Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations.

IF 4.3 3区医学 Q1 GASTROENTEROLOGY & HEPATOLOGY

Gut Pathogens Pub Date : 2023-09-20 DOI:10.1186/s13099-023-00569-6

Shainey Alokit Khakha, Tintu Varghese, Sidhartha Giri, Alan Durbin, Gene S Tan, Maheswari Kalaivanan, Jasmin Helan Prasad, Gagandeep Kang

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Abstract

Rotaviruses (RVs) are the most common etiological agent of acute gastroenteritis among young children, even after vaccine introduction in low-income countries. A whole-genome classification representing the 11 RV genes, was introduced for surveillance and characterization of RVs. This study characterized the common circulating strains in Vellore, India from 2002 to 2017 to understand rotavirus strain diversity and evolution using Whole genome sequencing (WGS) carried out on Illumina MiSeq. The 89% (92% of Wa-like, 86% of DS-1-like) of strains had classical constellations, while reassortant constellations were seen in 11% (8% of Wa-like, 14% of DS-1-like) of the strains. The rare E6-NSP4 in combination with DS-1 like G1P[8] and the emergence of the OP-354 subtype of P[8] were identified. Phylogenetics of RV strains revealed multiple subtypes circulating in the past 15 years, with strong evidence of animal to human gene transmission among several strains.

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2002年至2017年在印度Vellore流行的常见轮状病毒株的全基因组特征：非经典基因组星座的出现。

轮状病毒（RV）是幼儿急性肠胃炎最常见的病原体，即使在低收入国家引入疫苗后也是如此。介绍了代表11个RV基因的全基因组分类，用于RV的监测和表征。本研究对2002年至2017年印度Vellore的常见循环菌株进行了表征，以使用Illumina MiSeq进行的全基因组测序（WGS）来了解轮状病毒菌株的多样性和进化。89%（92%的Wa样，86%的DS-1样）的菌株具有经典星座，而在11%（8%的Wa类，14%的DS-1类）的菌株中观察到重配星座。鉴定出罕见的E6-NSP4与DS-1样G1P[8]结合以及P[8]的OP-354亚型的出现。RV菌株的系统发育遗传学揭示了在过去15年中流行的多种亚型，有强有力的证据表明几种菌株之间存在动物与人类的基因传播。

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来源期刊

Gut Pathogens GASTROENTEROLOGY & HEPATOLOGY-MICROBIOLOGY

CiteScore

7.70

自引率

2.40%

发文量

期刊介绍： Gut Pathogens is a fast publishing, inclusive and prominent international journal which recognizes the need for a publishing platform uniquely tailored to reflect the full breadth of research in the biology and medicine of pathogens, commensals and functional microbiota of the gut. The journal publishes basic, clinical and cutting-edge research on all aspects of the above mentioned organisms including probiotic bacteria and yeasts and their products. The scope also covers the related ecology, molecular genetics, physiology and epidemiology of these microbes. The journal actively invites timely reports on the novel aspects of genomics, metagenomics, microbiota profiling and systems biology. Gut Pathogens will also consider, at the discretion of the editors, descriptive studies identifying a new genome sequence of a gut microbe or a series of related microbes (such as those obtained from new hosts, niches, settings, outbreaks and epidemics) and those obtained from single or multiple hosts at one or different time points (chronological evolution).