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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Avian Influenza Virus (H11N9) in Migratory Shorebirds Wintering in the Amazon Region, Brazil</title><author><name sortKey="De Araujo, Jansen" sort="De Araujo, Jansen" uniqKey="De Araujo J" first="Jansen" last="De Araujo">Jansen De Araujo</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="De Azevedo Junior, Severino M" sort="De Azevedo Junior, Severino M" uniqKey="De Azevedo Junior S" first="Severino M." last="De Azevedo Júnior">Severino M. De Azevedo Júnior</name><affiliation><nlm:aff id="aff2"><addr-line>Departamento de Biologia da Universidade Federal Rural de Pernambuco, Pernambuco, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gaidet, Nicolas" sort="Gaidet, Nicolas" uniqKey="Gaidet N" first="Nicolas" last="Gaidet">Nicolas Gaidet</name><affiliation><nlm:aff id="aff3"><addr-line>CIRAD-ES, UR AGIRS, Montpellier, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Hurtado, Renata F" sort="Hurtado, Renata F" uniqKey="Hurtado R" first="Renata F." last="Hurtado">Renata F. Hurtado</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Walker, David" sort="Walker, David" uniqKey="Walker D" first="David" last="Walker">David Walker</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Thomazelli, Luciano M" sort="Thomazelli, Luciano M" uniqKey="Thomazelli L" first="Luciano M." last="Thomazelli">Luciano M. Thomazelli</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Ometto, Tatiana" sort="Ometto, Tatiana" uniqKey="Ometto T" first="Tatiana" last="Ometto">Tatiana Ometto</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Seixas, Marina M M" sort="Seixas, Marina M M" uniqKey="Seixas M" first="Marina M. M." last="Seixas">Marina M. M. Seixas</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodrigues, Roberta" sort="Rodrigues, Roberta" uniqKey="Rodrigues R" first="Roberta" last="Rodrigues">Roberta Rodrigues</name><affiliation><nlm:aff id="aff2"><addr-line>Departamento de Biologia da Universidade Federal Rural de Pernambuco, Pernambuco, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Galindo, Daniele B" sort="Galindo, Daniele B" uniqKey="Galindo D" first="Daniele B." last="Galindo">Daniele B. Galindo</name><affiliation><nlm:aff id="aff5"><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Da Silva, Adriana C S" sort="Da Silva, Adriana C S" uniqKey="Da Silva A" first="Adriana C. S." last="Da Silva">Adriana C. S. Da Silva</name><affiliation><nlm:aff id="aff6"><addr-line>SFA-PA- Superintendência Federal de Agricultura no estado do Pará. Ministério da Agricultura Pecuária e Abastecimento (MAPA), Distrito Federal, Brasília, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodrigues, Arlinea M M" sort="Rodrigues, Arlinea M M" uniqKey="Rodrigues A" first="Arlinéa M. M." last="Rodrigues">Arlinéa M. M. Rodrigues</name><affiliation><nlm:aff id="aff5"><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Bomfim, Leonardo L" sort="Bomfim, Leonardo L" uniqKey="Bomfim L" first="Leonardo L." last="Bomfim">Leonardo L. Bomfim</name><affiliation><nlm:aff id="aff5"><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Mota, Marcelo A" sort="Mota, Marcelo A" uniqKey="Mota M" first="Marcelo A." last="Mota">Marcelo A. Mota</name><affiliation><nlm:aff id="aff6"><addr-line>SFA-PA- Superintendência Federal de Agricultura no estado do Pará. Ministério da Agricultura Pecuária e Abastecimento (MAPA), Distrito Federal, Brasília, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Larrazabal, Maria E" sort="Larrazabal, Maria E" uniqKey="Larrazabal M" first="Maria E." last="Larrazábal">Maria E. Larrazábal</name><affiliation><nlm:aff id="aff7"><addr-line>Biologia Animal da Universidade Federal de Pernambuco, Pernambuco, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Branco, Joaquim O" sort="Branco, Joaquim O" uniqKey="Branco J" first="Joaquim O." last="Branco">Joaquim O. Branco</name><affiliation><nlm:aff id="aff8"><addr-line>Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Santa Catarina, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Serafini, Patricia" sort="Serafini, Patricia" uniqKey="Serafini P" first="Patricia" last="Serafini">Patricia Serafini</name><affiliation><nlm:aff id="aff9"><addr-line>Centro Nacional de Pesquisa e Conservação das Aves Silvestres (CEMAVE), Cabedelo, Paraíba, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Neto, Isaac S" sort="Neto, Isaac S" uniqKey="Neto I" first="Isaac S." last="Neto">Isaac S. Neto</name><affiliation><nlm:aff id="aff9"><addr-line>Centro Nacional de Pesquisa e Conservação das Aves Silvestres (CEMAVE), Cabedelo, Paraíba, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Franks, John" sort="Franks, John" uniqKey="Franks J" first="John" last="Franks">John Franks</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Webby, Richard J" sort="Webby, Richard J" uniqKey="Webby R" first="Richard J." last="Webby">Richard J. Webby</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Webster, Robert G" sort="Webster, Robert G" uniqKey="Webster R" first="Robert G." last="Webster">Robert G. Webster</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Durigon, Edison L" sort="Durigon, Edison L" uniqKey="Durigon E" first="Edison L." last="Durigon">Edison L. Durigon</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25329399</idno><idno type="pmc">4199675</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199675</idno><idno type="RBID">PMC:4199675</idno><idno type="doi">10.1371/journal.pone.0110141</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000B83</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B83</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Avian Influenza Virus (H11N9) in Migratory Shorebirds Wintering in the Amazon Region, Brazil</title><author><name sortKey="De Araujo, Jansen" sort="De Araujo, Jansen" uniqKey="De Araujo J" first="Jansen" last="De Araujo">Jansen De Araujo</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="De Azevedo Junior, Severino M" sort="De Azevedo Junior, Severino M" uniqKey="De Azevedo Junior S" first="Severino M." last="De Azevedo Júnior">Severino M. De Azevedo Júnior</name><affiliation><nlm:aff id="aff2"><addr-line>Departamento de Biologia da Universidade Federal Rural de Pernambuco, Pernambuco, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Gaidet, Nicolas" sort="Gaidet, Nicolas" uniqKey="Gaidet N" first="Nicolas" last="Gaidet">Nicolas Gaidet</name><affiliation><nlm:aff id="aff3"><addr-line>CIRAD-ES, UR AGIRS, Montpellier, France</addr-line></nlm:aff></affiliation></author><author><name sortKey="Hurtado, Renata F" sort="Hurtado, Renata F" uniqKey="Hurtado R" first="Renata F." last="Hurtado">Renata F. Hurtado</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Walker, David" sort="Walker, David" uniqKey="Walker D" first="David" last="Walker">David Walker</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Thomazelli, Luciano M" sort="Thomazelli, Luciano M" uniqKey="Thomazelli L" first="Luciano M." last="Thomazelli">Luciano M. Thomazelli</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Ometto, Tatiana" sort="Ometto, Tatiana" uniqKey="Ometto T" first="Tatiana" last="Ometto">Tatiana Ometto</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Seixas, Marina M M" sort="Seixas, Marina M M" uniqKey="Seixas M" first="Marina M. M." last="Seixas">Marina M. M. Seixas</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodrigues, Roberta" sort="Rodrigues, Roberta" uniqKey="Rodrigues R" first="Roberta" last="Rodrigues">Roberta Rodrigues</name><affiliation><nlm:aff id="aff2"><addr-line>Departamento de Biologia da Universidade Federal Rural de Pernambuco, Pernambuco, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Galindo, Daniele B" sort="Galindo, Daniele B" uniqKey="Galindo D" first="Daniele B." last="Galindo">Daniele B. Galindo</name><affiliation><nlm:aff id="aff5"><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Da Silva, Adriana C S" sort="Da Silva, Adriana C S" uniqKey="Da Silva A" first="Adriana C. S." last="Da Silva">Adriana C. S. Da Silva</name><affiliation><nlm:aff id="aff6"><addr-line>SFA-PA- Superintendência Federal de Agricultura no estado do Pará. Ministério da Agricultura Pecuária e Abastecimento (MAPA), Distrito Federal, Brasília, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Rodrigues, Arlinea M M" sort="Rodrigues, Arlinea M M" uniqKey="Rodrigues A" first="Arlinéa M. M." last="Rodrigues">Arlinéa M. M. Rodrigues</name><affiliation><nlm:aff id="aff5"><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Bomfim, Leonardo L" sort="Bomfim, Leonardo L" uniqKey="Bomfim L" first="Leonardo L." last="Bomfim">Leonardo L. Bomfim</name><affiliation><nlm:aff id="aff5"><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Mota, Marcelo A" sort="Mota, Marcelo A" uniqKey="Mota M" first="Marcelo A." last="Mota">Marcelo A. Mota</name><affiliation><nlm:aff id="aff6"><addr-line>SFA-PA- Superintendência Federal de Agricultura no estado do Pará. Ministério da Agricultura Pecuária e Abastecimento (MAPA), Distrito Federal, Brasília, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Larrazabal, Maria E" sort="Larrazabal, Maria E" uniqKey="Larrazabal M" first="Maria E." last="Larrazábal">Maria E. Larrazábal</name><affiliation><nlm:aff id="aff7"><addr-line>Biologia Animal da Universidade Federal de Pernambuco, Pernambuco, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Branco, Joaquim O" sort="Branco, Joaquim O" uniqKey="Branco J" first="Joaquim O." last="Branco">Joaquim O. Branco</name><affiliation><nlm:aff id="aff8"><addr-line>Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Santa Catarina, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Serafini, Patricia" sort="Serafini, Patricia" uniqKey="Serafini P" first="Patricia" last="Serafini">Patricia Serafini</name><affiliation><nlm:aff id="aff9"><addr-line>Centro Nacional de Pesquisa e Conservação das Aves Silvestres (CEMAVE), Cabedelo, Paraíba, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Neto, Isaac S" sort="Neto, Isaac S" uniqKey="Neto I" first="Isaac S." last="Neto">Isaac S. Neto</name><affiliation><nlm:aff id="aff9"><addr-line>Centro Nacional de Pesquisa e Conservação das Aves Silvestres (CEMAVE), Cabedelo, Paraíba, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Franks, John" sort="Franks, John" uniqKey="Franks J" first="John" last="Franks">John Franks</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Webby, Richard J" sort="Webby, Richard J" uniqKey="Webby R" first="Richard J." last="Webby">Richard J. Webby</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Webster, Robert G" sort="Webster, Robert G" uniqKey="Webster R" first="Robert G." last="Webster">Robert G. Webster</name><affiliation><nlm:aff id="aff4"><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></nlm:aff></affiliation></author><author><name sortKey="Durigon, Edison L" sort="Durigon, Edison L" uniqKey="Durigon E" first="Edison L." last="Durigon">Edison L. Durigon</name><affiliation><nlm:aff id="aff1"><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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>Aquatic birds are the natural reservoir for avian influenza viruses (AIV). Habitats in Brazil provide stopover and wintering sites for water birds that migrate between North and South America. The current study was conducted to elucidate the possibility of the transport of influenza A viruses by birds that migrate annually between the Northern and Southern Hemispheres. In total, 556 orotracheal/cloacal swab samples were collected for influenza A virus screening using real-time RT-PCR (rRT-PCR). The influenza A virus-positive samples were subjected to viral isolation. Four samples were positive for the influenza A matrix gene by rRT-PCR. From these samples, three viruses were isolated, sequenced and characterized. All positive samples originated from a single bird species, the ruddy turnstone (<italic>Arenaria interpres</italic>), that was caught in the Amazon region at Caeté Bay, Northeast Pará, at Ilha de Canelas. To our knowledge, this is the first isolation of H11N9 in the ruddy turnstone in South America.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Olsen, B" uniqKey="Olsen B">B Olsen</name></author><author><name sortKey="Munster, Vj" uniqKey="Munster V">VJ Munster</name></author><author><name sortKey="Wallensten, A" uniqKey="Wallensten A">A Wallensten</name></author><author><name sortKey="Waldenstrom, J" uniqKey="Waldenstrom J">J Waldenström</name></author><author><name sortKey="Osterhaus, Adme" uniqKey="Osterhaus A">ADME Osterhaus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, Jd" uniqKey="Brown J">JD Brown</name></author><author><name sortKey="Luttrell, Mp" uniqKey="Luttrell M">MP Luttrell</name></author><author><name sortKey="Berghaus, Rd" uniqKey="Berghaus R">RD Berghaus</name></author><author><name sortKey="Kistler, W" uniqKey="Kistler W">W Kistler</name></author><author><name 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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">25329399</article-id><article-id pub-id-type="pmc">4199675</article-id><article-id pub-id-type="publisher-id">PONE-D-14-00407</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0110141</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Veterinary Science</subject><subj-group><subject>Animal Types</subject><subj-group><subject>Wildlife</subject></subj-group></subj-group><subj-group><subject>Veterinary Diseases</subject><subj-group><subject>Veterinary Virology</subject><subj-group><subject>Animal Influenza</subject></subj-group></subj-group><subj-group><subject>Zoonoses</subject></subj-group></subj-group><subj-group><subject>Veterinary Microbiology</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Avian Influenza Virus (H11N9) in Migratory Shorebirds Wintering in the Amazon Region, Brazil</article-title><alt-title alt-title-type="running-head">Avian Influenza Virus (H11N9) in Amazon, Brazil</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>de Araujo</surname><given-names>Jansen</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>de Azevedo Júnior</surname><given-names>Severino M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gaidet</surname><given-names>Nicolas</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hurtado</surname><given-names>Renata F.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Walker</surname><given-names>David</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Thomazelli</surname><given-names>Luciano M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ometto</surname><given-names>Tatiana</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Seixas</surname><given-names>Marina M. M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rodrigues</surname><given-names>Roberta</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Galindo</surname><given-names>Daniele B.</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>da Silva</surname><given-names>Adriana C. S.</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rodrigues</surname><given-names>Arlinéa M. M.</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bomfim</surname><given-names>Leonardo L.</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mota</surname><given-names>Marcelo A.</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Larrazábal</surname><given-names>Maria E.</given-names></name><xref ref-type="aff" rid="aff7"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Branco</surname><given-names>Joaquim O.</given-names></name><xref ref-type="aff" rid="aff8"><sup>8</sup></xref></contrib><contrib contrib-type="author"><name><surname>Serafini</surname><given-names>Patricia</given-names></name><xref ref-type="aff" rid="aff9"><sup>9</sup></xref></contrib><contrib contrib-type="author"><name><surname>Neto</surname><given-names>Isaac S.</given-names></name><xref ref-type="aff" rid="aff9"><sup>9</sup></xref></contrib><contrib contrib-type="author"><name><surname>Franks</surname><given-names>John</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Webby</surname><given-names>Richard J.</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Webster</surname><given-names>Robert G.</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Durigon</surname><given-names>Edison L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>BSL3+ Laboratório de Virologia Clínica e Molecular do Instituto de Ciências Biomédicas (ICB-II), Universidade de São Paulo, São Paulo, Brazil</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Departamento de Biologia da Universidade Federal Rural de Pernambuco, Pernambuco, Brazil</addr-line></aff><aff id="aff3"><label>3</label><addr-line>CIRAD-ES, UR AGIRS, Montpellier, France</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Agência de Defesa Agropecuária do Estado do Pará- ADEPARA, Pará, Brazil</addr-line></aff><aff id="aff6"><label>6</label><addr-line>SFA-PA- Superintendência Federal de Agricultura no estado do Pará. Ministério da Agricultura Pecuária e Abastecimento (MAPA), Distrito Federal, Brasília, Brazil</addr-line></aff><aff id="aff7"><label>7</label><addr-line>Biologia Animal da Universidade Federal de Pernambuco, Pernambuco, Brazil</addr-line></aff><aff id="aff8"><label>8</label><addr-line>Centro de Ciências Tecnológicas da Terra e do Mar, Universidade do Vale do Itajaí (UNIVALI), Santa Catarina, Brazil</addr-line></aff><aff id="aff9"><label>9</label><addr-line>Centro Nacional de Pesquisa e Conservação das Aves Silvestres (CEMAVE), Cabedelo, Paraíba, Brazil</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Samaan</surname><given-names>Gina</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Australian National University, Australia</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>jansentequila@usp.br</email></corresp><fn fn-type="COI-statement"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: JA SMAJ JOB ELD RGW. Performed the experiments: JA SMAJ RFH DW LMT TO MMMS RR DG AMMR ACS LLB MAM MEL JOB PS ISN NG JF RW ELD. Analyzed the data: JA SMAJ RFH DW LMT TO MMMS NG RW ELD. Contributed reagents/materials/analysis tools: JA SMAJ RFH DW LMT TO NG JF RW RGW ELD. Wrote the paper: JA SMAJ DW LMT TO MMMS NG RW RGW ELD.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>16</day><month>10</month><year>2014</year></pub-date><volume>9</volume><issue>10</issue><elocation-id>e110141</elocation-id><history><date date-type="received"><day>6</day><month>1</month><year>2014</year></date><date date-type="accepted"><day>16</day><month>9</month><year>2014</year></date></history><permissions><copyright-statement>© 2014 de Araujo et al</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>de Araujo et al</copyright-holder><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>Aquatic birds are the natural reservoir for avian influenza viruses (AIV). Habitats in Brazil provide stopover and wintering sites for water birds that migrate between North and South America. The current study was conducted to elucidate the possibility of the transport of influenza A viruses by birds that migrate annually between the Northern and Southern Hemispheres. In total, 556 orotracheal/cloacal swab samples were collected for influenza A virus screening using real-time RT-PCR (rRT-PCR). The influenza A virus-positive samples were subjected to viral isolation. Four samples were positive for the influenza A matrix gene by rRT-PCR. From these samples, three viruses were isolated, sequenced and characterized. All positive samples originated from a single bird species, the ruddy turnstone (<italic>Arenaria interpres</italic>), that was caught in the Amazon region at Caeté Bay, Northeast Pará, at Ilha de Canelas. To our knowledge, this is the first isolation of H11N9 in the ruddy turnstone in South America.</p></abstract><funding-group><funding-statement>This work has been funded in part by the Fundacão de Amparo a Pesquisa do Estado de São Paulo (FAPESP), Conselho Nacional de Desenvolvimento a Pesquisa (CNPq), Ministério da Agricultura, Pecuária e Abastecimento (MAPA), the Wildlife Conservation Society (WCS) and the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, under contract number HHSN266200700005C and ALSAC. The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="10"></page-count></counts></article-meta></front><body><sec id="s1"><title>Introduction</title><p>Avian influenza viruses (AIV) are globally distributed in wild birds and have been isolated from a wide diversity of avian species <xref rid="pone.0110141-Olsen1" ref-type="bibr">[1]</xref>, <xref rid="pone.0110141-Brown1" ref-type="bibr">[2]</xref>. Wild aquatic birds are considered the natural reservoir for AIV <xref rid="pone.0110141-Stallknecht1" ref-type="bibr">[3]</xref>, and all known hemagglutinin (HA) and neuraminidase (NA) subtypes of AIV have been identified in these species <xref rid="pone.0110141-Beare1" ref-type="bibr">[4]</xref>. Charadriiformes, together with Anseriformes, serve as the main reservoir of low pathogenic avian influenza (LPAI) viruses <xref rid="pone.0110141-Gaidet1" ref-type="bibr">[5]</xref>. There are reports showing that LPAI are virus precursors of high pathogenic avian influenza (HPAI) viruses <xref rid="pone.0110141-Pasick1" ref-type="bibr">[6]</xref>. This relation is of concern because HPAI viruses cause enormous economic losses and have, in rare instances, become major public health issues. For example, deadly outbreaks of Influenza A virus include the H1N1 virus descended from the 1918 ‘Spanish flu’ pandemic, the H2N2 1957 ‘Asian flu’ pandemic strain, the 1968 ‘Hong Kong flu’ strain, the highly pathogenic H5N1 ‘bird flu’ virus of 1997, the 2009 H1N1 pandemic strain <xref rid="pone.0110141-Krauss1" ref-type="bibr">[7]</xref> and the most recent introduction of H7N9 in China that caused human fatalities <xref rid="pone.0110141-Chen1" ref-type="bibr">[8]</xref>. Brazil is considered free from highly pathogenic AIV in poultry, and, being a major global exporter of chicken meat, the emergence of such a disease could have a large economic impact due to trade restrictions <xref rid="pone.0110141-Thomazelli1" ref-type="bibr">[9]</xref>. Therefore, information on low-pathogenic viruses circulating among wild birds in Brazil may be useful for improving knowledge for Reference: Most shorebirds are long-distance migratory birds <xref rid="pone.0110141-Pearce1" ref-type="bibr">[10]</xref>. In the Americas, a large number of migratory shorebirds migrate from North America, where they breed, to South America, where they spend the boreal winter <xref rid="pone.0110141-Rodrigues1" ref-type="bibr">[11]</xref>. These birds have the potential to disperse AIV between the Northern and Southern hemispheres as they migrate.</p><p>The surveillance of migratory birds for AIV is conducted in several countries of the Pacific and Atlantic flyways in the New World <xref rid="pone.0110141-Pearce1" ref-type="bibr">[10]</xref>–<xref rid="pone.0110141-GonzlezReiche1" ref-type="bibr">[14]</xref>. However, AIV has been detected in different species, usually at low prevalence <xref rid="pone.0110141-Hanson1" ref-type="bibr">[15]</xref>, with the exception of a high prevalence in ruddy turnstones at Delaware Bay (USA) during the spring migration in May <xref rid="pone.0110141-Krauss1" ref-type="bibr">[7]</xref>. Delaware Bay represents the only site worldwide where AIV isolations from shorebirds (Scolopacidae) have consistently been reported <xref rid="pone.0110141-Gaidet1" ref-type="bibr">[5]</xref>, <xref rid="pone.0110141-Krauss1" ref-type="bibr">[7]</xref>.</p><p>The coast of Brazil offers several important stopover sites and wintering sites for migratory shorebirds, including ruddy turnstones (<xref ref-type="fig" rid="pone-0110141-g001"><bold>Figure 1</bold></xref>). Thus, at least two important questions must be addressed to better understand AIV dispersal: first, whether ruddy turnstones bring AIV from breeding areas in North America to their wintering sites in South America, and second, whether AIV persists in shorebirds in their wintering sites in South America, hence constituting a source of virus introduction to North America during the spring migration.</p><fig id="pone-0110141-g001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.g001</object-id><label>Figure 1</label><caption><title>Location of sampling sites along the Brazilian coast in relation to the main migration routes and congregation sites of ruddy turnstones in North and South America.</title><p>Samples were collected in Jan-May and Aug-Dec from 2006 to 2010. (map by M. Gély ©Cirad, adapted from Wings Over Wetlands UNEP-GEF Flyways Project and <xref rid="pone.0110141-Blanco1" ref-type="bibr">[34]</xref>.</p></caption><graphic xlink:href="pone.0110141.g001"></graphic></fig><p>The seasonal movements of shorebirds are generally associated with migrations to breeding sites or food <xref rid="pone.0110141-Sick1" ref-type="bibr">[16]</xref>. Shorebirds migrating from boreal winter arrive in Brazil, usually in September, via routes through the western Amazon, eastern Amazon, Central Plateau Brazil and Atlantic coast and remain in the country until April <xref rid="pone.0110141-Antas1" ref-type="bibr">[17]</xref>. During June and July, many species use breeding grounds in the Arctic, and only juveniles, sub-adults or adults that have not completed the molt cycle remain in wintering areas until the next migration season <xref rid="pone.0110141-AzevedoJnior1" ref-type="bibr">[18]</xref>. The largest flocks observed in Brazil are on the northern and southern coasts, and smaller flocks are found on the northeastern and eastern coasts <xref rid="pone.0110141-Morrison1" ref-type="bibr">[19]</xref>–<xref rid="pone.0110141-LyraNevesRM1" ref-type="bibr">[23]</xref>.</p><p>Before the emergence of HPAI (H5N1) in Asia (1997), the surveillance of AIV in migratory birds in Brazil was limited. Prior to 2003, only commercial poultry was routinely monitored for AIV due to export regulations from the Brazilian Agriculture Department (MAPA). Wild-bird surveillance was implemented in 2003–2005 within the framework of the Brazilian Ministry of Health <xref rid="pone.0110141-SecretariadeVigilnciaem1" ref-type="bibr">[24]</xref>. On occasion, the detection of AIV (H3) from Red Knot (<italic>Calidris canutus</italic>), Sanderling (<italic>Calidris alba</italic>), Least Sandpiper (<italic>Calidris minutilla</italic>), White-rumped Sandpiper (<italic>Calidris fuscicollis</italic>), Ruddy Turnstone (<italic>Arenaria interpres</italic>) and Semipalmated Sandpiper (<italic>Calidris pusilla</italic>) sampled on the coast of Brazil was reported <xref rid="pone.0110141-Arajo1" ref-type="bibr">[25]</xref>.</p><p>In the present study, shorebirds and sympatric species were selected for influenza A surveillance because of their status as reservoir species. Important sites for migratory birds were selected in accordance with migration patterns and logistical limitations. In the late spring and early autumn of the years 2006 to 2010, birds were sampled and tested for the presence of AIV at several of the main stopover and wintering sites in Brazil to characterize the pattern of dissemination of AIV in shorebirds.</p></sec><sec id="s2"><title>Material and Methods</title><sec id="s2a"><title>Study sites</title><p>Our study was conducted during 2006–2010 with field-sampling operations coordinated by the University of São Paulo (USP), University of Pernambuco (UFRPE), Brazilian Ministry of Agriculture (MAPA), University of Itajaí Valley (UNIVALI) and National Center of Research and Conservation of Wild Birds (CEMAVE). From February 2006 to November 2010, AIV surveillance was conducted at three locations on the Atlantic coast of Brazil: one site in the Amazon region within the state of Pará (Ilha de Canelas) and two sites on the northeastern coast in the states of Maranhão and Pernambuco (villages of Cururupu and Ilha de Itamaracá, respectively) (<xref ref-type="fig" rid="pone-0110141-g001"><bold>Figure 1</bold></xref>).</p></sec><sec id="s2b"><title>Sample collection</title><p>We collected orotrachael and cloacal swabs from birds captured by a mist net. Paired orotrachael and cloacal swabs were combined in the same vial with Virus Transport Media (VTM), which consisted of PBS-balanced salt solution supplemented with 0.5% bovine albumin (BSA), antimicrobial agents (200 U/mL penicillin G, 200 U/mL streptomycin, 25 µg/mL fungisone and 6 µg/mL gentamycin) and 10% glycerol. In addition, fresh fecal samples from shorebirds were collected from the ground after identification of the source taxon and placed in vials containing VTM. The samples were stored in dry shippers (liquid nitrogen) and then stored in the laboratory at −80°C until processed.</p></sec><sec id="s2c"><title>Avian influenza virus detection</title><p>The samples were analyzed at the Microbiology BSL3<sup>+</sup> Laboratory at the Biomedical Sciences Institute of the University of São Paulo. RNA was extracted from the orotrachael and cloacal swabs of the birds using the QIAmp RNeasy mini kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions. The samples were screened by real-time RT-PCR (rRT-PCR) using an AIV-M TaqMan Reagents Kit (Applied Biosystems, Foster City, CA, USA) <xref rid="pone.0110141-Curd1" ref-type="bibr">[26]</xref>.</p></sec><sec id="s2d"><title>Virus isolation</title><p>All samples that tested positive for the Influenza A virus matrix gene were subsequently submitted to the Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA for viral isolation using standard methods through inoculation in ten-day-old, embryonated chicken eggs <xref rid="pone.0110141-Shortridge1" ref-type="bibr">[27]</xref>. Each positive isolation was confirmed with an Avian Influenza Virus Type A Test Kit (Flu-DetectH<sup>®</sup> Synbiotics, San Diego, CA) <xref rid="pone.0110141-Das1" ref-type="bibr">[28]</xref>. Subtyping was performed using hemagglutination and neuraminidase inhibition tests and a panel of polyclonal reference sera <xref rid="pone.0110141-AymardHenry1" ref-type="bibr">[29]</xref>–<xref rid="pone.0110141-Webster1" ref-type="bibr">[31]</xref>. In addition, sequencing of the HA and NA genes of the isolates was performed.</p></sec><sec id="s2e"><title>RNA extraction and sequencing</title><p>Viral RNA was extracted from 400 µL of allantoic fluid with an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Extracted RNA was eluted in 80 µL of RNase-free water. The cDNA was transcribed using a High-Capacity cDNA Archive Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's directions. The full-length HA (1778 bp) and NA (1413 bp) genomic segments were sequenced using specific primers (<xref ref-type="table" rid="pone-0110141-t001"><bold>Table 1</bold></xref><bold>and</bold><xref ref-type="table" rid="pone-0110141-t002"><bold>Table 2</bold></xref>) on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems/Life Technologies) and the Big Dye Terminator v3.1 Cycle Sequencing Kit (Life Technologies) at the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital (Memphis, TN, USA).</p><table-wrap id="pone-0110141-t001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.t001</object-id><label>Table 1</label><caption><title>Primers used to sequence the complete HA gene.</title></caption><alternatives><graphic id="pone-0110141-t001-1" xlink:href="pone.0110141.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Sequence</td><td align="left" rowspan="1" colspan="1">Oligonucleotide Position (nt)</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">5′ GGA<named-content content-type="gene"> GTT CAC CAT CCT GCA ACT CT</named-content> 3′</td><td align="left" rowspan="1" colspan="1">H11-580</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ <named-content content-type="gene">TTC CTT TAG AGT TGC AGG ATG GTG</named-content> 3′</td><td align="left" rowspan="1" colspan="1">H11-600R</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ AA<named-content content-type="gene">C CAC CTT TCA TGA AAC CAG CTA TTG C</named-content> 3′</td><td align="left" rowspan="1" colspan="1">H11-1080R</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ <named-content content-type="gene">ACA GCT TCT CGT TTT ACT TGA AAA TGA</named-content> 3′</td><td align="left" rowspan="1" colspan="1">H11-1330</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ CAT<named-content content-type="gene"> TTT CAA GTA AAA CGA GAA GCT GTG CA</named-content> 3′</td><td align="left" rowspan="1" colspan="1">H11-1350R</td></tr></tbody></table></alternatives></table-wrap><table-wrap id="pone-0110141-t002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.t002</object-id><label>Table 2</label><caption><title>Primers used to sequence the complete NA gene.</title></caption><alternatives><graphic id="pone-0110141-t002-2" xlink:href="pone.0110141.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Sequence</td><td align="left" rowspan="1" colspan="1">Oligonucleotide Position (nt)</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">5′ TAT<named-content content-type="gene"> TCG TCT CAG GGA GCA AAA GCA GGG TC</named-content> 3′</td><td align="left" rowspan="1" colspan="1">‘Bm-N9-1</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ATA <named-content content-type="gene">TCG TCT CGT ATT AGT AGA AAC AAG GGT CTT</named-content> 3′</td><td align="left" rowspan="1" colspan="1">‘Bm-N9-1467R</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ ATA<named-content content-type="gene"> AAT TCA TGG CAC ATA TAT GG</named-content> 3′</td><td align="left" rowspan="1" colspan="1">N9×300</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ GTC<named-content content-type="gene"> AAG TAC TAG TTG CCA TGA TG</named-content> 3′</td><td align="left" rowspan="1" colspan="1">N9×560</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ CAT<named-content content-type="gene"> CAT GGC AAC TAG TAC TTG AC</named-content> 3′</td><td align="left" rowspan="1" colspan="1">N9×580R</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ <named-content content-type="gene">GGA TAA TTG GCA GGG CTC AAA TAG</named-content> 3′</td><td align="left" rowspan="1" colspan="1">N9×900</td></tr><tr><td align="left" rowspan="1" colspan="1">5′ GAT<named-content content-type="gene"> CTT GAA GCT GTG CTT ATT GT</named-content> 3′</td><td align="left" rowspan="1" colspan="1">N9×1137R</td></tr></tbody></table></alternatives></table-wrap></sec><sec id="s2f"><title>Genetic characterization and phylogenetic tree of the HA and NA genes</title><p>Nucleotide-level searches were performed for each genome segment of each virus isolate using the Basic Local Alignment Search Tool (BLAST) to identify the most closely related sequences available in public databases <xref rid="pone.0110141-Zhang1" ref-type="bibr">[32]</xref>. The sequences were initially aligned using the Bioedit Sequence Alignment Editor (v.7.1.5.0) (Ibis Biosciences Carlsbad, CA), and the nucleotide percentage similarities were calculated using the MegAlign program of the DNASTAR package (DNASTAR, Inc.).</p><p>To elucidate the relationships between the viruses isolated in this study, a phylogenetic analysis of the HA and NA genes, including all available H11 and N9 subtype influenza gene sequences between 2007–2009 in North America and other regions was performed. Phylogenetic analyses of the HA and NA genes were performed for specific-subtype group characterization using only the open reading frames (ORFs) of each segment, and the trees were generated by PAUP 4.0b10 using the maximum likelihood algorithm with the parameters indicated by the GTR Modeltest. Levels of bootstrap are shown for major clades <xref rid="pone.0110141-Swofford1" ref-type="bibr">[33]</xref> The sequences of the segments from the three isolates of influenza A virus were deposited with the following GenBank accession numbers for HA: KF824501 (A08), KF824502 (A17) and KF824503 (A51) and NA: KF824504 (A08), KF824505 (A17) and KF824506 (A51).</p></sec><sec id="s2g"><title>Ethics Statement</title><p>All procedures involving wild birds were approved by the Brazilian Society of Laboratory Animal Science (SBCAL) of the University of Sao Paulo (Permit Number: 105, page 74, book 2) and licensed by the Ministério do Meio Ambiente-MMA at the Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio/SISBIO), Number 25895-1.</p></sec></sec><sec id="s3"><title>Results</title><p>A total of 556 birds from 23 different species, representing 14 different families of the order Charadriiformes, were sampled (<xref ref-type="table" rid="pone-0110141-t003"><bold>Table 3</bold></xref>). Most of these species were migratory. AIV was only detected in ruddy turnstones (n = 4/68), all in Ilha de Canelas, Amazon region (Pará State) at the beginning of the wintering period in November 2008, using rRT-PCR amplification of the influenza A matrix gene. The proportion of ruddy turnstone that was infected with AIV was 5.8%. Of the four influenza A-positive samples, virus was isolated from three. BLAST searches of the surface glycoprotein genes of the three isolates from ruddy turnstones confirmed 94 to 99% sequence similarity to HA of the H11 subtypes, and all three isolates were 99% similar to Influenza A virus (A/ruddy turnstone/New Jersey/AI09-194/2009 (H11N8); ID: CY145907-1). The isolates were also 94 to 99% similar to NA of subtype N9 and 99% similar to Influenza A virus (A/shorebird/Delaware Bay/351/2009(H1N9); ID: CY137916.1) (<xref ref-type="table" rid="pone-0110141-t004"><bold>Table 4</bold></xref><bold> and </bold><xref ref-type="table" rid="pone-0110141-t005"><bold>Table 5</bold></xref>).</p><table-wrap id="pone-0110141-t003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.t003</object-id><label>Table 3</label><caption><title>Surveillance of influenza A viruses in wild birds in Brazil by real-time RT-PCR.</title></caption><alternatives><graphic id="pone-0110141-t003-3" xlink:href="pone.0110141.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><col align="center" span="1"></col><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">Site</td><td align="left" rowspan="1" colspan="1">Date</td><td align="left" rowspan="1" colspan="1">Scientific name</td><td align="left" rowspan="1" colspan="1">Sample<xref ref-type="table-fn" rid="nt101">*</xref></td><td align="left" rowspan="1" colspan="1">No. pos./No. birds</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Ilha de Canelas, PA</td><td align="left" rowspan="1" colspan="1">Nov. 06</td><td align="left" rowspan="1" colspan="1"><italic>Actitis macularius</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/10</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"><italic>Calidris canutus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/3</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"><italic>Calidris minutilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Sterna hirundo</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/4</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"><italic>Larus</italic> sp.</td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</td></tr><tr><td align="left" rowspan="1" colspan="1">Ajuruteua, PA</td><td align="left" rowspan="1" colspan="1">Nov. 06</td><td align="left" rowspan="1" colspan="1"><italic>Actitis macularius</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/5</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/2</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"><italic>Charadrius semipalmatus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</td></tr><tr><td align="left" rowspan="1" colspan="1">Ilha de Itamaracá, PE</td><td align="left" rowspan="1" colspan="1">Apr. 07</td><td align="left" rowspan="1" colspan="1"><italic>Arenaria interpres</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/7</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"><italic>Calidris alba</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/8</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/5</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"><italic>Charadrius semipalmatus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/3</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"><italic>Limnodromus griseus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Sterna hirundo</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</td></tr><tr><td align="left" rowspan="1" colspan="1">Ilha de Itamaracá, PE</td><td align="left" rowspan="1" colspan="1">Aug. 08</td><td align="left" rowspan="1" colspan="1"><italic>Charadrius semipalmatus/C. alba/A. interpres</italic></td><td align="left" rowspan="1" colspan="1">F</td><td align="left" rowspan="1" colspan="1">0/100</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"><italic>Sterna hirundo/Thalasseus sandvicensis</italic></td><td align="left" rowspan="1" colspan="1">F</td><td align="left" rowspan="1" colspan="1">0/64</td></tr><tr><td align="left" rowspan="1" colspan="1">Ilha de Itamaracá, PE</td><td align="left" rowspan="1" colspan="1">Oct. 08</td><td align="left" rowspan="1" colspan="1"><italic>Arenaria interpres</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/5</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"><italic>C. pusilla/A. interpres/C. alba/Pluvialis squatarola</italic></td><td align="left" rowspan="1" colspan="1">F</td><td align="left" rowspan="1" colspan="1">0/18</td></tr><tr><td align="left" rowspan="1" colspan="1">Ilha de Canela, PA</td><td align="left" rowspan="1" colspan="1">Nov. 08</td><td align="left" rowspan="1" colspan="1"><italic>Actitis macularius</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/31</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"><bold><italic>Arenaria interpres</italic></bold></td><td align="left" rowspan="1" colspan="1"><bold>C & O</bold></td><td align="left" rowspan="1" colspan="1"><bold>4/22</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"><italic>Calidris alba</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/2</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"><italic>Limnodromus griseus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/9</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"><italic>Tringa melanoleuca</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Charadrius semipalmatus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Gelochelidon nilotica</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</td></tr><tr><td align="left" rowspan="1" colspan="1">Cururupu, MA</td><td align="left" rowspan="1" colspan="1">May. 10</td><td align="left" rowspan="1" colspan="1"><italic>Actitis macularius</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/27</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"><italic>Arenaria interpres</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/12</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/98</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"><italic>Calidris canutus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/7</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"><italic>Limnodromus griseus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Vanellus chilensis</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/10</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"><italic>Charadrius collaris</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/6</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"><italic>Charadrius semipalmatus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/6</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"><italic>Haematopus palliatus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/6</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"><italic>Himantopus mexicanus</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/25</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"><italic>Chroicocephalus maculipennis</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Gelochelidon nilotica</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/4</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"><italic>Stercorarius skua</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/2</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"><italic>Jacana</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/2</td></tr><tr><td align="left" rowspan="1" colspan="1">Ilha de Itamaracá, PE</td><td align="left" rowspan="1" colspan="1">Oct. 10</td><td align="left" rowspan="1" colspan="1"><italic>Arenaria interpres</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/25</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"><italic>Calidris pusilla</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/11</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"><italic>Calidris alba</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/1</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"><italic>Sterna hirundo</italic></td><td align="left" rowspan="1" colspan="1">C & O</td><td align="left" rowspan="1" colspan="1">0/3</td></tr><tr><td align="left" rowspan="1" colspan="1">Total</td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><italic>21 species</italic></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">4/556</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="nt101"><label></label><p>*Sample type: C = Cloacal, O = Oral and F = Feces.</p></fn></table-wrap-foot></table-wrap><table-wrap id="pone-0110141-t004" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.t004</object-id><label>Table 4</label><caption><title>The closest sequences to HA of influenza A virus available in public databases based on percent nucleotide similarity.</title></caption><alternatives><graphic id="pone-0110141-t004-4" xlink:href="pone.0110141.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><col align="center" span="1"></col></colgroup><thead><tr><td align="left" rowspan="1" colspan="1">GenBank ID</td><td align="left" rowspan="1" colspan="1">Sequence name</td><td align="left" rowspan="1" colspan="1">A08/2008 (H11) [208614]</td><td align="left" rowspan="1" colspan="1">A17/2008 (H11) [208615]</td><td align="left" rowspan="1" colspan="1">A51/2008 (H11) [208617]</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">CY145907.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/AI09-194/2009(H11N8)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY145437.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/Sg-00557/2008(H11N5)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY145711.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/Sg-00564/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY127871.1</td><td align="left" rowspan="1" colspan="1">A/shorebird/Delaware Bay/257/2009(H11N8)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY127887.1</td><td align="left" rowspan="1" colspan="1">A/shorebird/Delaware Bay/549/2009(H11N1)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY145719.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/Sg-00567/2008(H11N2)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY145955.1</td><td align="left" rowspan="1" colspan="1">A/herring gull/New Jersey/AI09-335/2009(H11N1)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY138137.1</td><td align="left" rowspan="1" colspan="1">A/lesser black-backed gull/Iceland/145/2010(H11N2)</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">98%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY039532.1</td><td align="left" rowspan="1" colspan="1">A/green winged teal/California/AKS1305/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">97%</td></tr><tr><td align="left" rowspan="1" colspan="1">KF542875.1</td><td align="left" rowspan="1" colspan="1">A/Anas acuta/New Mexico/A00629381/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">96%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY096624.1</td><td align="left" rowspan="1" colspan="1">A/blue-winged teal/Guatemala/CIP049-10/2009(H11N2)</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">95%</td></tr><tr><td align="left" rowspan="1" colspan="1">HM193587.1</td><td align="left" rowspan="1" colspan="1">A/mallard/Alaska/44430-056/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">95%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY127638.1</td><td align="left" rowspan="1" colspan="1">A/mallard/Alberta/193/2000(H11N9)</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">94%</td></tr></tbody></table></alternatives></table-wrap><table-wrap id="pone-0110141-t005" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.t005</object-id><label>Table 5</label><caption><title>The closest sequences to NA of influenza A virus available in public databases based on percent nucleotide similarity.</title></caption><alternatives><graphic id="pone-0110141-t005-5" xlink:href="pone.0110141.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 align="left" rowspan="1" colspan="1">GenBank ID</td><td align="left" rowspan="1" colspan="1">Sequence name</td><td align="left" rowspan="1" colspan="1">A08/2008 (N9) [208614]</td><td align="left" rowspan="1" colspan="1">A17/2008 (N9) [208615]</td><td align="left" rowspan="1" colspan="1">A51/2008 (N9) [208617]</td></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">CY137916.1</td><td align="left" rowspan="1" colspan="1">(A/shorebird/Delaware Bay/351/2009(H1N9)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY146281.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/AI09-1082/2009(H1N9)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY145689.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/Sg-00561/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY146289.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/AI09-1144/2009(H11N9)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY038237.1</td><td align="left" rowspan="1" colspan="1">A/ruddy turnstone/New Jersey/Sg-00561/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">99%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY125351.1</td><td align="left" rowspan="1" colspan="1">A/ring-necked duck/New Brunswick/03449/2009(H11N9)</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">98%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY004368.1</td><td align="left" rowspan="1" colspan="1">A/mallard/Alberta/245/2003(H11N9)</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">97%</td></tr><tr><td align="left" rowspan="1" colspan="1">CY144334.1</td><td align="left" rowspan="1" colspan="1">A/red knot/Delaware/650666/2002(H11N9)</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">96%</td></tr><tr><td align="left" rowspan="1" colspan="1">JF323789.1</td><td align="left" rowspan="1" colspan="1">A/Steller's eider/Alaska/44422-253/2008(H11N9)</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">94%</td></tr></tbody></table></alternatives></table-wrap><p>The high similarity between the isolates and the formation of a clade indicates that these isolates are closely related. The HA and NA genes segments were most closely related to North American avian lineage viruses from New Jersey and Delaware Bay from 2009 (99% identity). The phylogenetic tree shows that these isolates are grouped in a different cluster from others H11 and N9 subtypes viruses and supported with high bootstrap values (<xref ref-type="fig" rid="pone-0110141-g002"><bold>Figure 2</bold></xref><bold> and </bold><xref ref-type="fig" rid="pone-0110141-g003"><bold>Figure 3</bold></xref>). In addition, we analyzed the isolates with sequences available from other continents (see <bold><xref ref-type="supplementary-material" rid="pone.0110141.s001">Figure S1</xref> and <xref ref-type="supplementary-material" rid="pone.0110141.s002">Figure S2</xref></bold>).</p><fig id="pone-0110141-g002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.g002</object-id><label>Figure 2</label><caption><title>Phylogenetic analysis of the hemagglutinin gene of the influenza A virus.</title><p>Trees were generated by PAUP 4.0b10 using the maximum likelihood algorithm with the parameters indicated by the GTR Modeltest (bootstrap values are shown for the branch points). The scale bar is shown on the bottom left. In this study, sequences that were available in the public database were used to construct the tree, and the accession numbers along with their branch data are shown.</p></caption><graphic xlink:href="pone.0110141.g002"></graphic></fig><fig id="pone-0110141-g003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0110141.g003</object-id><label>Figure 3</label><caption><title>Phylogenetic analysis of neuraminidase of the influenza A virus.</title><p>Trees were generated by PAUP 4.0b10 using the maximum likelihood algorithm with the parameters indicated by the GTR Modeltest (bootstrap values are shown for the branch points). The scale bar is shown on the bottom left. In this study, sequences that were available in public databases were used to construct the tree, and the accession numbers along with their branch data are shown.</p></caption><graphic xlink:href="pone.0110141.g003"></graphic></fig></sec><sec id="s4"><title>Discussion</title><p>Ilha de Canelas is an important stopover for migratory shorebirds in South America <xref rid="pone.0110141-Blanco1" ref-type="bibr">[34]</xref> and the only site in our study where AIV was detected. During our surveillance sampling effort, we detected AIV only in ruddy turnstones, which was consistent with other studies that found ruddy turnstones to be frequently infected with AIV <xref rid="pone.0110141-Gaidet1" ref-type="bibr">[5]</xref>, <xref rid="pone.0110141-Krauss1" ref-type="bibr">[7]</xref>. Reports indicate that AIV may occur at higher rates in ruddy turnstones than in other Scolopacidae <xref rid="pone.0110141-Hanson1" ref-type="bibr">[15]</xref>. H11 in combination with various NA subtypes has been reported throughout 2000–2010 in Asia <xref rid="pone.0110141-Okamatsu1" ref-type="bibr">[35]</xref>, <xref rid="pone.0110141-Karamendin1" ref-type="bibr">[36]</xref>, Europe <xref rid="pone.0110141-Munster1" ref-type="bibr">[37]</xref>–<xref rid="pone.0110141-Hoye1" ref-type="bibr">[39]</xref>, the USA and Canada <xref rid="pone.0110141-Senne1" ref-type="bibr">[40]</xref> as well as Central America <xref rid="pone.0110141-GonzlezReiche1" ref-type="bibr">[14]</xref>. It is therefore not surprising to find H11 in Brazil.</p><p>Previous outbreaks of highly pathogenic influenza in the Americas have originated from the introduction of low-pathogenic H5 or H7 precursors making their way into poultry populations with subsequent evolution to a highly pathogenic form <xref rid="pone.0110141-Senne1" ref-type="bibr">[40]</xref>. Although these two subtypes of greatest concern have not been detected in Brazil, the low number of subtypes that have been isolated in comparison with other countries raises the question as to whether the current surveillance strategy is adequately determining the full range of subtypes in the region. Thus, exploration of other possible sampling sites and species is warranted.</p><p>Our results suggest that it is possible for ruddy turnstones to carry AIV from the northern hemisphere to their wintering sites in South America. The virus was only detected during the arrival of the birds in Brazil, and we did not detect AIV in other shorebird species that occur in sympatry with the ruddy turnstones in Brazil. This raises the question as to whether there are inter-species transmission barriers among shorebird species. H11 was not a predominant HA subtype detected in shorebirds at Delaware Bay <xref rid="pone.0110141-Hanson1" ref-type="bibr">[15]</xref>, <xref rid="pone.0110141-Stallknecht2" ref-type="bibr">[41]</xref>. However, H11N9 AIVs have been detected (2002–2004, 2007–2009) in shorebirds at Delaware Bay in long-term monitoring studies. The existence of shared AIV subtypes in shorebirds between the South and North American staging sites suggests that virus exchange may occur between the two continents.</p><p><italic>Arenaria interpres</italic> is a long-distance migratory bird with circumpolar distribution. This species breeds in northeastern Alaska and the Canadian Arctic and then moves along the Pacific and Atlantic coasts toward Central and South America <xref rid="pone.0110141-Rodrigues1" ref-type="bibr">[11]</xref>. Delaware Bay represents a globally important site where AIV isolations from shorebirds (Scolopacidae) have consistently been reported <xref rid="pone.0110141-Krauss1" ref-type="bibr">[7]</xref>, <xref rid="pone.0110141-Zhang1" ref-type="bibr">[32]</xref>. Previous work showed that ruddy turnstone (<italic>Arenaria interpres</italic>) represented 40% of all AIV isolates, even though only 11.2% of the sampled birds were of the Charadriiformes order <xref rid="pone.0110141-Hanson1" ref-type="bibr">[15]</xref>, <xref rid="pone.0110141-Kawaoka1" ref-type="bibr">[42]</xref>. The combination of HA and NA that was most frequently isolated from shorebirds included H3N8 (7.1%) and H11N9 (7.6%) <xref rid="pone.0110141-Krauss2" ref-type="bibr">[43]</xref>.</p><p>Our work was performed over five years during two distinct time periods: the time of arrival of birds from the Northern Hemisphere in November and the time of return in April <xref rid="pone.0110141-Kober1" ref-type="bibr">[44]</xref>. Our results confirm the presence of low-pathogenic influenza A virus in wild birds during the arrival period in Brazil. The phylogenetic analysis of the HA and NA viral sequences revealed that the AIV isolates are of the H11N9 group and exhibit high similarity (99%) to viruses of the North American lineage found in shorebirds. One limitation of this study is not including the full virus genomes that would allow for more in depth molecular characterization for a better understanding of the eco-epidemiology and transcontinental transport of these viruses.</p><p>In Brazil, a small number of groups have worked with AIV in wild birds. Extensive data on the patterns of AI virus infection in wild birds only exist for Europe and North America <xref rid="pone.0110141-Stallknecht1" ref-type="bibr">[3]</xref>, <xref rid="pone.0110141-Munster1" ref-type="bibr">[37]</xref>, where the majority of surveillance has traditionally been focused, and similar information for many parts of the Southern Hemisphere is lacking <xref rid="pone.0110141-Gaidet1" ref-type="bibr">[5]</xref>, <xref rid="pone.0110141-Gaidet2" ref-type="bibr">[45]</xref>. The patterns of AIV circulation that are observed in Europe and North America cannot be directly transposed to the Southern Hemisphere, particularly to tropical regions, where differences in host ecology, climate and seasonality may produce different dynamics of infection <xref rid="pone.0110141-Gaidet2" ref-type="bibr">[45]</xref>.</p><p>The presence of AIV in wild birds in South America has been confirmed, and the detection or isolation of LPAI viruses in the following countries has been shown: subtypes H13N9, H1N1 and H6N2 <xref rid="pone.0110141-Pereda1" ref-type="bibr">[46]</xref>–<xref rid="pone.0110141-Rimondi1" ref-type="bibr">[48]</xref> were isolated in Argentina; H7N3 was isolated in Bolivia and Chile <xref rid="pone.0110141-Senne1" ref-type="bibr">[40]</xref>, <xref rid="pone.0110141-Spackman1" ref-type="bibr">[49]</xref>; H3 was isolated in Brazil <xref rid="pone.0110141-Arajo1" ref-type="bibr">[25]</xref>, <xref rid="pone.0110141-Kawamoto1" ref-type="bibr">[50]</xref>; H5N2 was isolated in Colombia <xref rid="pone.0110141-Karlsson1" ref-type="bibr">[51]</xref>; and H3N8, H4N5, H10N9 and H13N2 were isolated in Peru <xref rid="pone.0110141-Ghersi1" ref-type="bibr">[13]</xref>, <xref rid="pone.0110141-Ghersi2" ref-type="bibr">[52]</xref>, <xref rid="pone.0110141-Williams1" ref-type="bibr">[53]</xref>.</p></sec><sec id="s5"><title>Conclusion</title><p>An effective surveillance program for Influenza A viruses in migratory bird species may alert public health authorities of potential human and domestic animal pathogens and facilitate the implementation of response measures in Brazil.</p><p>The results of our surveillance of migratory birds demonstrated high similarity in the HA and NA genes to viruses of the North American lineage found in shorebirds.</p></sec><sec id="s6"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pone.0110141.s001"><label>Figure S1</label><caption><p><bold>Phylogenetic analysis of the hemagglutinin gene of the influenza A virus with sequences available from other continents.</bold> The accession numbers along with their branch data are shown.</p><p>(TIFF)</p></caption><media xlink:href="pone.0110141.s001.tiff"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0110141.s002"><label>Figure S2</label><caption><p><bold>Phylogenetic analysis of neuraminidase of the influenza A virus with sequences available from other continents.</bold> The scale bar is shown on the bottom left. The accession numbers along with their branch data are shown.</p><p>(TIFF)</p></caption><media xlink:href="pone.0110141.s002.tiff"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec><sec id="s7"><title>Biographical Sketch</title><p>Dr. Jansen de Araujo has a Ph.D. in Microbiology and is the coordinator of the field team in the Virology Laboratory at the Biomedical Science Institute. His research interests include ecoepidemiological studies of wildlife and emerging infectious diseases with zoonotic potential in Brazil.</p></sec></body><back><ack><p>We acknowledge the Ministério da Agricultura, Pecuária e Abastecimento (MAPA) and Centro Nacional de Pesquisa e Conservação das Aves Silvestres (CEMAVE) for supporting the logistic work and the Universidade Federal Rural de Pernambuco, Universidade Federal de Pernambuco, Universidade do Vale do Itajaí and Universidade de São Paulo for institutional support.</p><p>We would like to thank Dr. Andrew Ramey for valuable comments as a referee on an earlier version of this manuscript.</p></ack><ref-list><title>References</title><ref id="pone.0110141-Olsen1"><label>1</label><mixed-citation publication-type="journal"><name><surname>Olsen</surname><given-names>B</given-names></name>, <name><surname>Munster</surname><given-names>VJ</given-names></name>, <name><surname>Wallensten</surname><given-names>A</given-names></name>, 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