| Type A influenza viruses(IAVs)causes frequent infections and occasional pandemics in humans and various animals.Through continuous evolution,they exhibit complicated phylogenetic diversity and distribution.To reveal the diversity and distribution of IAV in time will not only help to predict the outbreak of IAV,but also help to clarify the epidemiology of IAV infection.Phylogenetic diversity and distribution of IAVs have been analyzed in a panorama view ten years ago.However,the analysis needs to be updated because some sequences of the viruses in Influenza Virus Resource have been revised,and many novel sequences have been uploaded in Database,and thereby some novel subtypes,lineages and subordinate lineages of IAVs have possibly emerged.Meanwhile,the analysis capacity of computers has been increased so greatly.In consideration of the above background,this study was aimed to update the most recent diversity and distribution of IAVs in a panorama view through analysis of more sequences,more accurate sequences and many new sequences.The groups of IAVs mainly circulating in birds,humans,pigs,horses and dogs were designated as type A avian influenza viruses(AIVs),human influenza viruses(Hu IVs),swine influenza viruses(SIVs),equine influenza viruses(EIVs),and canine influenza viruses(CIVs).In this study,139872 amino acid sequences of IAVs from Influenza Virus Resource were selected,and they were aligned and phylogenetically analyzed using the software tool MEGA 7.0.Compared with previous studies,more than 200 revisions have been made to describe the diversity and distribution of IAVs in this study,and the panorama view have been tested using representative sequences and an authentic survey of AIV.1.Distribution and diversity of IAVs circulating worldwideAfter statistical analysis of a large number of sequence information,the results showed that sequences of H1,H3,H5,and H9 were significantly more than those of other subtypes;H1N1,H1N2,H3N2,H5N1,and H9N2 were the predominant combination subtypes circulating worldwide;Birds,humans and pigs are the major hosts of IAVs;Most AIVs belong to H5N1 or H9N2 subtypes;Most Hu IVs belong to H1N1 or H3N2 subtypes;Most SIVs belong to H1N1,H1N2 or H3N2 subtypes;Most EIVs belong to H3N8 or H7N7 subtypes;Most CIVs belong to H3N8 or H3N2 subtypes.To a large extent,this result reflects the prevalence of IAVs and the epidemic potential of some subtypes of IAVs.It is of great significance to the epidemiological research and risk prediction of IAVs.2.Phylogenetic diversity and distribution of IAVsLarge number of IAV sequences were aligned and phylogenetically analyzed.Results showed that H1 subtype IAVs could be classified into H1.1 and H1.2,these lineages were both further designated four secondary lineages,each secondary lineage exhibited distinct host,temporal and spatial distribution characteristics,e.g.H1.1b corresponded to some AIVs from South America,and H1.2a corresponded to one Hu IV in 1918,and H1.2c corresponded to the classical H1 subtype SIVs which have been circulating worldwide for decades.Similarly,phylogenetic diversity and distribution of other 17 HA subtypes of H2-H18 were updated in a panorama view.N1 subtype IAVs could be classified into N1.1-N1.3,some lineages were further designated as two or three secondary lineages,some secondary lineages were further designated as tertiary lineages,quaternary lineages and fifth grade linegages,each secondary lineage,tertiary lineage,quaternary lineage and fifth grade linegage exhibited distinct host,temporal and spatial distribution characteristics,e.g.N1.1b corresponded to AIVs circulating in the Western Hemisphers,N1.1c2 a corresponded to the H5N1 subtype HPAIVs widely circulating in the Eastern Hemisphere in recent years.Similarly,phylogenetic diversity and distribution of other 10 NA subtypes of N2-N11 were updated in a panorama view.PB2 gene could be classified into PB2.1-PB2.4,some lineages were further designated as four secondary lineages,some secondary lineages were further designated tertiary lineages and quaternary lineages,each secondary lineage,tertiary lineage and quaternary lineage exhited distinct host,temporal and spatial distribution characteristics,e.g.PB2.1b corresponded to SIVs circulating in North America in 1990 s,PB2.1d corresponded to H3N2 subtype CIVs emerged in recent years.Similarly,phylogenetic diversity and distribution of other 5 internal genes of PB1,NP,PA,MP and NS were updated in a panorama view.the analysis in this studyCompared with previous studies,more than 200 revisions have been made to describe the diversity and distribution of IAVs in this study,mainly including:(1)Some lineages designated previously(e.g.S1.7,S1.8,S2.7,S3.8,S5.9,S5.10,h3.3,and h5.3 were deleted in this report because these lineages were with wrong sequences which have been revised thereafter.(2)This study summarized some new lineages of IAVs in recent years.Such as the lineage PB2.1b1 corresponded to the H7N9 subtype AIVs isolated in China which have caused many human infections and fatalities.(3)More groups,clades or lineages of SIVs in H1 and H3 subtypes were demonstrated directly in this study than our previously studies which were based on selected representative sequences.(4)The results further confirmed some previous conclusions,such as that none of the HA gene of H3,H13,the NA gene of N2 subtypes of AIVs and the viral NS gene of AIVs could be simply classified into two lineages according to the Eastern and Western Hemispheres.(5)This study revealed the epidemiology of IAV as a whole.For example,the SIVs circulating in the Eastern Hemisphere is seldom prevalent in the Western Hemisphere,but the SIVs circulating in the Western Hemisphere can often be prevalent in the Eastern Hemisphere.3.Test of the analysis using representative sequences and an authentic survey of AIVThe reliability of the updated panorama views of IAVs was further supported by the phylogenetic trees calculated using randomly selected representative sequences.The results suggested that most of the lineages and subordinate lineages designated in this report were supported by the bootstrap values calculated based on the representative sequences.The trend of phylogenetic tree of representative sequences was consistent with the large panorama phylogenetic trees in the above section,and most branches and subordinate branches were supported by high bootstrap values,which showed that the results of this study are reliable.At the same time,the epidemiological survey and monitoring of AIVs in 8914 samples in 67 sites of 11 provinces in China in 2018 were carried out.The NA genes of 2273 AIVs were sequenced and the phylogenetic analysis was carried out,the results further verified the practicability and reliability of the updated panorama views based on the diversity and distribution characteristics of IAVs.In summary,this study was a most recent update of the diversity and distribution of IAV.Compared with previous studies,more than 200 revisions have been made to describe the diversity and distribution of IAVs in this study,and shed novel insights to the diversity and distribution of IAVs.The results provided a comprehensive and important framework and background information for researchers and epidemic prevention and control personnels worldwide to carry out all kinds of epidemiological investigation,epidemic characteristics analysis and epidemic risk early warning of IAVs.So,it is of great significance for the prevention and control of all kinds of IAV.In addition,this study proposed a new reasonable and concise naming system for all branches and sub branches of IAV gene/subtypes,which is helpful to unify and simplify the academic exchanges of researchers on IAV. |
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