The genesis and source of the H7N9 influenza viruses causing human infections in China

Lam, Tommy Tsan-Yuk; Wang, Jia; Shen, Yongyi; Zhou, Boping; Duan, Lian; Cheung, Y. M.; Ma, Chi; Lycett, Samantha; Leung, Connie; Chen, Xinchun; Li, Lifeng; Hong, Wei; Chai, Yujuan; Zhou, Lingsha; Liang, Huyi; Ou, Zhihua; Liu, Yongmei; Farooqui, Amber; Kelvin, David J.; Poon, Leo L. M.; Smith, David K.; Pybus, Oliver G.; Leung, Gabriel M.; Shu, Yuelong; Webster, Robert G.; Webby, Richard J.; Peiris, J. S. Malik; Rambaut, Andrew; Zhu, Hua; Guan, Yi

doi:10.1038/nature12515

Cited by 424 publications

(410 citation statements)

References 26 publications

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“…Notably, this gene flow generally took the form of complex reassortments generally involving internal genes. Clearly, the genetic communication of AIVs amongst wild birds, domestic waterfowl and terrestrial poultry flocks is an important source of emerging AIVs, and similar reassortments have been observed in the highly pathogenic H5N1 and H7N9 viruses (Guan et al, 1999;Lam et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China

Chen

Lin

Guo

et al. 2016

Journal of General Virology

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The wide circulation of novel avian influenza viruses (AIVs) highlights the risk of pandemic influenza emergence in China. To investigate the prevalence and genetic diversity of AIVs in different ecological contexts, we surveyed AIVs in live poultry markets (LPMs), free-range poultry and the wetland habitats of wild birds in Zhejiang and Hubei provinces. Notably, LPMs contained the highest frequency of AIV infection, and the greatest number of subtypes (n59) and subtype co-infections (n514), as well as frequent reassortment, suggesting that they play an active role in fuelling AIV transmission. AIV-positive samples were also identified in wild birds in both provinces and free-range poultry in one sampling site close to a wetland region in Hubei. H9N2, H7N9 and H5N1 were the most commonly sampled subtypes in the LPMs from Zhejiang, whilst H5N6 and H9N2 were the dominant subtypes in the LPMs from Hubei. Phylogenetic analyses of the whole-genome sequences of 43 AIVs revealed that three reassortant H5 subtypes were circulating in LMPs in both geographical regions. Notably, the viruses sampled from the wetland regions and free-range poultry contained complex reassortants, for which the origins of some segments were unclear. Overall, our study highlights the extent of AIV genetic diversity in two highly populated parts of central and south-eastern China, particularly in LPMs, and emphasizes the need for continual surveillance.

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Section: Discussionmentioning

confidence: 99%

Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China

Chen

Lin

Guo

et al. 2016

Journal of General Virology

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“…To date, the novel virus has caused two outbreaks of human infection, including 375 known cases and 115 deaths as of 11 March 2014 (2). Phylogenetic analysis suggests that the virus is a triple reassortant of H7, N9, and H9N2 avian influenza viruses (3,4). The H7 and N9 genes may have been transferred from migratory birds to domestic ducks and then to chickens in the live poultry markets (3)(4)(5), after which reassortment with enzootic H9N2 viruses formed the H7N9 viruses identified in humans (3)(4)(5).…”

mentioning

confidence: 99%

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

Wang

Yin

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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315

340

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The emergence of human infection with a novel H7N9 influenza virus in China raises a pandemic concern. Chicken H9N2 viruses provided all six of the novel reassortant’s internal genes. However, it is not fully understood how the prevalence and evolution of these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that over more than 10 y of cocirculation of multiple H9N2 genotypes, a genotype (G57) emerged that had changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens in China, caused widespread outbreaks in 2010–2013 before the H7N9 viruses emerged in humans, and finally provided all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential.

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“…In addition, the NP gene presented a certain divergence, and the strain A/Shanghai/1/2013 is clustered together with A/chicken/ Shanghai/C1/2012(H9N2), rather than the other two H7N9 isolates 3 . Recently, the PB2, PB1, PA and M genes have also been found to form at least two clusters in the phylogenetic trees 10,11 . All these suggest that the H7N9 viruses of this outbreak might be diversified far beyond what we observed from preliminary studies, and consequently a more comprehensive study was called for to uncover the veil of the H7N9 virus.…”

mentioning

confidence: 99%

Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus

et al. 2014

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The genesis and source of the H7N9 influenza viruses causing human infections in China

Cited by 424 publications

References 26 publications

Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China

Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus

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