float" id="t4"><label>TABLE 4.</label>
<caption><p>Influenza A and B viral RNA copy numbers from two samples, as determined using quantitative real-time RT-PCR</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="2" align="center" valign="middle">Sample ID no. (yr of isolation)</th>
<th colspan="1" rowspan="2" align="center" valign="middle">Sample type</th>
<th colspan="1" rowspan="2" align="center" valign="middle">Influenza A virus subtype</th>
<th colspan="2" rowspan="1" align="center" valign="bottom">Viral RNA copy no./reaction mixture<xref ref-type="table-fn" rid="t4fn1"><italic>a</italic>
</xref>
<hr></hr>
</th>
</tr>
<tr><th colspan="1" rowspan="1" align="center" valign="bottom">Influenza A virus</th>
<th colspan="1" rowspan="1" align="center" valign="bottom">Influenza B virus</th>
</tr>
</thead>
<tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">1 (2005)</td>
<td colspan="1" rowspan="1" align="left" valign="top">Throat swab</td>
<td colspan="1" rowspan="1" align="center" valign="top">H3N2</td>
<td colspan="1" rowspan="1" align="center" valign="top">1.21E+06</td>
<td colspan="1" rowspan="1" align="center" valign="top">6.80E+02</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">1 (2005)</td>
<td colspan="1" rowspan="1" align="left" valign="top">RhMK1 culture</td>
<td colspan="1" rowspan="1" align="center" valign="top">H3N2</td>
<td colspan="1" rowspan="1" align="center" valign="top">2.21E+07</td>
<td colspan="1" rowspan="1" align="center" valign="top">6.71E+07</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">2 (2009)</td>
<td colspan="1" rowspan="1" align="left" valign="top">Pharyngeal swab</td>
<td colspan="1" rowspan="1" align="center" valign="top">H1N1</td>
<td colspan="1" rowspan="1" align="center" valign="top">4.21E+05</td>
<td colspan="1" rowspan="1" align="center" valign="top">1.00E+01</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">2 (2009)</td>
<td colspan="1" rowspan="1" align="left" valign="top">RhMK1 culture</td>
<td colspan="1" rowspan="1" align="center" valign="top">H1N1</td>
<td colspan="1" rowspan="1" align="center" valign="top">1.56E+07</td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">Negative extraction control</td>
<td colspan="1" rowspan="1" align="left" valign="top">PBS</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">No-template control</td>
<td colspan="1" rowspan="1" align="left" valign="top">Water</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
<td colspan="1" rowspan="1" align="center" valign="top">0</td>
</tr>
<tr><td colspan="1" rowspan="1" align="left" valign="top">Amplification control<xref ref-type="table-fn" rid="t4fn2"><italic>b</italic>
</xref>
</td>
<td colspan="1" rowspan="1" align="left" valign="top">Viral RNA</td>
<td colspan="1" rowspan="1" align="center" valign="top"></td>
<td colspan="1" rowspan="1" align="center" valign="top">2.00E+03</td>
<td colspan="1" rowspan="1" align="center" valign="top">1.00E+02</td>
</tr>
</tbody>
</table>
<table-wrap-foot><fn id="t4fn1"><label>a</label>
<p>Values represent RNA extracted from the original specimen and first-pass cell culture.</p>
</fn>
<fn id="t4fn2"><label>b</label>
<p>The amplification control for influenza A virus was diluted RNA extracted from an amplified New York A/H1N1 (2006) strain. The amplification control for influenza B virus was diluted RNA extracted from an amplified New York B (2006) strain.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</floats-wrap>
</pmc>
</record>
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