Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection

ABSTRACT

Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae. Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales. The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.

KEYWORDS:

• Viral metagenomics
• diarrhea
• Rotavirus A
• gut virome
• enteric virus
• phage

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors contribution

Wen Zhang, Ying Xiong, and Chenglin Zhou conceived this project. Chunying Lu, Liang Yong, Qing Zhang, Juan Xu, and Ping Ni participated in sample collections. The DNA library constructions were performed by Xiang Lu, Min Zhao, Juan Lu, Jia Liu, and Chukwudozie Kingsley Ikechukwu. The data analysis and the manuscript were completed done by Siwen Bao, Hao Wang, Wang Li, and Haisheng Wu. All authors read and approved the final manuscript.

Data availability statement

The raw sequence reads generated by Illumina in the study are available at the NCBI Sequence Read Archive database under the Biosample accession SAMN33574712 (https://www.ncbi.nlm.nih.gov/biosample/SAMN33574712/), and BioProject accession PRJNA940581 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA940581) and the accession numbers are listed in Supplementary Table S1. All viral sequences identified in this study were deposited in the GenBank database, and the accession numbers were listed in Supplementary Table S3.

Ethics approval

Sample collection and all experiments in the present were performed with Ethical Approval given by the Ethics Committee of The Affiliated Taizhou People’s Hospital.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2234653

Additional information

Funding

This research was supported by National Key Research and Development Programs of China No.2022YFC2603801 and Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents – Leading Talents No.202208170046.