Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
Youjiang Medical University for Nationalities, Baise, Guangxi, China.
Microbiol Spectr. 2023 Jun 15;11(3):e0488822. doi: 10.1128/spectrum.04888-22. Epub 2023 Apr 5.
Human astrovirus (HAstV) strains exhibit high levels of genetic diversity, and many recombinant strains with different recombination patterns have been reported. The aims of the present study were to investigate the emergence of HAstV recombinant strains and to characterize the recombination patterns of the strains detected in pediatric patients admitted to the hospital with acute gastroenteritis in Chiang Mai, Thailand. A total of 92 archival HAstV strains detected in 2011 to 2020 were characterized regarding their open reading frame 1a (ORF1a) genotypes in comparison with their ORF1b genotypes to identify recombinant strains. The recombination breakpoints of the putative recombinant strains were determined by whole-genome sequencing and were analyzed by SimPlot and RDP software. Three HAstV strains (CMH-N178-12, CMH-S059-15, and CMH-S062-15) were found to be recombinant strains of three different HAstV genotypes, i.e., HAstV5, HAstV8, and HAstV1 within the ORF1a, ORF1b, and ORF2 regions, respectively. The CMH-N178-12 strain displayed recombination breakpoints at nucleotide positions 2681 and 4357 of ORF1a and ORF1b, respectively, whereas the other two recombinant strains, CMH-S059-15 and CMH-S062-15, displayed recombination breakpoints at nucleotide positions 2612 and 4357 of ORF1a and ORF1b, respectively. This is the first study to reveal nearly full-length genome sequences of HAstV recombinant strains with a novel recombination pattern of ORF1a-ORF1b-ORF2 genotypes. This finding may be useful as a guideline for identifying other recombinant HAstV strains in other geographical regions and may provide a better understanding of their genetic diversity, as well as basic knowledge regarding virus evolution. Recombination is one of the mechanisms that plays a crucial role in the genetic diversity and evolution of HAstV. We wished to investigate the emergence of HAstV recombinant strains and to analyze the whole-genome sequences of the putative HAstV recombinant strains detected in pediatric patients with acute gastroenteritis in 2011 to 2020. We reported 3 novel intergenotype recombinant strains of HAstV5-HAstV8-HAstV1 at the ORF1a-ORF1b-ORF2 regions of the HAstV genome. The hot spots of recombination occur frequently near the ORF1a-ORF1b and ORF1b-ORF2 junctions of the HAstV genome. The findings indicate that intergenotype recombination of HAstV occurs frequently in nature. The emergence of a novel recombinant strain allows the new virus to adapt and successfully escape from the host immune system, eventually emerging as the predominant genotype to infect human populations that lack herd immunity against novel recombinant strains. The virus may cause an outbreak and needs to be monitored continually.
人星状病毒（HAstV）株表现出高度的遗传多样性，并且已经报道了许多具有不同重组模式的重组株。本研究的目的是调查 HAstV 重组株的出现，并分析在泰国清迈因急性胃肠炎住院的儿科患者中检测到的重组株的重组模式。对 2011 年至 2020 年间检测到的 92 株存档 HAstV 株的开放阅读框 1a（ORF1a）基因型与 ORF1b 基因型进行了特征分析，以确定重组株。通过全基因组测序确定推定重组株的重组断点，并通过 SimPlot 和 RDP 软件进行分析。发现 3 株 HAstV 株（CMH-N178-12、CMH-S059-15 和 CMH-S062-15）在 ORF1a、ORF1b 和 ORF2 区域内分别为三种不同的 HAstV 基因型（HAstV5、HAstV8 和 HAstV1）的重组株。CMH-N178-12 株在 ORF1a 和 ORF1b 的核苷酸位置 2681 和 4357 处显示重组断点，而其他两个重组株 CMH-S059-15 和 CMH-S062-15 在 ORF1a 和 ORF1b 的核苷酸位置 2612 和 4357 处显示重组断点。这是首次揭示具有新型 ORF1a-ORF1b-ORF2 基因型重组模式的 HAstV 重组株的全长基因组序列的研究。这一发现可能有助于在其他地理区域识别其他重组 HAstV 株，并更好地了解它们的遗传多样性，以及病毒进化的基础知识。重组是 HAstV 遗传多样性和进化中起关键作用的机制之一。我们希望调查 HAstV 重组株的出现，并分析 2011 年至 2020 年间在急性胃肠炎住院的儿科患者中检测到的推定 HAstV 重组株的全基因组序列。我们报道了在 HAstV 基因组的 ORF1a-ORF1b-ORF2 区域中，有 3 株新型的 HAstV5-HAstV8-HAstV1 种间重组株。重组的热点经常发生在 HAstV 基因组的 ORF1a-ORF1b 和 ORF1b-ORF2 连接处附近。研究结果表明，HAstV 种间重组在自然界中经常发生。新型重组株的出现使新病毒能够适应并成功逃避宿主免疫系统，最终成为感染缺乏针对新型重组株的群体免疫力的人群的主要基因型。该病毒可能会引发疫情，需要持续监测。
