Diversity of A(H5N1) clade 2.3.2.1c avian Influenza viruses with evidence of reassortment in Cambodia, 2014-2016

Suttie, Annika, Tok, Songha, Yann, Sokhoun, Keo, Ponnarath, Horm, Srey Viseth, Roe, Merryn, Kaye, Matthew, Sorn, San, Holl, Davun, Tum, Sothyra, Buchy, Philippe, Barr, Ian, Hurt, Aeron, Greenhill, Andrew R., Karlsson, Erik A., Vijaykrishna, Dhanasekaran, Deng, Yi-Mo, Dussart, Philippe, and Horwood, Paul F. (2019) Diversity of A(H5N1) clade 2.3.2.1c avian Influenza viruses with evidence of reassortment in Cambodia, 2014-2016. PLoS ONE, 14 (12). e0226108.

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Abstract

In Cambodia, highly pathogenic avian influenza A(H5N1) subtype viruses circulate endemically causing poultry outbreaks and zoonotic human cases. To investigate the genomic diversity and development of endemicity of the predominantly circulating clade 2.3.2.1c A(H5N1) viruses, we characterised 68 AIVs detected in poultry, the environment and from a single human A(H5N1) case from January 2014 to December 2016. Full genomes were generated for 42 A(H5N1) viruses. Phylogenetic analysis shows that five clade 2.3.2.1c genotypes, designated KH1 to KH5, were circulating in Cambodia during this period. The genotypes arose through multiple reassortment events with the neuraminidase (NA) and internal genes belonging to H5N1 clade 2.3.2.1a, clade 2.3.2.1b or A(H9N2) lineages. Phylogenies suggest that the Cambodian AIVs were derived from viruses circulating between Cambodian and Vietnamese poultry. Molecular analyses show that these viruses contained the hemagglutinin (HA) gene substitutions D94N, S133A, S155N, T156A, T188I and K189R known to increase binding to the human-type α2,6-linked sialic acid receptors. Two A(H5N1) viruses displayed the M2 gene S31N or A30T substitutions indicative of adamantane resistance, however, susceptibility testing towards neuraminidase inhibitors (oseltamivir, zanamivir, lananmivir and peramivir) of a subset of thirty clade 2.3.2.1c viruses showed susceptibility to all four drugs. This study shows that A(H5N1) viruses continue to reassort with other A(H5N1) and A(H9N2) viruses that are endemic in the region, highlighting the risk of introduction and emergence of novel A(H5N1) genotypes in Cambodia.

Item ID: 61393
Item Type: Article (Research - C1)
ISSN: 1932-6203
Keywords: avian influenza, poultry, Phylogenetic analysis, viral genomics, Cambodia, population genetics.
Copyright Information: © 2019 Suttie et al. 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 credited.
Funders: Office of the Assistant Secretary for Preparedness and Response, USA, US Agency for International Development (USAID), UK Research and Innovation Global Challenges Research Fund to The Consortium of Animal Market Networks to Assess Risk of Emerging Infectious Diseases Through Enhanced Surveillance (CANARIES)
Projects and Grants: IDSEP140020-01-00, USAID grant no. AID-442-G-14-00005, CANARIES; grant No. GCRFNGR3\1497
Date Deposited: 24 Jan 2020 03:52
FoR Codes: 07 AGRICULTURAL AND VETERINARY SCIENCES > 0707 Veterinary Sciences > 070712 Veterinary Virology @ 100%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences @ 100%
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