Identification of a Novel Recombinant Type 2 Porcine Reproductive and Respiratory Syndrome Virus in China

Abstract

Since the emergence of NADC30-like porcine reproductive and respiratory syndrome virus (PRRSV) in China in 2013, PRRSVs have undergone rapid evolution. In this study, a novel variant of PRRSV strain (designated SCcd17) was successfully isolated from piglets with clinical signs in Sichuan Province in China in 2017, and the complete genomic sequence was determined. The genome of this new isolate was 15,015 nucleotides (nt) long, and comparative analysis revealed that SCcd17 exhibited 90.2%, 85.2%, 84.9%, and 84.0% nucleotide similarity to PRRSVs NADC30, JXA1, CH-1a, and VR-2332, respectively. Phylogenetic analysis indicated that the SCcd17 strain was classified into the NADC30-like sub-genotype, in which all the strains contained the unique discontinuous 131-amino acid deletion in nonstructural protein 2 (nsp2) when compared to VR-2332-like viruses. Notably, extensive amino acid substitutions were observed in nsp2 and a unique single amino acid deletion at position 33 of the GP5 is being described for the first time. Strikingly, recombination analysis revealed that SCcd17 was the result of recombination between the NADC30-like, JXA1-like, and VR-2332-like strains at five recombination breakpoints: nsp1α (nt 641), nsp3 (nt 5141), nsp10 (nt 9521), open reading frame 3 (ORF3) (nt 12,581), and ORF4 (nt 13,021). The genomic data of SCcd17 will be helpful for understanding the role of genomic recombination in the evolution of PRRSV.

Emergence of a novel highly pathogenic recombinant virus from three lineages of porcine reproductive and respiratory syndrome virus 2 in China 2017

“…The co‐existence of different lineages of PRRSV2 not only complicates the control of PRRSV2 infection in China, but also provides a suitable condition for PRRSV recombination in the field. Distinct recombination patterns between/among different lineages of PRRSV2 were observed in the latest reports (Liu et al., ; Zhou et al., ). In this study, we isolated a novel PRRSV2 variant, denominated SD17‐38, in Shandong province of China in 2017.…”

“…One amino acid deletion at position 34 of GP5 was first found in GZ1101 isolate, which is a RespPRRS MLV‐like virus (Zhou et al., ). The amino acid deletion at position 33 of GP5 was first found in SCcd17, which is a NADC30‐like PRRSV isolate (Zhou et al., ). Here, we first described the SD17‐38 isolate, which simultaneously contains the S/N 33 deletion and N 60 insertion in hypervariable regions of GP5.…”

“…Moreover, recombination events between HP‐PRRSV and NADC30‐like PRRSV have been frequently reported in recent years (Zhao et al., ; Liu et al., ; Wang et al., ). NADC30‐like PRRSV recombined with VR‐2332‐like and CH‐1a‐like classical PRRSV has also been identified (Li, Ji et al., ; Liu et al., ; Zhou et al., ). A latest study identified a triple recombinant virus SDhz1512 that was recombined from NADC30, classical and HP‐PRRSV isolates (Liu et al., ).…”

“…A latest study identified a triple recombinant virus SDhz1512 that was recombined from NADC30, classical and HP‐PRRSV isolates (Liu et al., ). Another recently reported SCcd17 isolate, which contains the amino acid deletion at position 33 of GP5, is also a recombination virus among NADC30‐like, JXA1‐like and VR‐2332‐like isolates (Zhou et al., ). Each fragment alignment and recombination analyses by RDP4 and SimPlot all indicated that our isolate SD17‐38 is also a recombination virus among three lineages of PRRSV2; however, it has distinct recombination patterns compared with the SDhz1512 and SCcd17 isolates.…”

Helicase of Type 2 Porcine Reproductive and Respiratory Syndrome Virus Strain HV Reveals a Unique Structure

“…However, the C-terminal domain (CTD) is variable among nidoviruses. Besides, nsp10 can vary up to approximately 42% on the amino acid level between the two genotypes, and the strains within PRRSV-2 also vary considerably with amino acid differences as high as 8% [21,22]. We previously reported the first structure of the nidovirus helicase, equine arteritis virus (EAV; family Arteriviridae) nsp10, and demonstrated that the CTD perhaps exerts a regulatory function on the helicase core, facilitating coupling between NTPase and polynucleotide binding activities [23].…”