Complete Genomic Sequence of a Novel Natural Recombinant H6N2 Influenza Virus from Chickens in Guangdong, Southern China

Abstract

Here, we reported the complete genome sequence of a novel H6N2 avian influenza virus (AIV) isolated from chicken in Guangdong, Southern China, in 2011 which was a natural recombinant virus between the H6N2 and H5N1 subtypes. It will help to understand the epidemiology and molecular characteristics of H6N2 influenza virus in Southern China.

GENOME ANNOUNCEMENT

Avian influenza (AI) is caused by type A influenza viruses, which result mainly in systemic or respiratory infection diseases of birds. Based on the antigenicity of hemagglutinin (HA) and neuraminidase (NA), avian influenza virus (AIV) can be divided into H1 to H16 and N1 to N9, respectively (5, 7, 9). In recent years, there have been several subtypes of AIVs (H5, H6, and H9 subtypes) circulating and evolving in Southern China (1, 4, 10), which might provide an opportunity for these virus subtypes to recombine. In 1997, H5N1 highly pathogenic AIV derived its HA gene from A/Goose/Guangdong/1/96(H5N1)-like virus and its other seven genes from A/teal/HongKong/W312/97(H6N1)-like virus and caused disease outbreaks in chickens in Hong Kong (2) and caused 6 deaths among 18 people infected (3, 8). Therefore, it is necessary to examine the epidemiological research to understand the evolution and recombination of AIVs in Southern China.

In November 2011, we isolated a natural recombinant H6N2 influenza virus (A/Chicken/Guangdong/C273/2011 [C273]) from healthy chickens that was between the H6N2 and H5N1 subtypes, a strain which was rarely reported in Guangdong.

To investigate more information about this recombinant virus, we determined the complete genomic sequence with an ABI 3730 genetic analyzer. The 8 genome segments of the virus encoded 10 proteins (PB2, PB1, PA, HA, NP, NA, M1, M2, NS1, and NS2) with the amino acid lengths 759, 757, 716, 566, 498, 469, 252, 80, 230, and 121, respectively. The C273 virus possessed the low-pathogenic influenza A virus sequence PQIETR↓G at the cleavage site between HA1 and HA2. The receptor-binding pocket of HA1 retains the amino acid residues Q226 and G228 (H3 numbering), which preferentially bind to the avian influenza virus receptor. The consensus amino acid sequences revealed eight potential N-linked glycosylation sites in HA (26 or 27, 39, 182, 306, 311, 498, and 557) and nine potential N-linked glycosylation sites in NA (61 or 69, 70, 86, 146, 200, 234, 331, and 402). Amino acid residue 627 of PB2 was E rather than K and amino acid residue 701 of PB2 was D, showing residues which are characteristic of the avian influenza virus.

Phylogenetic analysis of the C273 surface genes HA and NA showed that they belonged to ST339-like [A/duck/Shantou/339/2000(H6N2)-like] viruses (6) and that their nucleotide homologies were 95.4% and 94.8% compared with the ST339-like virus, respectively. The internal genes showed that the PB1, NP, M, and NS genes belonged to ST339-like viruses, and nucleotide homologies were above 95.3%, 93.8%, 97.1%, and 96.8% compared with the ST339-like virus, respectively. The PA gene belonged to HN573-like [A/duck/Hunan/573/2002(H6N2)-like] virus (6) and had nucleotide homology above 95.7% compared with the HN573-like virus. However, the PB2 gene of C273 was derived from the GS/GD96-like H5N1 virus lineage, and nucleotide homology was 90.7% compared with the A/Goose/Guangdong/1/96-like H5N1 virus. Thus, we isolated a natural recombinant H6N2 influenza virus from chicken that was between the H6N2 and H5N1 subtypes.

Therefore, continuing influenza virus surveillance in poultry is critical to understanding the genesis and emergence of coming pandemic strains in Southern China.

Nucleotide sequence accession numbers.

The genome sequences of A/Chicken/Guangdong/C273/2011 (C273) have been deposited in GenBank under accession numbers JQ924794 to JQ924801.