Establishment of an H6N2 influenza virus lineage in domestic ducks in southern China

Abstract

Multiple reassortment events between different subtypes of endemic avian influenza viruses have increased the genomic diversity of influenza viruses circulating in poultry in southern China. Gene exchange from the natural gene pool to poultry has contributed to this increase in genetic diversity. However, the role of domestic ducks as an interface between the natural gene pool and terrestrial poultry in the influenza virus ecosystem has not been fully characterized. Here we phylogenetically and antigenically analyzed 170 H6 viruses isolated from domestic ducks from 2000 to 2005 in southern China, which contains the largest population of domestic ducks in the world. Three distinct hemagglutinin lineages were identified. Group I contained the majority of isolates with a single internal gene complex and was endemic in domestic ducks in Guangdong from the late 1990s onward. Group II was derived from reassortment events in which the surface genes of group I viruses were replaced with novel H6 and N2 genes. Group III represented H6 viruses that undergo frequent reassortment with multiple virus subtypes from the natural gene pool. Surprisingly, H6 viruses endemic in domestic ducks and terrestrial poultry seldom reassort, but gene exchanges between viruses from domestic ducks and migratory ducks occurred throughout the surveillance period. These findings suggest that domestic ducks in southern China mediate the interaction of viruses between different gene pools and facilitate the generation of novel influenza virus variants circulating in poultry.

FIG. 1.

Phylogenetic relationships of the H6 HA (a) and N2 NA (b) genes of representative H6 influenza viruses. The phylogenetic trees were generated by the maximum-likelihood method using Garli (version 0.96). Numbers above and below branches indicate Bayesian posterior probabilities and neighbor-joining (NJ) bootstrap values, using MrBayes 3.1 and PAUP* 4b10 programs, respectively. Analysis was based on coding nucleotides 1 to 1704 and 1 to 1410 of the H6 HA and N2 NA gene segments, respectively. The H6 HA and N2 NA trees are both rooted to turkey/Canada/63 (H6N2). Viruses highlighted in blue are those characterized in this study. Viruses highlighted in green were those isolated from minor poultry, and the ones in red are reference strains. Abbreviations: Ck, chicken; Ck/Bei, chicken/Beijing/1/94-like; Cu, chukar; Dk, duck; FJ, Fujian; G1, Qa/HK/G1/97-like; GD, Guangdong; Gf, guinea fowl; Gs, goose; Gs/GD, goose/Guangdong/1/96-like; GX, Guangxi; HK, Hong Kong; HN, Hunan; JX, Jiangxi; Mall, mallard; MDk, migratory duck; Pa, partridge; Ph, pheasant; Qa, quail; SAU, southern Australia; ST, Shantou; TW, Taiwan; Ty, turkey; WDk, wild duck; W312, teal/HK/W312-like. The length of the scale bar corresponds to 0.01 nucleotide substitution per site.

FIG. 2.

Phylogenetic relationships of the PB2 (a), PB1 (b), and PA (c) polymerase genes of representative H6 influenza viruses. Analysis was based on the indicated nucleotides: PB2, 1 to 2280; PB1, 1 to 2274; and PA, 1 to 2151. The PB2, PB1, and PA trees were rooted to equine/Prague/1/56 (H7N7), pintail duck/Alberta/628/79, and Ann Arbor/6/60, respectively. Viruses characterized in this study are highlighted in blue. Viruses shown in green were those isolated from minor poultry, while viruses in red represent prototype viruses. Abbreviations are the same as those defined in the legend to Fig. 1. The length of the scale bar corresponds to 0.01 nucleotide substitution per site.

FIG. 3.

Phylogenetic relationships of nucleoprotein (NP) (a), matrix (M) (b), and nonstructural (NS) protein (c) genes of representative H6 influenza viruses. Analysis was based on the indicated nucleotides: NP, 1 to 1494; M, 1 to 982; and NS, 1 to 844. The NP, M, and NS trees are rooted to equine/Prague/1/56 (H7N7). Viruses characterized in this study are highlighted in blue. Viruses highlighted in green were those isolated from minor poultry, while viruses in red represent prototype viruses. Abbreviations are the same as the ones listed in the legend to Fig. 1. The length of the scale bar corresponds to 0.01 nucleotide substitution per site.