Submitted to: Virus Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2005
Publication Date: 12/1/2005
Citation: Spackman, E., Stallknecht, D.E., Slemons, R.D., Winker, K., Suarez, D.L., Scott, M.A., Swayne, D.E. 2005. Phylogenetic analyses of type a influenza genes in natural reservoir species in North America reveals genetic variation. Virus Research. 114:89-100.
Interpretive Summary: The natural hosts of avian influenza virus (AIV) or bird flu virus are ducks, shorebirds and gulls. These species serve as the main reservoir of the virus world-wide and do not get sick from the virus. In order for the virus to cross species, into chickens and turkeys for example, genetic changes must occur. These changes can be used to determine how long the virus has been in a new species and in some cases where the virus came from. Previously most work with AIV has been done with isolates from non-natural hosts such as chickens and mammals, little is known about the genetics of the virus in its natural host. In order to develop an understanding of AIV in the natural hosts, which can be used to both understand genetic mechanisms which allow cross species transmission, and to develop and epidemiological map to trace the origin of a virus during an outbreak, a multi-institutional (Southeast Poultry Research Laboratory USDA-ARS, University of Georgia, The Ohio State University, and University of Alaska) surveillance study was undertaken. In this study five of the eight genes of influenza were sequenced and analyzed from over 100 isolates collected between 1969 and 2003 through-out North America. A higher than expected level of variation was observed in some of the genes, indicating that development of a geographical and temporal molecular epidemiological map may not be possible.
Technical Abstract: 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 sequence from isolates from gallinaceous poultry and mammalian host species. Among the wild aquatic bird isolates the NP, NS subtype B NS1 and subtype B NS2 proteins were the most conserved with minimum amino acid identities of 95.7, 98.0 and 99.0% respectively, although the NP gene had as little as 82.1% nucleotide identity. 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, 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.