Abstract
BackgroundType A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. Currently, the viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view.Methodology/Principal FindingsThe panorama phylogenetic trees of influenza A viruses were calculated with representative sequences selected from approximately 23000 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.Conclusions/SignificanceHere, two panorama phylogenetic trees of type A influenza virus covering all the 16 hemagglutinin subtypes and 9 neuraminidase subtypes, respectively, were generated. 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.
Highlights
Influenza A virus causes frequent epidemics and occasional pandemics in various animals, including humans, pigs, horses, marine mammals and birds [1]
(3100 N1, 3967 N2, 192 N3, 26 N4, 58 N5, 125 N6, 75 N7, N8, 69 N9) influenza viruses with clear background were available in GenBank, after excluding the sequences of unclear background, the same viruses or manipulated materials and the ones shorter than 500 bp or with sequencing errors
During the analysis of the sequences, we found that the topology of phylogenetic trees changed little if calculated with different software packages like MEGA, PHYLIP or PAUP, or calculated with different methods like neighboring-joining or maximum parsimony
Summary
Influenza A virus causes frequent epidemics and occasional pandemics in various animals, including humans, pigs, horses, marine mammals and birds [1]. The viral genome comprises 8 segments which totally encode at least 10 proteins. The fourth and sixth segments encode the viral hemagglutinin (HA) and neuraminidase (NA), respectively, both of which are highly variable and diversified. 9 NA subtypes (N1,N9) of influenza A virus have been identified [2]. The phylogenetic diversity and distribution of influenza. Type A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. The viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view
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