Molecular Characterization of the Nsp2 and ORF5s of PRRSV Strains in Sichuan China during 2012-2020

Jun Zhao; Zhiwen Xu; Tong Xu; Yuancheng Zhou; Jiangling Li; Huidan Deng; Fengqing Li; Lei Xu; Xiangang Sun; Ling Zhu

doi:10.3390/ani12233309

Molecular Characterization of the Nsp2 and ORF5s of PRRSV Strains in Sichuan China during 2012-2020

Animals (Basel). 2022 Nov 26;12(23):3309. doi: 10.3390/ani12233309.

Authors

Jun Zhao^{1

2}, Zhiwen Xu^{1

3}, Tong Xu¹, Yuancheng Zhou⁴, Jiangling Li⁴, Huidan Deng¹, Fengqing Li^{1

5}, Lei Xu¹, Xiangang Sun¹, Ling Zhu^{1

3}

Affiliations

¹ College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
² Chia Tai Animal Husbandry Investment (Beijing) Co., Ltd., Beijing 101301, China.
³ Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu 611130, China.
⁴ Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610058, China.
⁵ College of Animal Science, Xichang University, Xichang 615012, China.

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that poses a serious threat to the global pig industry. Sichuan Province is one of the largest pig breeding provinces in China. There is a lack of reports on the continuous surveillance and systematic analysis of prevalent strains of PRRSV in Sichuan Province in recent years. To fill this gap, a total of 539 samples were collected from 13 breeding regions in Sichuan during 2012-2020. The detection result showed that the positive rate of PRRSV was 52.32% (282/539). The ORF5s and Nsp2 were obtained and further analyzed, with Chinese reference strains downloaded from the GenBank. Phylogenetic analysis showed that the PRRSV strains sequenced in this study belonged to PRRSV-1 and PRRSV-2 (lineage 1, 3, 5 and 8). In total, 168 PRRSV-2 strains were selected for ORF5 analyses, and these strains were classified into sub-lineage 8.7 (HP-PRRSV), sub-lineage 5.1 (classical PRRSV), sub-lineage 1.8 (NADC30-like), sub-lineage 1.5 (NADC34-like) and sub-lineage 3.5 (QYYZ-like), accounting for 60.71% (102/168), 11.31% (19/168), 18.45% (31/168), 2.97% (5/168) and 6.55% (11/168) of the total analyzed strains, respectively. The Nsp2 of identified PRRSV strains exhibited a nucleotide identity of 44.5-100%, and an amino acid identity of 46.82-100%. The ORF5 of the identified PRRSV strains exhibited a nucleotide identity of 81.3-100%, and an amino acid identity of 78.5-100%. A sequence analysis of ORF5 revealed that the mutation sites of GP5 were mainly concentrated in HVR1 and HVR2 and the virulence sites. In summary, the HP-PRRSV, NADC30-like PRRSV, Classic-PRRSV, QYYZ-like PRRSV, NADC34-like PRRSV and PRRSV-1 strains exist simultaneously in pigs in Sichuan. NADC30-like PRRSV was gradually becoming the most prevalent genotype currently in Sichuan province. This study suggested that PRRSV strains in Sichuan were undergoing genomic divergence.

Keywords: NADC34-like strain; Sichuan China; phylogenetic analysis; porcine reproductive and respiratory syndrome virus.

Abstract

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