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

Abstract

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.

Genetic characterization of an H5N6 avian influenza virus with multiple origins from a chicken in southern China, October 2019

“…These observations indicate a potential mammalian adaptation of H5N6 AIV. Fortunately, our results showed that DG/19 possessed 226Q and 228G (H3 numbering) in the HA, which suggested a typical avian receptor preference and were consistent with previous studies [ 16 ]. However, DG/19 has 222Q and 227R in the HA, which has been shown to facilitate virus binding to fucosylated sialosides [ 20 ].…”

“…A further comparison with the reference sequence of the sub-clades of 2.3.4.4 suggested DG/19 belongs to the 2.3.4.4 h subclade. The internal genes of DG/19 had high identity with strains isolated from ducks in 2017–2018 in Hunan by a recent study [ 16 ]. The HA gene has the highest nucleic acid homology with A/duck/Hunan/1.12_YYGK 72H3-OC/2018(H5N6) (98.35%).…”

“…The 222Q and 227R on HA of DG/19 suggested that H5N6 AIV has been well adapted to terrestrial birds, which made H5N6 AIV easier to adapt to mammalian hosts. The 226Q and loss of the glycosylation site at 158 suggested DG/19 prefers avian-type receptors [ 13 , 16 ].…”

“…To date, since the first case of human infection with HPAIV H5N6 in Sichuan province in April 2014 [ 13 ], more than 23 cases of infection and 9 deaths were recorded ( www.who.int/influenza/human_animal_interface ). During the past several years, the HPAIV H5N6 subtype has continuously evolved and has replaced H5N1 as one of the main HPAIV subtypes in domestic poultry in China [ 13 – 16 ]. A more recent study suggested that the positive rate of H5N6 in live poultry markets (LPM) is 7.87%, which became the second most dominant subtype currently circulating in LPMs in China [ 16 ].…”

“…During the past several years, the HPAIV H5N6 subtype has continuously evolved and has replaced H5N1 as one of the main HPAIV subtypes in domestic poultry in China [ 13 – 16 ]. A more recent study suggested that the positive rate of H5N6 in live poultry markets (LPM) is 7.87%, which became the second most dominant subtype currently circulating in LPMs in China [ 16 ]. Moreover, human infection of HPAIV H5N6 subtype even had a higher mortality than H5N1 subtype based on the clinical statistical data thus far [ 17 ].…”