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Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021

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. F...

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Autores principales: Xu, Hu, Xiang, Lirun, Tang, Yan-Dong, Li, Chao, Zhao, Jing, Gong, Bangjun, Sun, Qi, Leng, Chaoliang, Peng, Jinmei, Wang, Qian, Zhou, Guohui, An, Tongqing, Cai, Xuehui, Tian, Zhi-Jun, Zhang, Hongliang, Song, Mingxin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9280713/
https://www.ncbi.nlm.nih.gov/pubmed/35847645
http://dx.doi.org/10.3389/fvets.2022.945381
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author Xu, Hu
Xiang, Lirun
Tang, Yan-Dong
Li, Chao
Zhao, Jing
Gong, Bangjun
Sun, Qi
Leng, Chaoliang
Peng, Jinmei
Wang, Qian
Zhou, Guohui
An, Tongqing
Cai, Xuehui
Tian, Zhi-Jun
Zhang, Hongliang
Song, Mingxin
author_facet Xu, Hu
Xiang, Lirun
Tang, Yan-Dong
Li, Chao
Zhao, Jing
Gong, Bangjun
Sun, Qi
Leng, Chaoliang
Peng, Jinmei
Wang, Qian
Zhou, Guohui
An, Tongqing
Cai, Xuehui
Tian, Zhi-Jun
Zhang, Hongliang
Song, Mingxin
author_sort Xu, Hu
collection PubMed
description 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.
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spelling pubmed-92807132022-07-15 Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021 Xu, Hu Xiang, Lirun Tang, Yan-Dong Li, Chao Zhao, Jing Gong, Bangjun Sun, Qi Leng, Chaoliang Peng, Jinmei Wang, Qian Zhou, Guohui An, Tongqing Cai, Xuehui Tian, Zhi-Jun Zhang, Hongliang Song, Mingxin Front Vet Sci Veterinary Science 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. Frontiers Media S.A. 2022-06-30 /pmc/articles/PMC9280713/ /pubmed/35847645 http://dx.doi.org/10.3389/fvets.2022.945381 Text en Copyright © 2022 Xu, Xiang, Tang, Li, Zhao, Gong, Sun, Leng, Peng, Wang, Zhou, An, Cai, Tian, Zhang and Song. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Xu, Hu
Xiang, Lirun
Tang, Yan-Dong
Li, Chao
Zhao, Jing
Gong, Bangjun
Sun, Qi
Leng, Chaoliang
Peng, Jinmei
Wang, Qian
Zhou, Guohui
An, Tongqing
Cai, Xuehui
Tian, Zhi-Jun
Zhang, Hongliang
Song, Mingxin
Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
title Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
title_full Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
title_fullStr Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
title_full_unstemmed Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
title_short Genome-Wide Characterization of QYYZ-Like PRRSV During 2018–2021
title_sort genome-wide characterization of qyyz-like prrsv during 2018–2021
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9280713/
https://www.ncbi.nlm.nih.gov/pubmed/35847645
http://dx.doi.org/10.3389/fvets.2022.945381
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