Panorama Phylogenetic Diversity And Distribution Of HA Gene Of Type A Influenza Virus And Molecular Evolution Analysing Of HA Genes Of Subtype H9 Avain Influenza Viruses Isolated In 2007-2008 From Part Of China

Type A influenza virus, belongs to the Orthomyxoviridae family, is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. It was able to cause frequent epidemics and occasional pandemics. The viral genome comprises 8 segments which totally encode at least 11 proteins. It was further divided into multiple subtypes based on the antigenic differences in the viral surface glycoproteins, hemagglutinin (HA). Till date, 16 HA (H1-H16) subtypes of type A influenza virus have been recognized.This study mainly include: panorama phylogenetic diversity and distribution of HA gene of type A influenza virus and molecular evolution analysing of HA genes of subtype H9 avain influenza viruses isolated in 2007-2008 from part of China.1. Panorama phylogenetic diversity and distribution of HA gene of type A influenza virus Till date, the phylogenetic diversity and distribution of influenza A viruses have been widely studied within some regions, periods, hosts or viral lineages, but seldom detailed within the type or a subtype from the panorama view. In addition, some of the lineages and sublineages have been designated as the North American lineage, swine human-like H1 viruses, A/chicken/Hong Kong/G9/97(H9N2)-like viruses, Fujian-like viruses, etc., as required by the studies on evolution, ecology and epidemiology of influenza A virus. These nomenclatures are ambiguous, miscellaneous, self-limited and sometimes even misleading. Therefore, it is of significance to identify all the lineages and sublineages within type A influenza virus and unify their nomenclature with a more rational system. Here, The panorama phylogenetic trees of HA genes of influenza A viruses were calculated with representative sequences selected from approximately 14328 candidates available in GenBank using web servers in NCBI and the software MEGA 4.0. Lineages and sublineages were classified according to genetic distances, topology of the phylogenetic trees and distributions of the viruses in hosts, regions and time.The trees provided us whole views and some novel information to recognize influenza A viruses including that some subtypes of avian influenza viruses are more complicated than Eurasian and North American lineages as we thought in the past. They also provide us a framework to generalize the history and explore the future of the viral circulation and evolution in different kinds of hosts. In addition, a simple and comprehensive nomenclature system for the dozens of lineages and sublineages identified within the viral type was proposed, which if universally accepted, will facilitate communications on the viral evolution, ecology and epidemiology.2. Molecular evolution analysing of HA genes of subtype H9 avain influenza viruses isolated in 2007-2008 from part of China.Subtype H9 AIVs were first isolated in Hong Kong in the 1970s, but have not been widespread in China mainland until the 1990s. To control the infections in poultry, inactivated vaccines have been widely used in China mainland since the late 1990s. In recent years, subtype H9 avian influenza viruses circulating in China have aroused high concerns for their impact on poultry and risk to public health.We had done epidemiological investigation with domestic poultry in part region of China mainland, and separated 70 strains H9 subtype AIV in 2007-2008. For explore the evolution of genetic variation and molecular evolution of subtype H9 avian influenza in our country in recent years, HA gene segments of 44 strains were amplified by RT-PCR and sequenced. Homology analysis and evolution analysis of these sequences were generated by using MEGA4.0 and DNAStar software. Come to the following conclusions:1. Isolated 70 H9 isolates from 5260 swab samples from 14 provinces in China in 2007-2008, isolating rate of H9 AIVs is 1.33%.2. Poultry in our country exist much more healthy-infected phenomenon than waterfowl.3. The deduced amino acids sequence showed that all the strains possesse one or two basic aminos at the cleavage site.4. All the strains were of human influenza virus-like receptor specificity, which suggested the viruses were posing higher risk to public health.5. Most H9 AIVs isolated in the past decade in China mainland belonged to sublineage h9.4.2, the ones isolated in this study were distributed in multiple clades within this sublineage.And a presumably predominant clade was identified as it covered strains isolated from 13 provinces in China mainland in 2007-2008. The representative virus is A/chicken/Guangxi/ 55/2005. 6. Six specific mutations were found in the HA gene of the viruses within the presumably predominant clade in China mainland in 2007-2008.