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Title: Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh

Abstract

Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh weremore » phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. Here these findings, combined with the seven year timeframe of sampling, indicate a continuous circulation of these viruses in the country.« less

Authors:
 [1];  [2];  [1];  [1];  [2];  [2];  [2];  [2];  [3];  [4];  [2];  [2];  [1];  [1];  [5];  [1];  [6]
  1. Centers for Disease Control and Prevention, Atlanta, GA (United States)
  2. International Centre for Diarrhoeal Disease Research, Dhaka (Bangladesh)
  3. Ministry of Fisheries and Livestock, Dhaka (Bangladesh)
  4. EcoHealth Alliance, New York, NY (United States)
  5. Centers for Disease Control and Prevention, Atlanta, GA (United States); International Centre for Diarrhoeal Disease Research, Dhaka (Bangladesh)
  6. Linneaus Univ. (Sweden)
Publication Date:
Research Org.:
Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1377073
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 3; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; H7N9; Animal phylogenetics; Poultry; Bird genetics; Microbial genetics; Viral pathogens; Birds; Bangladesh

Citation Formats

Gerloff, Nancy A., Khan, Salah Uddin, Zanders, Natosha, Balish, Amanda, Haider, Najmul, Islam, Ausraful, Chowdhury, Sukanta, Rahman, Mahmudur Ziaur, Haque, Ainul, Hosseini, Parviez, Gurley, Emily S., Luby, Stephen P., Wentworth, David E., Donis, Ruben O., Sturm-Ramirez, Katharine, Davis, C. Todd, and Waldenstrom, Jonas. Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0152131.
Gerloff, Nancy A., Khan, Salah Uddin, Zanders, Natosha, Balish, Amanda, Haider, Najmul, Islam, Ausraful, Chowdhury, Sukanta, Rahman, Mahmudur Ziaur, Haque, Ainul, Hosseini, Parviez, Gurley, Emily S., Luby, Stephen P., Wentworth, David E., Donis, Ruben O., Sturm-Ramirez, Katharine, Davis, C. Todd, & Waldenstrom, Jonas. Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh. United States. doi:10.1371/journal.pone.0152131.
Gerloff, Nancy A., Khan, Salah Uddin, Zanders, Natosha, Balish, Amanda, Haider, Najmul, Islam, Ausraful, Chowdhury, Sukanta, Rahman, Mahmudur Ziaur, Haque, Ainul, Hosseini, Parviez, Gurley, Emily S., Luby, Stephen P., Wentworth, David E., Donis, Ruben O., Sturm-Ramirez, Katharine, Davis, C. Todd, and Waldenstrom, Jonas. Thu . "Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh". United States. doi:10.1371/journal.pone.0152131. https://www.osti.gov/servlets/purl/1377073.
@article{osti_1377073,
title = {Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh},
author = {Gerloff, Nancy A. and Khan, Salah Uddin and Zanders, Natosha and Balish, Amanda and Haider, Najmul and Islam, Ausraful and Chowdhury, Sukanta and Rahman, Mahmudur Ziaur and Haque, Ainul and Hosseini, Parviez and Gurley, Emily S. and Luby, Stephen P. and Wentworth, David E. and Donis, Ruben O. and Sturm-Ramirez, Katharine and Davis, C. Todd and Waldenstrom, Jonas},
abstractNote = {Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. Here these findings, combined with the seven year timeframe of sampling, indicate a continuous circulation of these viruses in the country.},
doi = {10.1371/journal.pone.0152131},
journal = {PLoS ONE},
number = 3,
volume = 11,
place = {United States},
year = {Thu Mar 24 00:00:00 EDT 2016},
month = {Thu Mar 24 00:00:00 EDT 2016}
}

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