Genome Characterization of a Recombinant Porcine Reproductive and Respiratory Syndrome Virus

Porcine reproductive and respiratory syndrome virus (PRRSV) mutates continuously, and it is increasingly difficult to control it. To monitor the genetic evolution characteristics of PRRSV timely under the condition of natural infection, a novel PRRSV variant named SHpd1/2018 was isolated from PRRSV positive clinical samples. The results showed that the SHpd1/2018, with a total genome length of 15 018 bp (excluding poly A), showed similar proliferation characteristics to HP-PRRSV strain HuN4. However, it could not be recognized by the monoclonal antibody against HuN4-Nsp2. The sequence analysis indicated that SHpd1/2018 had the greatest homology with HP-PRRSV-like strains, reaching 94.3% with HuN4 strain. The results of recombination analysis showed that SHpd1/2018 was recombined from HP-PRRSV-like strain (main parent strain) and NADC30 strain (secondary parent strain), and both the two recombination breakpoints nt2002 and nt3205 are located in the hypervariable regions of the Nsp2 gene. In short, we confirmed that the isolated strain SHpd1/2018 is a recombinant PRRSV, which may be the main cause of the disease in the pig farm in Shanghai.