Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O. Box 29053, Nairobi 00625, Kenya.
Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA.
Viruses. 2020 Nov 5;12(11):1262. doi: 10.3390/v12111262.
Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus . Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.
星状病毒（AstVs）广泛分布，与人类和动物的胃肠炎有关。关于非洲星状病毒的遗传多样性和流行病学知识有限。本研究旨在描述肯尼亚和乌干达无症状小农户仔猪中的星状病毒。从最初为轮状病毒研究收集的 446 头 6 个月以下仔猪中随机选择了 24 个样本进行全基因组分析。13 个（13/24）样本的序列与属具有高同源性。对具有完整（或近乎完整）AstV 基因组的 7 株病毒进行分析，发现与已知猪星状病毒（PoAstV）株的核苷酸和氨基酸序列具有不同的同源性。U083 和 K321 株与已知的 PoAstV2 株的核苷酸序列同源性在 66.4%至 75.4%之间；U460 株与已知的 PoAstV3 株的核苷酸序列同源性在 57.0%至 65.1%之间；而 K062、K366、K451 和 K456 株与已知的 PoAstV4 株的核苷酸序列同源性在 63.5%至 80%之间。较低的序列同一性（<90%）表明，研究区域中存在新型猪星状病毒基因型。使用全基因组进行重组分析表明，PoAstV4 中存在多种重组事件的证据，这表明重组可能导致了观察到的遗传多样性。线性抗原表位预测和对我们田间毒株衣壳蛋白的比较分析确定了潜在的候选表位，这可能有助于设计免疫诊断工具和亚单位疫苗。这些发现为东非猪星状病毒的分子流行病学提供了新的见解。
