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Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014

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ABSTRACT

Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngeal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4–6.0). Subtyping was performed on 468 pooled swabs with M gene Ct < 26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of interaction between H9 and H5 virus detection rates. We sequenced 17 whole genomes of A/H9N2, 2 of A/H5N6, and 11 partial genomes. All H9N2 viruses had internal genes that clustered with genotype 57 and were closely related to Chinese human isolates of A/H7N9 and A/H10N8. Using a nucleotide divergence cutoff of 98%, we identified 9 distinct H9 genotypes. Phylogenetic analysis suggested multiple introductions of H9 viruses to northern Vietnam rather than in-situ transmission. Further investigations of H9 prevalence and diversity in other regions of Vietnam are warranted to assess H9 endemicity elsewhere in the country.

No MeSH data available.


Genotype constellations for H9N2. Segments of different colours represent > 2% nucleotide difference. Different genotypes were assigned an arbitrary ‘Vietnam genotype #’ (VNG#).
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f0015: Genotype constellations for H9N2. Segments of different colours represent > 2% nucleotide difference. Different genotypes were assigned an arbitrary ‘Vietnam genotype #’ (VNG#).

Mentions: Each of the 17 whole genomes of H9N2 possessed the G57-like internal gene cassette, similar to zoonotic H7N9 and H10N8 viruses in mainland China. For example, the genes most closely related to the PB2 and PB1 segments of H7F-14-BN4-437 belonged to the human H10N8 and H7N9 isolates, A/Jiangxi/IPB13/2013(H10N8) and A/Guangdong/04/2013(H7N9) with percentage nucleotide homologies of 99.6% and 99.5% respectively. Additionally H7F-14-CB4-2, H7F-14-CB4-29, H7F-14-CB4-31 and H7F-14-CB4-34 possessed PB1 and NS genes closely related to human and avian H7N9 isolates from 2013 with homologies of over 99.9%, and their PA, NP and MP genes were related to H10N8 viruses with homologies > 99.3%. Using an > 98% nucleotide difference cutoff for each segment, we determined patterns of clustering at the sub-genotype level, and identified 9 distinct sub-genotypes, all of which appeared to be reassortants between closely related H9N2 viruses (Fig. 3). (For reference, the comparable divergence level used for clade designations in H5 viruses is 1.5%) (WHO/OIE/FAO, 2012). Previous investigations of nucleotide substitution rates of H9N2 viruses have suggested that 2% divergence signifies approximately 4.5 to 9 years of evolution (Fusaro et al., 2011).


Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014
Genotype constellations for H9N2. Segments of different colours represent > 2% nucleotide difference. Different genotypes were assigned an arbitrary ‘Vietnam genotype #’ (VNG#).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036934&req=5

f0015: Genotype constellations for H9N2. Segments of different colours represent > 2% nucleotide difference. Different genotypes were assigned an arbitrary ‘Vietnam genotype #’ (VNG#).
Mentions: Each of the 17 whole genomes of H9N2 possessed the G57-like internal gene cassette, similar to zoonotic H7N9 and H10N8 viruses in mainland China. For example, the genes most closely related to the PB2 and PB1 segments of H7F-14-BN4-437 belonged to the human H10N8 and H7N9 isolates, A/Jiangxi/IPB13/2013(H10N8) and A/Guangdong/04/2013(H7N9) with percentage nucleotide homologies of 99.6% and 99.5% respectively. Additionally H7F-14-CB4-2, H7F-14-CB4-29, H7F-14-CB4-31 and H7F-14-CB4-34 possessed PB1 and NS genes closely related to human and avian H7N9 isolates from 2013 with homologies of over 99.9%, and their PA, NP and MP genes were related to H10N8 viruses with homologies > 99.3%. Using an > 98% nucleotide difference cutoff for each segment, we determined patterns of clustering at the sub-genotype level, and identified 9 distinct sub-genotypes, all of which appeared to be reassortants between closely related H9N2 viruses (Fig. 3). (For reference, the comparable divergence level used for clade designations in H5 viruses is 1.5%) (WHO/OIE/FAO, 2012). Previous investigations of nucleotide substitution rates of H9N2 viruses have suggested that 2% divergence signifies approximately 4.5 to 9 years of evolution (Fusaro et al., 2011).

View Article: PubMed Central - PubMed

ABSTRACT

Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngeal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4–6.0). Subtyping was performed on 468 pooled swabs with M gene Ct < 26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of interaction between H9 and H5 virus detection rates. We sequenced 17 whole genomes of A/H9N2, 2 of A/H5N6, and 11 partial genomes. All H9N2 viruses had internal genes that clustered with genotype 57 and were closely related to Chinese human isolates of A/H7N9 and A/H10N8. Using a nucleotide divergence cutoff of 98%, we identified 9 distinct H9 genotypes. Phylogenetic analysis suggested multiple introductions of H9 viruses to northern Vietnam rather than in-situ transmission. Further investigations of H9 prevalence and diversity in other regions of Vietnam are warranted to assess H9 endemicity elsewhere in the country.

No MeSH data available.