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

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.


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(a) Influenza A prevalence estimates in 5 district markets each for 7 northern provinces from Oct.–Dec. 2014; (b) map showing provinces surveyed by the H7F programme. Yellow = Lao Cai province; orange = Ha Giang province; red = Cao Bang province; green = Ha Noi province; purple = Bac Giang province.
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f0005: (a) Influenza A prevalence estimates in 5 district markets each for 7 northern provinces from Oct.–Dec. 2014; (b) map showing provinces surveyed by the H7F programme. Yellow = Lao Cai province; orange = Ha Giang province; red = Cao Bang province; green = Ha Noi province; purple = Bac Giang province.

Mentions: A total of 1207 of 2450 pooled swabs (49%) screened positive for influenza A by matrix gene real time RT-PCR. Using a maximum likelihood modeling approach that accounts for pooling (Suppl Appendix A), this detection level corresponded to an overall influenza A prevalence of 5.45% (95% Confidence Interval [CI] 5.4–6.0%). Fig. 1(a) presents estimated prevalence of influenza A per weekly sampling round (x-axis), depicted by province (rows) and by market (individual graphs). None of the 1207 influenza positive pools were found positive for H7 subtype. Further molecular subtyping to detect H5 and H9 viruses was conducted on all pooled swabs with an influenza A matrix gene Ct < 26 (n = 468) (Table 1). Detection rates for H9 and H5 subtype varied dramatically between provinces and individual markets, with H9 accounting for 64–100% of influenza A positive pools; H5 was detected in 4.7% (22/468) of positive pools; 3.8% (18/468) pools screened positive for both H5 and H9 subtypes; and 8.9% (42/468) were classified as ‘subtype unknown’. The maximum likelihood prevalence (accounting for pooling) for H9 and H5 was 3.7% (95%CI 3.3–4.1%) and 1.09% (95%CI 0.7–1.6%), respectively. We found no evidence of significant interaction between H5 and H9 when using a maximum likelihood modeling approach (Suppl Appendix B). Virus isolation in embryonated eggs was attempted on selected representative H9 positive pools with Ct < 24 (n = 25), and all H5 positive pools and pools the were ‘unknown subtype’, regardless of Ct value (n = 22 and 42, respectively). We isolated 25 H9 viruses, however none of the H5 positive pools or the pools of ‘unknown subtype’ yielded a virus isolate.


Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014
(a) Influenza A prevalence estimates in 5 district markets each for 7 northern provinces from Oct.–Dec. 2014; (b) map showing provinces surveyed by the H7F programme. Yellow = Lao Cai province; orange = Ha Giang province; red = Cao Bang province; green = Ha Noi province; purple = Bac Giang province.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036934&req=5

f0005: (a) Influenza A prevalence estimates in 5 district markets each for 7 northern provinces from Oct.–Dec. 2014; (b) map showing provinces surveyed by the H7F programme. Yellow = Lao Cai province; orange = Ha Giang province; red = Cao Bang province; green = Ha Noi province; purple = Bac Giang province.
Mentions: A total of 1207 of 2450 pooled swabs (49%) screened positive for influenza A by matrix gene real time RT-PCR. Using a maximum likelihood modeling approach that accounts for pooling (Suppl Appendix A), this detection level corresponded to an overall influenza A prevalence of 5.45% (95% Confidence Interval [CI] 5.4–6.0%). Fig. 1(a) presents estimated prevalence of influenza A per weekly sampling round (x-axis), depicted by province (rows) and by market (individual graphs). None of the 1207 influenza positive pools were found positive for H7 subtype. Further molecular subtyping to detect H5 and H9 viruses was conducted on all pooled swabs with an influenza A matrix gene Ct < 26 (n = 468) (Table 1). Detection rates for H9 and H5 subtype varied dramatically between provinces and individual markets, with H9 accounting for 64–100% of influenza A positive pools; H5 was detected in 4.7% (22/468) of positive pools; 3.8% (18/468) pools screened positive for both H5 and H9 subtypes; and 8.9% (42/468) were classified as ‘subtype unknown’. The maximum likelihood prevalence (accounting for pooling) for H9 and H5 was 3.7% (95%CI 3.3–4.1%) and 1.09% (95%CI 0.7–1.6%), respectively. We found no evidence of significant interaction between H5 and H9 when using a maximum likelihood modeling approach (Suppl Appendix B). Virus isolation in embryonated eggs was attempted on selected representative H9 positive pools with Ct < 24 (n = 25), and all H5 positive pools and pools the were ‘unknown subtype’, regardless of Ct value (n = 22 and 42, respectively). We isolated 25 H9 viruses, however none of the H5 positive pools or the pools of ‘unknown subtype’ yielded a virus isolate.

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&ndash;6.0). Subtyping was performed on 468 pooled swabs with M gene Ct&nbsp;&lt;&nbsp;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.


Related in: MedlinePlus