Whole Genome Analysis of Two Novel Type 2 Porcine Reproductive and Respiratory Syndrome Viruses with Complex Genome Recombination between Lineage 8, 3, and 1 Strains Identified in Southwestern China

Abstract

Recombination among porcine reproductive and respiratory syndrome viruses (PRRSVs) is thought to contribute to the emergence of new PRRSV variants. In this study, two newly emerged PRRSV strains, designated SCcd16 and SCya17, are isolated from lung tissues of piglets in Southwestern China. Genome comparative analysis reveals that SCcd16/SCya17 exhibit 93.1%/93.2%, 86.9%/87.0%, 85.3%/85.7%, and 83.6%/82.0% nucleotide similarity to PRRSVs JXA1, VR-2332, QYYZ and NADC30, respectively. They only exhibit 44.8%/45.1% sequence identity with LV (PRRSV-1), indicating that both emergent strains belong to the PRRSV-2 genotype. Genomic sequence alignment shows that SCcd16 and SCya17 have the same discontinuous 30-amino acid (aa) deletion in Nsp2 of the highly pathogenic Chinese PRRSV strain JXA1, when compared to strain VR-2332. Notably, SCya17 shows a unique 5-nt deletion in its 3’-UTR. Phylogenetic analysis shows that both of the isolates are classified in the QYYZ-like lineage based on ORF5 genotyping, whereas they appear to constitute an inter-lineage between JXA1-like and QYYZ-like lineages based on their genomic sequences. Furthermore, recombination analyses reveal that the two newly emerged PRRSV isolates share the same novel recombination pattern. They have both likely originated from multiple recombination events between lineage 8 (JXA1-like), lineage 1 (NADC30-like), and lineage 3 (QYYZ-like) strains that have circulated in China recently. The genomic data from SCcd16 and SCya17 indicate that there is on going evolution of PRRSV field strains through genetic recombination, leading to outbreaks in the pig populations in Southwestern China.

Two novel recombinant porcine reproductive and respiratory syndrome viruses belong to sublineage 3.5 originating from sublineage 3.2

“…Subsequently, lineage 3 PRRSV emerged in Hong Kong (2004) and mainland China (2005). However, the reemerged lineage 3 PRRSV strains in southern China display increased genetic diversity (Brar et al, ; Dong et al, ; Gao et al, ; Liu et al, ; Lu et al, ; Shi et al, ; Sun et al, ; Zhou et al, ). In this study, SD110‐1608 and SDWH27‐1710 were classified into sublineage 3.5 and maintained a close relationship with representative strains QYYZ and GDsg, respectively.…”

“…Lineage 3 has widely spread throughout Guangdong Province (Gao et al, ; Xie et al, ). Consequently, lineage 3 strains have been constantly detected in neighbouring provinces in southern China (Liu et al, ; Zhou et al, ). Considering the collected data, analysed phylogenies, geographic distribution and circulation of pigs in the swine trade, the hypothesized transmission route is that the disease was initially transmitted to the peripheral provinces (Gao et al, ).…”

Genetic Characterization and Pathogenicity of a Novel Recombined Porcine Reproductive and Respiratory Syndrome Virus 2 among Nadc30-Like, Jxa1-Like, and Mlv-Like Strains

“…However, the complex recombination pattern among a NADC30-like, a JXA1-like, and the classical PRRSV-2-derived MLV vaccine strain (RespPRRS MLV) has never been described. In our previous investigation, we found that JXA1-like, NADC30-like, VR-2332-like, and QYYZ-like strains had coexisted in some pig herds in the Sichuan Province since 2016, and the following different recombination patterns were observed in this region: (i) NADC30-like + JXA1-like [ 23 ]; (ii)NADC30-like + JXA1-like + VR-2332-like [ 27 ]; and (iii) NADC30-like + JXA1-like + QYYZ-like [ 28 ]. This evidence thus further supported the possible recombination among the PRRSV strains, NADC30-like and JXA1-like, and the vaccine strain, RespPRRS MLV (VR-2332-like).…”

“…Additionally, NADC30-like strains were found to recombine with JXA1-like strains (HENAN-HEB, JL580, FJ1402, TJnh1501, 15HEN1, HNhx, and SCnj16) [ 17 , 18 , 19 , 20 , 21 , 22 , 23 ] or VR-2332-like strains (Chsx1401, HENAN-XINX, and HNyc15) [ 14 , 20 , 24 ]. Moreover, several complex recombinants among the three lineages of PRRSV-2 strains (SDhz1512, SD17-38, SCcd16, SCcd17, and SCya17) have also been observed in China [ 25 , 26 , 27 , 28 ].…”

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

“…The increasing diversity of the type 2 PRRSV is related to point mutations and genetic recombination among the field strains or in between the field and modified live vaccine (MLV) strains, which can lead to some new emerging antigenic variant strains ( 6 , 18 – 24 ). In the present study, we identify two novel recombinant PRRSV strains circulating in swine farms in Guangxi, a province of southern China.…”