Speaker
Description
Hemagglutinin (HA) and neuraminidase (NA) proteins are the primary antigenic targets of influenza A virus (IAV) infections. IAV infections are generally classified into subtypes of HA and NA proteins, e.g., H3N2. Most of the known subtypes were originally defined by a lack of antibody cross-reactivity with pre-existing subtypes. However, genome sequencing has played an increasingly important role in characterizing the evolving diversity of IAV. Novel subtypes have recently been described solely by their genome sequences, and IAV infections are routinely subtyped by molecular assays, e.g., real-time PCR, or by comparing sequences to reference genomes. I carried out a phylogenetic analysis of all available IAV protein sequences in the NCBI Genbank database (over 1.1 million records) to determine whether the serologically-defined subtypes can be reproduced with molecular criteria. I show that a robust molecular taxonomy of HA and NA subtypes can be obtained with a simple clustering method, namely by progressively partitioning the phylogeny on its longest internal branches. However, this taxonomy also requires some revisions to the existing IAV nomenclature. For example, two IAV isolates from bats previously characterized as a divergent lineage of H9N2 should be separated into their own subtype. With the exception of these small, highly divergent lineages, phylogenies relating each of the other six IAV genomic segments do not support partitions into major subtypes.
