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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">PhyloFlu, a DNA Microarray for Determining the Phylogenetic Origin of Influenza A Virus Gene Segments and the Genomic Fingerprint of Viral Strains</title><author><name sortKey="Paulin, Luis F" sort="Paulin, Luis F" uniqKey="Paulin L" first="Luis F." last="Paulin">Luis F. Paulin</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="Soto Del Rio, Maria De Los D" sort="Soto Del Rio, Maria De Los D" uniqKey="Soto Del Rio M" first="María De Los D." last="Soto-Del Río">María De Los D. Soto-Del Río</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="Sanchez, Ivan" sort="Sanchez, Ivan" uniqKey="Sanchez I" first="Iván" last="Sánchez">Iván Sánchez</name><affiliation><nlm:aff id="aff2">Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff></affiliation></author><author><name sortKey="Hernandez, Jesus" sort="Hernandez, Jesus" uniqKey="Hernandez J" first="Jesús" last="Hernández">Jesús Hernández</name><affiliation><nlm:aff id="aff3">Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico</nlm:aff></affiliation></author><author><name sortKey="Gutierrez Rios, Rosa M" sort="Gutierrez Rios, Rosa M" uniqKey="Gutierrez Rios R" first="Rosa M." last="Gutiérrez-Ríos">Rosa M. Gutiérrez-Ríos</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="L Pez Martinez, Irma" sort="L Pez Martinez, Irma" uniqKey="L Pez Martinez I" first="Irma" last="L Pez-Martínez">Irma L Pez-Martínez</name><affiliation><nlm:aff id="aff4">Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaria de Salud, Mexico City, Mexico</nlm:aff></affiliation></author><author><name sortKey="Wong Chew, Rosa M" sort="Wong Chew, Rosa M" uniqKey="Wong Chew R" first="Rosa M." last="Wong-Chew">Rosa M. Wong-Chew</name><affiliation><nlm:aff id="aff5">Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff></affiliation></author><author><name sortKey="Parissi Crivelli, Aurora" sort="Parissi Crivelli, Aurora" uniqKey="Parissi Crivelli A" first="Aurora" last="Parissi-Crivelli">Aurora Parissi-Crivelli</name><affiliation><nlm:aff id="aff6">Laboratorio Estatal de Salud Pública, Servicios de Salud de Veracruz, Veracruz, Veracruz, Mexico</nlm:aff></affiliation></author><author><name sortKey="Isa, P" sort="Isa, P" uniqKey="Isa P" first="P." last="Isa">P. Isa</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="L Pez, Susana" sort="L Pez, Susana" uniqKey="L Pez S" first="Susana" last="L Pez">Susana L Pez</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="Arias, Carlos F" sort="Arias, Carlos F" uniqKey="Arias C" first="Carlos F." last="Arias">Carlos F. Arias</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24353006</idno><idno type="pmc">3957772</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957772</idno><idno type="RBID">PMC:3957772</idno><idno type="doi">10.1128/JCM.03134-13</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000624</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000624</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">PhyloFlu, a DNA Microarray for Determining the Phylogenetic Origin of Influenza A Virus Gene Segments and the Genomic Fingerprint of Viral Strains</title><author><name sortKey="Paulin, Luis F" sort="Paulin, Luis F" uniqKey="Paulin L" first="Luis F." last="Paulin">Luis F. Paulin</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="Soto Del Rio, Maria De Los D" sort="Soto Del Rio, Maria De Los D" uniqKey="Soto Del Rio M" first="María De Los D." last="Soto-Del Río">María De Los D. Soto-Del Río</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="Sanchez, Ivan" sort="Sanchez, Ivan" uniqKey="Sanchez I" first="Iván" last="Sánchez">Iván Sánchez</name><affiliation><nlm:aff id="aff2">Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff></affiliation></author><author><name sortKey="Hernandez, Jesus" sort="Hernandez, Jesus" uniqKey="Hernandez J" first="Jesús" last="Hernández">Jesús Hernández</name><affiliation><nlm:aff id="aff3">Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico</nlm:aff></affiliation></author><author><name sortKey="Gutierrez Rios, Rosa M" sort="Gutierrez Rios, Rosa M" uniqKey="Gutierrez Rios R" first="Rosa M." last="Gutiérrez-Ríos">Rosa M. Gutiérrez-Ríos</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="L Pez Martinez, Irma" sort="L Pez Martinez, Irma" uniqKey="L Pez Martinez I" first="Irma" last="L Pez-Martínez">Irma L Pez-Martínez</name><affiliation><nlm:aff id="aff4">Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaria de Salud, Mexico City, Mexico</nlm:aff></affiliation></author><author><name sortKey="Wong Chew, Rosa M" sort="Wong Chew, Rosa M" uniqKey="Wong Chew R" first="Rosa M." last="Wong-Chew">Rosa M. Wong-Chew</name><affiliation><nlm:aff id="aff5">Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico</nlm:aff></affiliation></author><author><name sortKey="Parissi Crivelli, Aurora" sort="Parissi Crivelli, Aurora" uniqKey="Parissi Crivelli A" first="Aurora" last="Parissi-Crivelli">Aurora Parissi-Crivelli</name><affiliation><nlm:aff id="aff6">Laboratorio Estatal de Salud Pública, Servicios de Salud de Veracruz, Veracruz, Veracruz, Mexico</nlm:aff></affiliation></author><author><name sortKey="Isa, P" sort="Isa, P" uniqKey="Isa P" first="P." last="Isa">P. Isa</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="L Pez, Susana" sort="L Pez, Susana" uniqKey="L Pez S" first="Susana" last="L Pez">Susana L Pez</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author><author><name sortKey="Arias, Carlos F" sort="Arias, Carlos F" uniqKey="Arias C" first="Carlos F." last="Arias">Carlos F. Arias</name><affiliation><nlm:aff id="aff1">Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Clinical Microbiology</title><idno type="ISSN">0095-1137</idno><idno type="eISSN">1098-660X</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Recent evidence suggests that most influenza A virus gene segments can contribute to the pathogenicity of the virus. In this regard, the hemagglutinin (HA) subtype of the circulating strains has been closely surveyed, but the reassortment of internal gene segments is usually not monitored as a potential source of an increased pathogenicity. In this work, an oligonucleotide DNA microarray (PhyloFlu) designed to determine the phylogenetic origins of the eight segments of the influenza virus genome was constructed and validated. Clades were defined for each segment and also for the 16 HA and 9 neuraminidase (NA) subtypes. Viral genetic material was amplified by reverse transcription-PCR (RT-PCR) with primers specific to the conserved 5′ and 3′ ends of the influenza A virus genes, followed by PCR amplification with random primers and Cy3 labeling. The microarray unambiguously determined the clades for all eight influenza virus genes in 74% (28/38) of the samples. The microarray was validated with reference strains from different animal origins, as well as from human, swine, and avian viruses from field or clinical samples. In most cases, the phylogenetic clade of each segment defined its animal host of origin. The genomic fingerprint deduced by the combined information of the individual clades allowed for the determination of the time and place that strains with the same genomic pattern were previously reported. PhyloFlu is useful for characterizing and surveying the genetic diversity and variation of animal viruses circulating in different environmental niches and for obtaining a more detailed surveillance and follow up of reassortant events that can potentially modify virus pathogenicity.</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 Clin Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">J. Clin. Microbiol</journal-id><journal-id journal-id-type="hwp">jcm</journal-id><journal-id journal-id-type="pmc">jcm</journal-id><journal-id journal-id-type="publisher-id">JCM</journal-id><journal-title-group><journal-title>Journal of Clinical Microbiology</journal-title></journal-title-group><issn pub-type="ppub">0095-1137</issn><issn pub-type="epub">1098-660X</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24353006</article-id><article-id pub-id-type="pmc">3957772</article-id><article-id pub-id-type="publisher-id">03134-13</article-id><article-id pub-id-type="doi">10.1128/JCM.03134-13</article-id><article-categories><subj-group subj-group-type="heading"><subject>Virology</subject></subj-group></article-categories><title-group><article-title>PhyloFlu, a DNA Microarray for Determining the Phylogenetic Origin of Influenza A Virus Gene Segments and the Genomic Fingerprint of Viral Strains</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Paulin</surname><given-names>Luis F.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Soto-Del Río</surname><given-names>María de los D.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="author-notes" rid="fn1">*</xref></contrib><contrib contrib-type="author"><name><surname>Sánchez</surname><given-names>Iván</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hernández</surname><given-names>Jesús</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gutiérrez-Ríos</surname><given-names>Rosa M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>López-Martínez</surname><given-names>Irma</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wong-Chew</surname><given-names>Rosa M.</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Parissi-Crivelli</surname><given-names>Aurora</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author"><name><surname>Isa</surname><given-names>P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>López</surname><given-names>Susana</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Arias</surname><given-names>Carlos F.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><aff id="aff1"><label>a</label>Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Chamilpa, Cuernavaca, Morelos, Mexico</aff><aff id="aff2"><label>b</label>Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico</aff><aff id="aff3"><label>c</label>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico</aff><aff id="aff4"><label>d</label>Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaria de Salud, Mexico City, Mexico</aff><aff id="aff5"><label>e</label>Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico</aff><aff id="aff6"><label>f</label>Laboratorio Estatal de Salud Pública, Servicios de Salud de Veracruz, Veracruz, Veracruz, Mexico</aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>McAdam</surname><given-names>A. J.</given-names></name><role>Editor</role></contrib></contrib-group><author-notes><corresp id="cor1">Address correspondence to Carlos F. Arias, <email>arias@ibt.unam.mx</email>.</corresp><fn id="fn1" fn-type="present-address"><label>*</label><p>Present address: María de los D. Soto-Del Río, Department of Animal Pathology, University of Turin, Grugliasco, Turin, Italy.</p></fn></author-notes><pub-date pub-type="ppub"><month>3</month><year>2014</year></pub-date><volume>52</volume><issue>3</issue><fpage>803</fpage><lpage>813</lpage><history><date date-type="received"><day>7</day><month>11</month><year>2013</year></date><date date-type="rev-request"><day>10</day><month>12</month><year>2013</year></date><date date-type="accepted"><day>16</day><month>12</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © 2014, American Society for Microbiology. All Rights Reserved.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>American Society for Microbiology</copyright-holder></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zjm00314000803.pdf"></self-uri><abstract><p>Recent evidence suggests that most influenza A virus gene segments can contribute to the pathogenicity of the virus. In this regard, the hemagglutinin (HA) subtype of the circulating strains has been closely surveyed, but the reassortment of internal gene segments is usually not monitored as a potential source of an increased pathogenicity. In this work, an oligonucleotide DNA microarray (PhyloFlu) designed to determine the phylogenetic origins of the eight segments of the influenza virus genome was constructed and validated. Clades were defined for each segment and also for the 16 HA and 9 neuraminidase (NA) subtypes. Viral genetic material was amplified by reverse transcription-PCR (RT-PCR) with primers specific to the conserved 5′ and 3′ ends of the influenza A virus genes, followed by PCR amplification with random primers and Cy3 labeling. The microarray unambiguously determined the clades for all eight influenza virus genes in 74% (28/38) of the samples. The microarray was validated with reference strains from different animal origins, as well as from human, swine, and avian viruses from field or clinical samples. In most cases, the phylogenetic clade of each segment defined its animal host of origin. The genomic fingerprint deduced by the combined information of the individual clades allowed for the determination of the time and place that strains with the same genomic pattern were previously reported. PhyloFlu is useful for characterizing and surveying the genetic diversity and variation of animal viruses circulating in different environmental niches and for obtaining a more detailed surveillance and follow up of reassortant events that can potentially modify virus pathogenicity.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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