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Genomic Evolution and Selective Pressure Analysis of a Novel Porcine Sapovirus in Shanghai, China

文献类型： 外文期刊

作者： Tao, Jie 1 ; Li, Benqiang 1 ; Shi, Ying 1 ; Cheng, Jinghua 1 ; Tang, Pan 1 ; Jiao, Jiajie 1 ; Liu, Huili 1 ;

作者机构： 1.Shanghai Acad Agr Sci, Inst Anim Husb & Vet Med, Shanghai 201106, Peoples R China

2.Shanghai Key Lab Agr Genet & Breeding, Shanghai 201106, Peoples R China

3.Shanghai Engn Res Ctr Pig Breeding, Shanghai 201302, Peoples R China

关键词： metagenomic sequencing; porcine sapovirus; genomic evolution; recombination; selective pressure

期刊名称：MICROORGANISMS （ 影响因子：4.5； 五年影响因子：4.8 ）

ISSN：

年卷期： 2024 年 12 卷 3 期

页码：

收录情况： SCI

摘要： Porcine sapovirus (PoSaV) is one of the most significant pathogens causing piglet diarrhea, and one with limited genetic characterization. In this study, the prevalence, infection pattern, and genetic evolution of porcine sapovirus were elucidated in detail. The positive rate of PoSaV was 10.1% (20/198), with dual, triple, and quadruple infections of 45%, 40%, and 5%, respectively. To further explore the viral composition in the PoSaV-positive diarrhea feces, metagenomic sequencing was carried out. The results confirmed that RNA viruses accounted for a higher proportion (55.47%), including the two primary viruses of PoSaV (21.78%) and porcine astrovirus (PAstV) (24.54%) in the tested diarrhea feces samples. Afterward, a full-length sequence of the PoSaV isolate was amplified and named SHCM/Mega2023, and also given the identifier of GenBank No. PP388958. Phylogenetic analysis identified the prevalent PoSaV strain SHCM/Mega2023 in the GIII genogroup, involving a recombinant event with MK962338 and KT922089, with the breakpoint at 2969-5132 nucleotides (nt). The time tree revealed that the GIII genogroup exhibits the widest divergence time span, indicating a high likelihood of viral recombination. Moreover, SHCM/Mega2023 had three nucleotide "RPL" insertions at the 151-153 nt site in the VP2 gene, compared to the other GIII strains. Further selective pressure calculations demonstrate that the whole genome of the SHCM/Mega2023 strain was under purifying selection (dN/dS < 1), with seven positively selected sites in the VP1 protein, which might be related to antigenicity. In conclusion, this study presents a novel genomic evolution of PoSaV, offering valuable insights into antigenicity and for vaccine research.

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