Genome Properties And Phylogenic Analysis Of H6N2 And H11N9 Avian Influenza Virus Strains From Wildbirds

Avian influenza viruses (AIV) are widely distributed in wild birds. The wild waterfowls are particularly natural reservoirs of avian influenza virus. Migration of wild birds could not be overlooked during the prevalence of avian influenza virus. In this study, the whole genome was sequenced and their genetic characteristics and phylogenetic relationships were compared for two H6N2 AIVs [A/mallard/HeiLongjiang/131/2006(H6N2), A/Mallard/SanJiang/113/2006 (H6N2)] isolated from Sanjiang natural Reserve and a H11N9 AIV [A/OrientalWhite Stork/ZhaLong/183/2006(H11N9)] isolate from Zhalong natural Reserve.Reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify the full-length cDNAs of the AIVs.Furthermore, the cDNAs were cloned into pMD18-T and then sequenced. These sequences were compared with the corresponding sequences published in GenBank. The panorama phylogenetic trees of H6 and H11 genes of AIV and the phylogenetic trees of the other genes were drawn. Results show that eight cDNA fragments all contain the whole open reading frame of corresponding gene. There are seven potential glycosylation sites in HA gene. The amino acid sequence of the cleavage site with the typical characteristics of the low pathogenic avian influenza virus (LPAIV). The results of comparative sequence analysis indicate that the gene of the isolate viruses are recombinant. The PB1 gene of A/Mallard/ SanJiang/113/2006(H6N2) was closely related to A/environment/Qinghai/1/2008 (H5N1),as high as 99.9% homology. And the phylogenetic trees revealed that the PA gene of H6N2 viruses belonged to the American avian AIV lineage, whereas the other 7 genes belonged to the Eurasian avian lineage.In this study, the phenomenon of gene recombination was found in all of the 3 AIV isolates, especially isolate A/Mallard/SanJiang/113/2006(H6N2) has the characteristics with recombinant gene fragments of both Eurasian and American lineages of AIV. Our findings indicate the natural geographical distribution of AIVs is more complicated than previously known, with original distribution division of Eurasian and American lineages, though the reassortment between these two AIV lineages is generally limited due to geographical constraints. Also it could be speculated that the AIV gene recombination might be related to the close contaction among the wild birds which carrying variety of different subtypes of AIV and frequent infection of AIV in migration process, and the continuous or simultaneity infection of different subtypes of LPAIV is a very common situation in wild bird populations.This study can be concluded that LPAIVs circulating in wildbirds have been experiencing the genetic reassortment among the different subtypes of AIVs. Therefore, the LPAIV in birds should be given adequate attention.