Revised and updated nomenclature for highly pathogenic avian influenza A (H5N1) viruses

Abstract

The divergence of the hemagglutinin gene of A/goose/Guangdong/1/1996-lineage H5N1 viruses during 2011 and 2012 (807 new sequences collected through December 31, 2012) was analyzed by phylogenetic and p-distance methods to define new clades using the pre-established nomenclature system. Eight new clade designations were recommended based on division of clade 1·1 (Mekong River Delta), 2·1·3·2 (Indonesia), 2·2·2 (India/Bangladesh), 2·2·1·1 (Egypt/Israel), and 2·3·2·1 (Asia). A simplification to the previously defined criteria, which adds a letter rather than number to the right-most digit of fifth-order clades, was proposed to facilitate this and future updates.

Keywords: H5N1; hemagglutinin; highly pathogenic avian influenza; molecular epidemiology; nomenclature; phylogenetics; viral evolution.

Figure 1

Phylogenetic relationships of recently diverged A/goose/Guangdong /1/1996-like H5 hemagglutinin (HA) genes. A maximum likelihood tree of 198 HA nucleotide sequences from H5N1 viruses was constructed with 10 000 local support bootstraps (above branches) using FastTree2 (GTR+GAMMA) and rooted to A/goose/Guangdong /1/1996. Newly designated clades are underlined. Solid triangles denote HA clades of viruses that have not been in circulation since 2010 or earlier. Scale bar denotes nucleotide substitutions per site. Sequence data (FASTA) used to generate this figure are provided in Data S4.