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Phylogenetically evolutionary analysis provides insights into the genetic diversity and adaptive evolution of porcine deltacoronavirus

文献类型： 外文期刊

作者： Guo, Zhenhua 1 ; Lu, Qingxia 1 ; Jin, Qianyue 1 ; Li, Peng 4 ; Xing, Guangxu 1 ; Zhang, Gaiping 1 ;

作者机构： 1.Henan Acad Agr Sci, Key Lab Anim Immunol, Minist Agr, Henan Prov Key Lab Anim Immunol, Zhengzhou 450002, Peoples R China

2.Peking Univ, Sch Adv Agr Sci, Beijing, Peoples R China

3.Jiangsu Coinnovat Ctr Prevent & Control Important, Yangzhou, Peoples R China

4.Iowa State Univ, Vet Diagnost & Prod Anim Med, Ames, IA USA

关键词： Porcine deltacoronavirus; Genetic diversity; Recombination; Adaptive evolution; Spike protein

期刊名称：BMC VETERINARY RESEARCH （ 影响因子：2.6； 五年影响因子：2.9 ）

ISSN：

年卷期： 2024 年 20 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundPorcine deltacoronavirus (PDCoV) is one of the emerging swine enteric coronaviruses (SECoVs), which has been widely prevalent in the North America and Asia. In addition to causing severe diarrhea in piglets, PDCoV also shows the potential to infect diverse host species, including calves, chickens, turkey poults, and humans. However, the clinical pathogenicity and genetic evolution of PDCoV is still not fully understood.ResultsHere, we recorded an outbreak of a novel recombinant PDCoV strain (CHN-HeN06-2022) in a large nursery fattening pig farm. Genomic analysis showed that the CHN-HeN06-2022 strain shared 98.3-98.7% sequence identities with the Chinese and American reference strains. To clarify the evolutionary relationships, phylogenetic analysis was performed using the PDCoV genome sequences available in the GenBank database. Based on genetic distance and geographical distribution, the phylogenetic tree clearly showed that all the PDCoV sequences could be divided into lineage 1 and lineage 2, which were further classified into sublineage 1.1 (Chinese strains), 1.2 (the North American strains), 2.1 (the Southeast Asian strains), and 2.2 (Chinese strains). Corresponding to the evolutionary tree, we found that, compared to lineage 1, lineage 2 strains usually contain a continuous 6-nt deletion in Nsp2 and a 9-nt deletion in Nsp3, respectively. Furthermore, recombination analysis suggested that the CHN-HeN06-2022 occurred segments exchange crossed Nsp2 and Nsp3 region between sublineage 1.1 and sublineage 2.1. Combined with previously reported recombinant strains, the highest recombination frequency occurred in Nsp2, Nsp3, and S gene. Additionally, we identified a total of 14 amino acid sites under positive selection in spike protein, most of which are located in the regions related with the viral attachment, receptor binding, and membrane fusion.ConclusionsTaken together, our studies provide novel insights into the genetic diversity and adaptive evolution of PDCoV. It would be helpful to the development of vaccine and potential antiviral agent.

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