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Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing

Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next...

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Autores principales: Song, Ke, Lin, Xiaojuan, Liu, Yao, Ji, Feng, Zhang, Li, Chen, Peng, Zhao, Chenxu, Song, Yanyan, Tao, Zexin, Xu, Aiqiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7985922/
https://www.ncbi.nlm.nih.gov/pubmed/33755873
http://dx.doi.org/10.1007/s12560-021-09469-x
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author Song, Ke
Lin, Xiaojuan
Liu, Yao
Ji, Feng
Zhang, Li
Chen, Peng
Zhao, Chenxu
Song, Yanyan
Tao, Zexin
Xu, Aiqiang
author_facet Song, Ke
Lin, Xiaojuan
Liu, Yao
Ji, Feng
Zhang, Li
Chen, Peng
Zhao, Chenxu
Song, Yanyan
Tao, Zexin
Xu, Aiqiang
author_sort Song, Ke
collection PubMed
description Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12560-021-09469-x.
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spelling pubmed-79859222021-03-23 Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing Song, Ke Lin, Xiaojuan Liu, Yao Ji, Feng Zhang, Li Chen, Peng Zhao, Chenxu Song, Yanyan Tao, Zexin Xu, Aiqiang Food Environ Virol Original Paper Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12560-021-09469-x. Springer US 2021-03-23 2021 /pmc/articles/PMC7985922/ /pubmed/33755873 http://dx.doi.org/10.1007/s12560-021-09469-x Text en © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Original Paper
Song, Ke
Lin, Xiaojuan
Liu, Yao
Ji, Feng
Zhang, Li
Chen, Peng
Zhao, Chenxu
Song, Yanyan
Tao, Zexin
Xu, Aiqiang
Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing
title Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing
title_full Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing
title_fullStr Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing
title_full_unstemmed Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing
title_short Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing
title_sort detection of human sapoviruses in sewage in china by next generation sequencing
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7985922/
https://www.ncbi.nlm.nih.gov/pubmed/33755873
http://dx.doi.org/10.1007/s12560-021-09469-x
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