Metagenomies Analysis And Genetic Diversity Study Of Porcine Viruses In Ningxia Yinchuan Region

Metagenomies is a new technology that uses the genetic material of all viruses in the environment to quickly identify the viral components in the environment and obtain the viral sequence by high-throughput sequencing of the virus.At present,the characteristics of viral metagenomics are able to systematically alert the occurrence of known viruses and the emergence of new viruses in various environments and various intermediate hosts in the current occurrence of viral zoonosis and these are the technologies that the current virus research institute needs.At present,the prevalence data of swine virus in Ningxia is relatively scarce in China.Therefore,this study aimed to carry out high-throughput sequencing of piglets after weaning in two large-scale swine farms in Ningxia,and then carried out virus metagenomic analysis and selected relative epidemic survey.We celected the virus with less popular investigation,high positive rate or infected humanity and take verification by RT-PCR,in order to grasp the epidemic situation of the swine farm virus group in Ningxia,and provide important basic data for the study of the prevalence of various viruses in swines in China.The research shows that the high-throughput sequencing of weaned piglets in Ningxia can directly annotate the number of reads of the virus sequence to 9.16%of the total number of reads.The annotated virus belongs to 30 known families of viruses,including double-stranded DNA(dsDNA)virus,double-stranded RNA(dsRNA)virus,single-stranded DNA(ssDNA)and single-stranded RNA(ssRNA).By analyzing the splicing results of the virus metagenomic reads,we found that the number of reads obtained by sequencing is not proportional to the number of contigs of the splicing results.Five viruses of the Sapelovirus,Teschovirus,Mamastrovirus,Torovirus and Sapovirus found in weaned piglets were designed for each of the five viruses.A specific detection primer for viruses,and the positive detection rate of these five viruses in two swine farms in Ningxia was obtained by RT-PCR test,and the total positive detection rate of Sapelovirus was 61.25%,The total positive detection rate of Teschovirus was 61.25%,the total positive detection rate of Mamastrovirus was 21.25%,the total positive detection rate of Torovirus was 31.25%,and the total positive detection rate of Sapovirus was 1.25%.In this experiment,the detected viral sequences were compared by phylogenetic relationship,and the relationship between these five viruses and other homologous viruses was determined.This study uses virus metagenomics technology to analyze the virus carrying in weaned piglets in Ningxia,and enriches the background data of Ningxia virus.The genetic diversity of the Sapelovirus,Teschovirus,Mamastrovirus,Torovirus,Sapovirus and the possibility of cross-species transmission of some viruses were analyzed.