Genetic characterization and evolution of H6N6 subtype avian influenza viruses

Abstract

H6-subtype avian influenza virus (AIV) was prevalent in the world and could sporadically infect humans. Here, a new chicken-derived H6N6-subtype AIV strain A/chicken/Zhejiang/49/2021 (ZJ49) was isolated in Zhejiang Province, China in 2021. Phylogenetic analysis by Maximum likelihood methods showed that H6-subtype AIVs were classed into 13 groups according to HA gene. The ZJ49 strain belonged to the G12 group, which mainly consisted of strains from Asian and dominated in recent years. Based on NA gene, H6-subtype AIVs were divided into N6.1 and N6.2 clades according to the NA gene. The ZJ49 isolate was located in the N6.2e clade, which mainly consisted of the H5N6-subtype AIVs. Phylogenetic analysis by Bayesian methods showed that the effective quantity size of H6-subtype AIVs increased around 1990, reached a peak around 2015, declined after 2015, then kept in a stable level after 2018. The reassortment analysis predicted that the PB2, PA, and NA genes of ZJ49 may recombine with H5-subtype AIVs. The amino acid at 222 position of HA gene of ZJ49 strain mutated from A to V, suggesting that ZJ49 has a potential ability to cross species barriers. The four glycosylation sites were highly conserved, implying less impact on the fold and conception of HA stem structure. Our results revealed the complicated evolution, reassortment, and mutations of receptor binding sites of H6-subtype AIVs, which emphasize the importance to continuously monitor the epidemiology and evolution of H6-subtype AIVs.

Evolution and Reassortment of H6 Subtype Avian Influenza Viruses

“…H6 AIVs found have been LPAIV [13]. Despite H6 AIV being an LPAIV A/teal/HK/W312/97 (H6N1) has been identified as a potential precursor of A/Hong Kong/156/1997 (H5N1) [14], and some of the H6NX strains have been identified as donors for H5 and H9N2 subtype AIV [15,16].…”

“…The main distribution of H6NX subtypes were as follows: North America and Asia covered nine subtypes, South America and Africa were dominated by H6N1, H6N2, and H6N8, Europe was dominated by H6N1, H6N2, H6N5, H6N6, and H6N8, and Oceania included H6N1, H6N2, H6N5, and H6N9 [11], and notably, a strain of H6N8 AIV was isolated in Antarctica in 2011. The global distribution of H6NX is shown in Figure 2a-g China, the epicenter of influenza [23], has an extremely high isolation rate of H6 subtypes [13]. N1, N2, and N6 were the major H6 AIV subtypes in China, with duck derived H6N2 predominating from 2000-2005.…”

“…This trend is essentially in line with the trend of H6 AIV in China. China, the epicenter of influenza [23], has an extremely high isolation rate of H6 subtypes [13]. N1, N2, and N6 were the major H6 AIV subtypes in China, with duck derived H6N2 predominating from 2000-2005.…”

“…A foreign surveillance study including more than 36,000 wild birds from Europe and America (1998–2006) found that H6 was the most frequently detected influenza virus subtype [ 22 ]. H6NX AIV spread from North America to Eurasia around 1976, with a population size increase around 1990, peaking around 2015, declining after 2015, and maintaining stable levels after 2018 [ 13 ]. As of 3 October 2022, GISAID included a total of 3234 H6 AIV sequences (HA), of which H6N2 had the highest detection rate (1069 strains) and H6N7 had the lowest number (9 strains), and the number of each subtype was shown in Figure 1 .…”

“…Moreover, positive detection rates for H6 AIV are increasing in both wild and domestic waterfowl and terrestrial birds [ 12 ]. Today, all H6 AIVs found have been LPAIV [ 13 ]. Despite H6 AIV being an LPAIV, A/teal/HK/W312/97 (H6N1) has been identified as a potential precursor of A/Hong Kong/156/1997 (H5N1) [ 14 ], and some of the H6NX strains have been identified as donors for H5 and H9N2 subtype AIV [ 15 , 16 ].…”