The Transcriptomic Analysis Of Influenza Virus Infection And Establishment Of A Viral Clonotype Methodology

Influenza A virus(IAV)belongs to the Orthomyxoviridae family.IAV causes a highly contagious respiratory disease in humans that exacts severe economic losses globally.The virus uses strategies developed to exploit and subvert cellular proteins and pathways to increase its own replication and to inhibit antiviral immune response.In this work,influenza virus is taken as the object to study transcriptome of the virus infected host cells,to find out the changes of molecular biological level of virus invasion of the host,and to establish the method of studying virus gene clonotype.First,A/bar-headed goose/Qinghai/1/2005(A/QH)was uesd to infect A549 and 293 T cells,respectively,in which the virus had a high infection rate on A549 cells.To identify host cellular responses of human cells to influenza infection,differentially expressed genes(DEGs)between AIV-infected groups and uninfected controls were identified using RNA-sequencing.The DEGs were annotated by Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses,which revealed that the DEGs were mainly linked to cellular function and metabolic processes.The global transcriptome analysis results revealed that sensitive genes and pathways of the cells were infected with the influenza virus and provided further evidence to investigate the complicated relationship between IAV and host cells.In addition,a clonotype research has been carried out to help determine whether a disease is associated with the emergence of specific viral clonotypes and makes it more direct disease and gene association.Clonotype research helps to determine whether the virus causing a particular disease has the same clonotype and makes it more direct than disease and gene association.Here,we evaluated emerging direct RNA sequencing and cDNA sequencing with the MinION platform and established a novel approach that combines the high accuracy of Illumina sequencing technology and long reads of MinION sequencing technology to resolve both variants and clonotypes of influenza virus.The approach can quickly discriminate the clonotypes of virus gene with more than 40 variation sites and correct the error rate of MinION sequencing platform,which is capable to further diagnose the composition and distribution of influenza virus gene clonotype in the host,and to understand the virus adaptation and evolution in population level.