Dominant subtype switch in avian influenza viruses during 2016–2019 in China

We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIV-positive samples and perform next generation sequencing. AIV-positive rates (12.73%) from samples had decreased substantially since 2016, compared to that during 2014–2016 (26.90%). Additionally, H9N2 has replaced H5N6 and H7N9 as the dominant AIV subtype in both chickens and ducks. Notably, novel reassortants and variants continually emerged and disseminated in avian populations, including H7N3, H9N9, H9N6 and H5N6 variants. Importantly, almost all of the H9 AIVs and many H7N9 and H6N2 strains prefer human-type receptors, posing an increased risk for human infections. In summary, our nation-wide surveillance highlights substantial changes in the circulation of AIVs since 2016, which greatly impacts the prevention and control of AIVs in China and worldwide.


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Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi) and the GISAID on 2019. The source data underlying  have been provided as a Source Data file, respectively. Extra data are available from the corresponding authors upon request.
A total of 16,091 samples were collected from May 2016 to February 2019 from 37 cities in 23 provinces, municipalities and minority autonomous regions in China (Fig. 1a), in which 2,048 samples were identified to be AIV-positive by next generation sequencing (NGS), with a positive rate of 12.73% (Supplementary Data 1-5).
Only full-length genome sequences were analyzed and partial genome sequences were not included in our phylogenetic analyses.
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Virus-receptor binding was detected with rabbit antisera against the influenza viruses (H1, H5, H6

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Embryonated chicken eggs obtained from Beijing Vital River Laboratory Animal Technology Company were incubated at ‫خ73‬ " and 80% hum i di t y f or 10 days bef or e bei ng used f or vi r us i sol at i on.
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Oropharyngeal and cloacal swabs from apparently healthy poultry, as well as environmental samples, were collected in LPMs in 37 cities and counties across 23 provinces or municipalities or minority municipalities in China. Poultry included chickens, ducks, geese, and pigeons. Environmental samples included swabs from cages, poultry drinking water, defeathering machines, chopping boards, and feces in the LPMs. Sampling was collected from May 2016 to February 2019 (samples collected once a month, unless the LPM was closed, and there was no samples being collected in the corresponding month), a period of 26 months spanning three flu seasons. Selection criteria of cities and provinces, and the LPMs chosen for sampling are same as described previously13. The swabs were placed into viral transport media and transported to the laboratory within 24 hours in a handheld portable 4°C refrigerator, and frozen at -80°C immediately for future use.
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