The Whole Genome Sequencing And Diagnosis Method Established Of Liao Ning Swine GETV

Getah virus(Getah virus,GETV)is an arbovirus that endangers the swine industry.It can cause sows(especially in the pre-pregnancy period)to give birth to stillbirths,tremors in newborn swinelets,red skin,mental depression,brownish diarrhea and more High mortality rate.When weaned swinelets are subject to stress reaction,GETV infection is likely to occur,often mixed infection with some bacteria or viruses,and the mortality rate can reach more than50%in severe cases.Sick swines,diseased swines and vector sources are important sources of infection of this disease.Therefore,analyzing the characteristics of Liao Ning swine GETV gene provides an important reference for a comprehensive understanding of the phylogenetic relationship between Liao Ning swine GETV strains,molecular epidemiological characteristics and the establishment of diagnostic methods.In this study,RT-PCR was used to amplify swine GETV gene fragments.After sequencing,the whole genome sequence of swine GETV was assembled using bioinformatics software,and its nucleotide and amino acid homology and phylogenetic tree characteristics were analyzed to understand the genetics of swine GETV genes.Variation characteristics,fluorescent probes and nested PCR detection methods were established for the NSP1 gene of swine GETV,and optimized in terms of sensitivity and specificity.The results showed that the whole genome of Liao Ning swine GETV had a nucleotide homology of 97.5%to 99.7%with the genome of other GETV representative strains;among them,CAP,E1,E2,E3,NSP1,NSP2,NSP3,NSP4,6K genes and other GETV representatives The gene nucleotide homology of the strains were 97.4%?99.6%,98.4%?99.8%,97.9%?99.1%,94.8%?99.6%,96.3%?99.6%,97.0%?99.4%,96.7%?99.3%,95.3%?99.4%,97.4%?99.4%,97.5%?99.7%;Liao Ning swine GETV whole genome and its 9 genes have amino acid homology with other representative GETV strains of 96.2%?99.6%,92.3%?98.7%,94.5%?97.9%,96.3%?98.2%,86.0%?99.0%,97.3%?99.5%,91.3%?97.6%,90.1%?97.4%,86.9%?98.2%,97.6%?98.8%.It shows that the amino acid positions of the GETV gene of Liao Ning swines are different to different degrees from the corresponding genes of the GETV representative strain.The phylogenetic tree results showed that the whole genome of Liao Ning swine GETV and its 9 genes have the closest homology relationship with He Nan HNJZ-S2 strain,and they belong to the Asian strain.In this study,the optimum concentration of primer was 4umol/L,the optimum concentration of probe was 6umol/L,the optimum annealing temperature was 50°C,and the minimum amount of nucleic acid was 8.8369×10~1copies/?L.The optimum concentration of primers was 3umol/L,the optimum annealing temperature was 52°C,and the minimum amount of nucleic acid was 8 copies/?L,the minimum number of copies detected by the two methods was higher than that detected by commercial porcine Geta virus RT-PCR(90copies/?L),and no other porcine pathogens were detected,the results showed that the fluorescence probe and nested PCR assay for Liaoning pig GETV NSP1were sensitive and specific.In this paper,we studied the homology and genetic evolution of Liaoning pig GETV genome and single gene.At the same time,a Liao Ning swine with better specificity and sensitivity was established.The GETV fluorescent probe and Nest's PCR diagnostic method provide a theoretical basis for the prevention and control of Liao Ning swine GETV,which has important guiding significance.