Genomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus 1 Revealed Extensive Recombination and Potential Introduction Events in China

SIMPLE SUMMARY: Porcine reproductive and respiratory syndrome, caused by the porcine reproductive and respiratory syndrome virus, is considered one of the most devastating swine diseases worldwide. Porcine reproductive and respiratory syndrome virus 1 was first isolated in China in 2006, and there have been few reports concerning its genetic characteristics in China. We hope to find out the regularity of genetic diversity, recombination, and evolution of the virus by analyzing all available genomic sequences during 1991–2018. We found that high-frequency recombination regions were concentrated in non-structural protein 2 and structural proteins 2 to 4 and extensive deletions in non-structural protein 2; phylogenetic analysis revealed four independent introductions in China. Our results suggest that attention should be paid to the prevention and control of porcine reproductive and respiratory syndrome virus 1 and the rational use of vaccine strains. These results will help us to understand the recombination of porcine reproductive and respiratory syndrome virus and strengthen viral inspection before mixing herds of swine to reduce the probability of novel recombinant variants. Moreover, our study might form the basis of monitoring and control measures to prevent the spread of this economically important virus. ABSTRACT: Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is considered one of the most devastating swine diseases worldwide. PRRSV-1 was first isolated in China in 2006. However, there were few reports concerning the genetic characteristics of PRRSV-1 in China. In this study, three PRRSV-1 strains (HL85, HeB3, and HeB47) were detected by a general RT-qPCR method from clinical samples in 2018. HeB47 was identified as a recombinant between the BJEU06-1 and CReSA228-like strains. To further analyze the recombination and deletion features of PRRSV-1, all the available 88 complete genome sequences (isolated in 19 countries) from 1991 to 2018 in GenBank were analyzed. The high-frequency recombination regions were concentrated in NSP2 and GP2 to GP4. More importantly, phylogenetic analysis of PRRSV-1 revealed four independent introductions in China. Therefore, it is necessary to strengthen the important monitoring of breeding pigs and pork products and epidemiological surveys on pig farms to prevent the further spread of PRRSV-1.