Investigation And Analysis On Etiology Of Major Respiratory Virus Diseases In Pigs In Shandong Province From 2018 To 2019

With the development of pig industry,the incidence of porcine disease becomes more frequent and complicated.Diseases of respiratory system,digestive system,and reproduction system are the major problems in the pig industry of China.According to previous studies,immunosuppression associated disease is the major cause of respiratory illness in pigs,including Classical swine fever virus(CSFV),Porcine Circovirus Type 2(PCV2),Respiratory Syndrome Virus(PRRSV),Pseudorabies virus(PRV),etc.Immunosuppression virus infects the host and makes them more susceptible to other viruses and bacteria to invade.Therefore,it is essential to survey the possible pathogens assosicatted porcine respiratory disease.This study aims to understand the prevalence of porcine respiratory diseases,genetic evolution of CSFV,PRRS,and PCV.This study will lay a foundation for future diagnoses,treatment,and preventions on porcine respiratory disease.Major findings of this study are listed as follows:1.During 2018-2019,a total of 2650 sets of swine tissues and swine nose swabs were detected for PRRSV,CSFV,PCV2 and PRV by fluorescent quantitative PCR or RT-PCR.The positive rates of PRRSV,PCV2,CSFV,and PRV were 3.81%(101/2650),8.45%(224/2650),4.42%(117/2650),and 0.07%(2/2650),respectively.The data analysis showed that the trend of the difference in the positive rate of pathogens in different seasons was basically the same.PRRSV,CSFV,and PCV2 infections were common in different swine herds,and there were some differences in the positive rates of tested samples in different regions.2.Sequence analysis of the E2 genes of nine CSFV viruses showed that compared with the HCLV vaccine strain,11 mutations were observed in key amino acid sites of E2 that could cause immune escape.The phylogenetic trees of 5?UTR and E2 showed that the 9 strains belong to the 2.1d subgroup,which was distinctive from Shimen strain and HCLV vaccine strain.In conclusion,CSFV circulating in Shandong has evolved significantly under the immune pressure of swine fever attenuated vaccine.3.Gentic analysis of PRRSV indeified in this study.Phylogenetic tree and genetic analysis based on the ORF5 gene revealed that 11 PPRV strains were classified as lineage 1and were in the same branch as the NADC30-like strain.The other 9 strains belong to lineage8,of which 8 strains are in the same branch as the JXA1 highly pathogenic strain,indicating that NADC30 PRRSV is predominantly circulating in Shandong Province.nsp2 has highvariability,which led to the emergence of a new HP-PRRSV strain.Deletions and insertions of amino acids in the HVR were observed in nsp2 gene of the PRRSV found in this study,which might cause the emergence of highly pathogenic strains.4.Genome-wide genetic variation analysis of the 22 strains of PCV2 detected in this study showed that PCV2 b and PCV2 e were the main pandemic strains in shandong province.Compared with the vaccine strain,our experimental strain have several amino acid site mutations.Especially whether the high degree of variation rigeon can lead to the unsatisfactory immune effect of the current vaccine still needs further study.The antigen index prediction analysis found that the antigen index of PCV2 e subtype strains was the most different from the four vaccine strains,suggesting that we need to carry out epidemic analysis of the PCV2 gene subtype in this district before the vaccine immunity.In particular,if the PCV2 e subtype is prevalent,we need to consider whether to immunize animal with the current commercial vaccine.