AUTHOR=Wang Jinglong , Lin Siyuan , Quan Dongqun , Wang Hao , Huang Jiabin , Wang Yuxu , Ren Tongwei , Ouyang Kang , Chen Ying , Huang Weijian , Luo Tingrong , Wei Zuzhang 

TITLE=Full Genomic Analysis of New Variants of Porcine Reproductive and Respiratory Syndrome Virus Revealed Multiple Recombination Events Between Different Lineages and Sublineages

JOURNAL=Frontiers in Veterinary Science

VOLUME=Volume 7 - 2020

YEAR=2020

URL=https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2020.00603

DOI=10.3389/fvets.2020.00603

ISSN=2297-1769

ABSTRACT=Porcine reproductive and respiratory syndrome virus (PRRSV) has had a devastating impact on the pig industry in China and monitoring its genetic diversity is important for epidemiological surveillance and understanding its evolution. Here, we determined the complete genome sequences of two PRRSV strains, GXYL1403 and GXNN1839.  Comparative, phylogenetic and recombination detection program analyses showed that the two isolates were recombinant strains with large fragment amino acid deletions in nsp2. GXYL1403 possessed a unique deletion region of 124 amino acids in nsp2 and GXNN1839 contained a deletion of 131 amino acids in nsp2 when compared with VR2332. Further analysis of the full-length sequence suggests that GXYL1403 is a natural recombinant between the sublineage 8.1 (CH-1a like) and sublineage 8.3 (JXA1-like). The recombination site of GXYL1403 is located in nsp9-nsp12 (8961nt-11181nt). GXNN1839 is a natural recombinant between the lineage 5 (VR-2332-like) and lineage 1 (NADC30-like) strains. The recombination events occurred in nsp9 (7872nt-8162nt) and in ORF2 (12587nt-13282nt) in the genome of GXNN1839. These results provide new evidence that PRRSV strains circulating in the field underwent recombination among the different lineages or sublineages of field strains and add to our understanding of RNA combination events which occur in PRRSV.