基于全基因组分析2017—2021年福建省猪繁殖与呼吸综合征病毒基因组特征

doi:10.11843/j.issn.0366-6964.2023.04.021

Abstract

Abstract: To investigate the prevalence and genomic characterization of porcine reproductive and respiratory syndrome virus (PRRSV) in Fujian province and provid a theoretical basis for the prevention and control of PRRS, the complete genome of 32 isolates from Fujian province from 2017 to 2021 were analyzed. Tissues and serum were collected from suspected of being infected with PRRSV in Fujian during 2017-2021 were used for virus isolation and full-length genomics sequences amplification by RT-PCR. Genome analyses were performed using the DNASTAR 7.0 package. Phylogenetic trees were constructed by the MEGA 7.0 software using the neighbor-joining method, the genomic recombination of PRRSV were analyzed by using RDP 4.10 and Simplet SimPlot 3.51 softwares. Thirty-two PRRSV-2 strains were successfully isolated. The full length of 32 isolates were determined to be 14938-15439 bp, excluding the poly (A) tail and shared 81.4%-99% identity with PRRSV-2 representative strains and only 59.8%-60.6% with LV. Genotyped of 32 PRRSVs were tested by genetic evolutionary tree constructed by the whole genome and ORF5 gene, and the results showed 75% agreement. Genomic sequence analysis showed Nsp2 and ORF5 are the most variable protein in PRRSV genome, Nsp2 protein has different degrees of amino acid deletion (1-155 aa) and GP5 had high variability in the primary neutralizing epitope (PNE). Recombination analyses revealed a high recombination probability (27/32) and complex recombination patterns were found in the 32 PRRSV strains, including:L1+L8, L1+L3, L8+L5, L8+L3, L1 (Sublineage1.8+Sublineage1.5)+L8, L1+L5+L8, L1+L3+L8, L1+L3+L5, L1+L3+L5+L8. Additionally, PRRSV genomic recombination hotspots mainly distributed in Nsp1, Nsp2, Nsp9 and ORF3 genes. In summary, the epidemiological and evolutionary characteristics of PRRSV indicating the circulating strains in Fujian Province are recombinant strains with NADC30-like PRRSV as the main parent. Genotypes of PRRSV should be based on the results of the full-length genome.

Key words: porcine reproductive and respiratory syndrome virus (PRRSV), virus isolation and identification, full-length genome, genetic diversity, recombination

CLC Number:

S852.659.6

LIU Jiankui, XU Ye, LIU Chen, YU Hui, YANG Yuan, HE Le, LI Jiarui, DAN Huijuan, DAI Ailing, YANG Xiaoyan, WEI Chunhua. Genomic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in Fujian Province from 2017 to 2021 based on Whole Genome[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1579-1589.

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Genomic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in Fujian Province from 2017 to 2021 based on Whole Genome

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