TY - JOUR
T1 - Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
AU - Xu, Hu
AU - Xiang, Lirun
AU - Tang, Yan Dong
AU - Li, Chao
AU - Zhao, Jing
AU - Gong, Bangjun
AU - Sun, Qi
AU - Leng, Chaoliang
AU - Peng, Jinmei
AU - Wang, Qian
AU - Zhou, Guohui
AU - An, Tongqing
AU - Cai, Xuehui
AU - Tian, Zhi Jun
AU - Zhang, Hongliang
AU - Song, Mingxin
N1 - Publisher Copyright:
Copyright © 2022 Xu, Xiang, Tang, Li, Zhao, Gong, Sun, Leng, Peng, Wang, Zhou, An, Cai, Tian, Zhang and Song.
PY - 2022/6/30
Y1 - 2022/6/30
N2 - In the last decade, the emergence of QYYZ-like porcine reproductive and respiratory syndrome virus (PRRSV) has attracted increasing attention due to the high incidence of PRRSV mutation and recombination. However, the endemic status and genomic characteristics of the QYYZ-like strains are unclear. From 2018 to October 2021, 24 QYYZ-like PRRSV isolates were obtained from 787 PRRSV-positive clinical samples. Only one QYYZ-like positive sample was from a northern province, and the rest were from central and southern provinces. We selected 9 samples for whole-genome sequencing, revealing genome lengths of 15,008–15,316 nt. We retrieved all the available whole-genome sequences of QYYZ-like PRRSVs isolated in China from 2010 to 2021 (n = 28) from GenBank and analyzed them together with the new whole-genome sequences (n = 9). Phylogenetic tree analysis based on the ORF5 gene showed that all QYYZ-like PRRSV strains belonged to sublineage 3.5 but were clustered into three lineages (sublineage 1.8, sublineage 3.5, and sublineage 8.7) based on whole-genome sequences. Genomic sequence alignment showed that QYYZ-like strains, have characteristic amino acids insertions or deletions in the Nsp2 region (same as NADC30, JXA1 and QYYZ) and that thirteen strains also had additional amino acid deletions, mostly between 468 and 518 aa. Moreover, QYYZ-like strains (sublineage 3.5) have seven identical characteristic amino acid mutations in ORF5. Recombination analysis revealed that almost all QYYZ-like complete genome sequences (36/37) were products of recombination and mainly provided structural protein fragments (GP2-N) for the recombinant strains. Overall, QYYZ-like strains were mainly prevalent in central and southern China from 2018 to 2021, and these strains provided recombinant fragments in the PRRSV epidemic in China.
AB - In the last decade, the emergence of QYYZ-like porcine reproductive and respiratory syndrome virus (PRRSV) has attracted increasing attention due to the high incidence of PRRSV mutation and recombination. However, the endemic status and genomic characteristics of the QYYZ-like strains are unclear. From 2018 to October 2021, 24 QYYZ-like PRRSV isolates were obtained from 787 PRRSV-positive clinical samples. Only one QYYZ-like positive sample was from a northern province, and the rest were from central and southern provinces. We selected 9 samples for whole-genome sequencing, revealing genome lengths of 15,008–15,316 nt. We retrieved all the available whole-genome sequences of QYYZ-like PRRSVs isolated in China from 2010 to 2021 (n = 28) from GenBank and analyzed them together with the new whole-genome sequences (n = 9). Phylogenetic tree analysis based on the ORF5 gene showed that all QYYZ-like PRRSV strains belonged to sublineage 3.5 but were clustered into three lineages (sublineage 1.8, sublineage 3.5, and sublineage 8.7) based on whole-genome sequences. Genomic sequence alignment showed that QYYZ-like strains, have characteristic amino acids insertions or deletions in the Nsp2 region (same as NADC30, JXA1 and QYYZ) and that thirteen strains also had additional amino acid deletions, mostly between 468 and 518 aa. Moreover, QYYZ-like strains (sublineage 3.5) have seven identical characteristic amino acid mutations in ORF5. Recombination analysis revealed that almost all QYYZ-like complete genome sequences (36/37) were products of recombination and mainly provided structural protein fragments (GP2-N) for the recombinant strains. Overall, QYYZ-like strains were mainly prevalent in central and southern China from 2018 to 2021, and these strains provided recombinant fragments in the PRRSV epidemic in China.
KW - QYYZ-like PRRSV
KW - complex patterns of recombination
KW - epidemiological characteristics
KW - recombination hotspots
KW - whole-genome analysis
UR - http://www.scopus.com/inward/record.url?scp=85134198377&partnerID=8YFLogxK
U2 - 10.3389/fvets.2022.945381
DO - 10.3389/fvets.2022.945381
M3 - Article
AN - SCOPUS:85134198377
SN - 2297-1769
VL - 9
JO - Frontiers in Veterinary Science
JF - Frontiers in Veterinary Science
M1 - 945381
ER -