| The main influenza viruses that infect humans are H1N1 and H3N2,which threaten human life and health worldwide.Influenza viruses are highly variable,and adaptive mutations occur at intervals to escape the host immune system and adapt to the environment.Therefore,strengthening the monitoring and evolutionary dynamics of influenza viruses can provide an important basis for influenza virus prevention and control.In this study,the influenza surveillance data and bioinformatics methods were used to analyze the evolutionary dynamics of H1N1/pdm2009 in India from 2009 to 2018 and the adaptive evolution of H3 subtype influenza virus transmission among different hosts.A global outbreak of the H1N1 influenza virus in 2009 caused tens of thousands of infections and thousands of deaths in India.This new recombinant virus replaced the previous seasonal H1N1 and became epidemic in the population.Then H1N1 influenza virus broke out in India in 2015 and 2017 respectively.In order to better understand the causes of the three outbreaks,the evolutionary dynamics of the H1N1/pdm2009 in this region,and whether H1N1/pdm2009 has undergone adaptive evolution.This study collected all the H1N1 influenza virus sequence from India and compared it with data from some tropical countries in South and Southeast Asia(Bangladesh,Myanmar,Nepal,Singapore,and Vietnam)that are geographically close to India.Then using d N/d S,Tajima’s D test,Fu & Li’D * tset,Bayesian skygrid model and site model to analysis the H1N1 influenza virus in these countries after 2009.The H3 subtype influenza virus has a wide host range,can infect humans,pigs,birds,and horses.The adaptive evolution of influenza virus plays an important role in cross-host transmission.At the same time,HA of influenza virus is the main factor that determines receptor specificity and has an important influence on host range.Therefore,the HA gene sequences of all H3 subtype viruses in the influenza virus database were collected.Then positive selection analysis and parallel/convergent evolution analysis were performed to detection whether the adaptive evolution of H3 subtype influenza virus between different hosts occurred.The results of the research on the evolutionary dynamics of H1N1/pdm2009 outbreaks in India from 2009 to 2018 showed that in the 2014/2015 influenza season,HA and NA genes have population expansion,and in 2012/2013 and 2013/2014,Positive selection signals of HA were detected.And 8 sites of HA gene have undergone positive selection: 45,94,104,124,166,188,225,and 238.In the parallel/convergent evolution of the HA gene of the H3 subtype influenza virus,a significant positive selection signal was found in the dog-cat branch.In addition,29 parallel/convergent evolutionary sites have been identified,of which 144,145,158,188,226,229,and 275 in HA have been reported to affect the antigenicity and cross-host transmission of influenza viruses.In summary,before the outbreak of H1N1 influenza virus in India in 2015,they experienced population expansion and adaptive evolution.H3 subtype influenza viruses have undergone adaptive evolution,enabling them to adapt to new host environments.This study provides clues for further experimental verification and clarify the adaptation process. |
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