Phylogenetic analyses of type A influenza genes in natural reservoir species in North America reveals genetic variation

The matrix (M) (98 isolates), nucleoprotein (NP) (67 isolates), non-structural (NS) (107 isolates), H4 subtype HA1 (21 isolates) and H6 (38 isolates) subtype HA1 region of the hemagglutinin (HA) gene were sequenced from avian influenza viruses isolated from North American wild aquatic birds between 1969 and 2003. Sequences were compared phylogenetically with all available wild aquatic bird isolate sequences and sequences from isolates from gallinaceous poultry and mammalian host species. Among the wild aquatic bird isolates the NS subtype B NS1 and subtype B NS2 proteins were the most conserved with minimum amino acid identities of 98.0 and 99.0%, respectively. The H6 HA1, M and NS subtype A genes were more divergent; both nucleotide and amino acid divergence levels were similar to those of the same genes from gallinaceous poultry and mammalian origin type A influenza isolates. Phylogenetically none of the genes assorted geographically (within North America), chronologically or by species of origin, unlike isolates from non-natural host species, suggesting that selection pressure is low. A lack of clear temporal or spatial grouping shows that multiple lineages of virus co-circulate and precludes the development of an epidemiological map for influenza virus from these species.