Characterization of low-pathogenic H5 subtype influenza viruses from Eurasia: implications for the origin of highly pathogenic H5N1 viruses

Abstract

Highly pathogenic avian influenza (HPAI) H5N1 viruses are now endemic in many Asian countries, resulting in repeated outbreaks in poultry and increased cases of human infection. The immediate precursor of these HPAI viruses is believed to be A/goose/Guangdong/1/96 (Gs/GD)-like H5N1 HPAI viruses first detected in Guangdong, China, in 1996. From 2000 onwards, many novel reassortant H5N1 influenza viruses or genotypes have emerged in southern China. However, precursors of the Gs/GD-like viruses and their subsequent reassortants have not been fully determined. Here we characterize low-pathogenic avian influenza (LPAI) H5 subtype viruses isolated from poultry and migratory birds in southern China and Europe from the 1970s to the 2000s. Phylogenetic analyses revealed that Gs/GD-like virus was likely derived from an LPAI H5 virus in migratory birds. However, its variants arose from multiple reassortments between Gs/GD-like virus and viruses from migratory birds or with those Eurasian viruses isolated in the 1970s. It is of note that unlike HPAI H5N1 viruses, those recent LPAI H5 viruses have not become established in aquatic or terrestrial poultry. Phylogenetic analyses revealed the dynamic nature of the influenza virus gene pool in Eurasia with repeated transmissions between the eastern and western extremities of the continent. The data also show reassortment between influenza viruses from domestic and migratory birds in this region that has contributed to the expanded diversity of the influenza virus gene pool among poultry in Eurasia.

FIG. 1.

Numerical analysis of HI titers (see Table 2) by nonmetric multidimensional ordination in two dimensions (A) and using hierarchical agglomerative clustering (B). Colors indicate viruses isolated from Italy (blue), southern China (green), and A/goose/Guangdong/1/96-like (red). Abbreviations: IDN, Indonesia; Mall, mallard; MDk, migratory duck; BHG, bar-hooded goose; QH, Qinghai.

FIG. 2.

Phylogenetic relationships of the HA (A) and M (B) genes of representative influenza A viruses isolated in Asia, America, and Europe. Numbers above and below the branch nodes indicate neighbor-joining bootstrap values of ≥50% and Bayesian posterior probabilities of >95, respectively. Analyses were based on nucleotides 22 to 1032 of the HA gene and 26 to 947 of the M gene. The HA and M gene trees were rooted to A/Japan/305/57 and A/equine/Prague/1/56, respectively. Colors indicate viruses isolated from Italy (blue), southern China (green), and A/goose/Guangdong/1/96 (red). Red branches indicate A/goose/Guangdong/1/96-like highly pathogenic influenza virus and its variants. Bar, 0.1 nucleotide substitution per site. Abbreviations: Am, America; Mall, mallard; MDk, migratory duck; Gf, guinea fowl; SCk, silky chicken; BH goose, bar-hooded goose; QH, Qinghai; Qa, quail; WDk, wild duck.

FIG. 3.

Phylogenetic relationships of the NP (A), PA (B), and PB2 (C) genes of representative influenza A viruses isolated in Asia, America (Am), and Europe. Numbers above and below the branch nodes indicate neighbor-joining bootstrap values of ≥50% and Bayesian posterior probabilities of >95, respectively. Analyses of NP, PA, and PB2 genes were based on nucleotides 41 to 984, 1425 to 2135, and 1065 to 2085, respectively. The gene trees were rooted to A/equine/Prague/1/56 (NP, PB2) and B/Lee/40 (PA), respectively. Colors indicate viruses isolated from Italy (blue), southern China (green), and A/goose/Guangdong/1/96 (red). Red branches indicate A/goose/Guangdong/1/96-like highly pathogenic influenza virus and its variants. Bar, 0.01 nucleotide substitution per site. Abbreviations: Am, America; Qa, quail; Mall, mallard; Mdk, migratory duck; Gf, guinea fowl; Sck, silky chicken; BH goose, bar-hooded goose; QH, Qinghai; Ph, pheasant.