Sequence characteristics and phylogenetic analysis of H9N2 subtype avian influenza A viruses detected from poultry and the environment in China, 2018

Abstract

H9N2 subtype avian influenza A virus (AIV) is a causative agent that poses serious threats to both the poultry industry and global public health. In this study, we performed active surveillance to identify H9N2 AIVs from poultry (chicken, duck, and goose) and the environment of different regions in China, and we phylogenetically characterized the sequences. AIV subtype-specific reverse transcription polymerase chain reaction (RT-PCR) showed that 5.43% (83/1529) samples were AIV positive, and 87.02% (67/77) of which were H9N2 AIVs. Phylogenetic analysis revealed that all H9N2 field viruses belonged to the Y280-like lineage, exhibiting 93.9–100% and 94.6–100% of homology in the hemagglutinin (HA) gene and 94.4–100% and 96.3–100% in the neuraminidase (NA) gene, at the nucleotide (nt) and amino acid (aa) levels, respectively. All field viruses shared relatively lower identities with vaccine strains, ranging from 89.4% to 97.7%. The aa sequence at the cleavage site (aa 333–340) in HA of all the isolated H9N2 AIVs was PSRSSRG/L, which is a characteristic of low pathogenic avian influenza virus (LPAIV). Notably, all the H9N2 field viruses harbored eight glycosylation sites, whereas a glycosylation site 218 NRT was missing and a new site 313 NCS was inserted. All field viruses had NGLMR as their receptor binding sites (RBS) at aa position 224–229, showing high conservation with many recently-isolated H9N2 strains. All H9N2 field isolates at position 226 had the aa Leucine (L), indicating their ability to bind to sialic acid (SA) α, a 2–6 receptor of mammals that poses the potential risk of transmission to humans. Our results suggest that H9N2 AIVs circulating in poultry populations that have genetic variation and the potential of infecting mammalian species are of great significance when monitoring H9N2 AIVs in China.

That H9N2 avian influenza viruses circulating in different regions gather in the same live-poultry market poses a potential threat to public health

“…However, since the implementation of the new live-poultry trading policy in Guangdong Province, the proportion of H9N2 subtype AIVs isolated in Southern China has decreased. After 2013, the viruses isolated from several provinces were most similar to the strains from Eastern China ( Zhang et al, 2019 ; Gao et al, 2021 ; Guo et al, 2021 ; Hu et al, 2021 ; Liu et al, 2022 ), which is consistent with our analysis that the epidemiological center of H9N2 AIVs has shifted to Eastern China. With our monitoring of the live-poultry market in Foshan, we found that Eastern China was an early epidemic center for clade A and clade B.…”

Mutual antagonism of mouse-adaptation mutations in HA and PA proteins on H9N2 virus replication

“…H9 seropositivity is particularly common among poultry market workers in southern China ( Li et al., 2017 ; Ma et al., 2018 ; Song and Qin, 2020 ), suggesting that direct exposure is a risk factor for H9N2 infection. In poultry, the hemagglutinin (HA) receptor preference of most H9N2 viruses seemed to have gained the ability to bind human-receptor ( Gao et al., 2021 ), indicating an increased risk of cross-species transmission to mammals. Though some studies have described the molecular mechanisms associated with the adaptation of H9N2 viruses to mammals, the molecular basis remains to be supplemented.…”

Emergence of a new designated clade 16 with significant antigenic drift in hemagglutinin gene of H9N2 subtype avian influenza virus in eastern China

“…H9N2 subtype avian influenza virus (AIV) was first isolated in turkeys in 1966 in United States and then became endemic in many countries in Asia, Eurasian, Middle East, and Africa [ 1 , 2 ]. Since the first H9N2 virus in mainland China was isolated in Guangdong in 1994 [ 3 ], it has been prevalent in many provinces [ 4–7 ]. According to the surveillance of AIVs from 16 provinces in China during 2014-2016, H9N2 was isolated in 54.1% of apparently healthy chickens [ 8 ].…”

“…H9N2 subtype AIV has become a severe concern in China because of its threat to the poultry industry and public health. On the one hand, the circulation of H9N2 in poultry can cause significant economic losses due to declined egg production, weight loss and susceptibility to co-infection with other pathogens [ 4 ]. On the other hand, H9N2 AIVs pose a threat to human health.…”