Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1)

Abstract

Highly pathogenic avian influenza (HPAI) virus (H5N1) has appeared in >60 countries and continues to evolve and diversify at a concerning rate. Because different names have been used to describe emerging lineages of the virus, this study describes a unified nomenclature system to facilitate discussion and comparison of subtype H5N1 lineages.

Figure 1

Neighbor-joining tree of 859 H5N1 isolates constructed by using PAUP* version 4.0b10 (9) with 1,000 bootstrap replicates. The tree was rooted by using the highly pathogenic avian influenza virus (H5N1) strain A/turkey/England/50–92/91, a historical European H5N1 virus closely related to the Gs/GD lineage (10). Clades are color coded with isolates not given a clade designation in light green. Maximum-likelihood trees used for comparison were constructed by using GARLI version 0.951 (11). Bayesian analysis for comparison was conducted with MrBayes version 3.1 (12) by using 4 replicates of 2 million generations, sampled every 100 generations, with 6 chains. The convergence of Markov Chain Monte Carlo chains was confirmed for each dataset by using Tracer version 1.3 (http://tree.bio.ed.ac.uk/software/tracer). Estimates of the statistical significance of phylogenies were calculated by performing 1,000 NJ bootstrap replicates, and Bayesian posterior probabilities were calculated from the consensus of 60,000 trees after excluding the first 20,000 trees (25%) as burn-in. Scale bar represents 0.01-nt changes.

Figure 2

Neighbor-joining tree of 158 H5N1 isolates constructed by using PAUP* version 4.0b10 (9). Estimates of the phylogenies were calculated by performing 1,000 neighbor-joining bootstrap replicates. Distinct amino acid residues shared only by isolates within a particular clade are shown on the line above the clade-defining node when present. Amino acid substitutions represent change relative to Gs/GD/1/96. The small tree was rooted at the clade 0 node for larger scaling. Scale bar represents 0.01-nt changes. Ck, chicken; Gs, goose; Dk, duck; Ph, pheasant; CPH, Chinese pond heron; Ty, turkey; Gf, Guinea fowl; MDk, migratory duck; BHGs, bar-headed goose; WDk, wild duck; Qa, quail; Pg, pigeon.