About: Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

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About: Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
Creator	Li, Min Yang, Lin Wang, Jian Zhao, Jincun Wang, Yanqun Chen, Weijun Zhang, Yanyan Chen, Tian Chen, Fang Li, Yimin Liu, Xiaoqing Yang, Huanming Wu, Honglong Li, Jiandong Zhao, Yanping Li, Junhua Sun, Wanying Cheng, Xinyi Deng, Ziqing Feng, Taiqing Gong, Yanping Ji, Jingkai Ou, Zhihua Ren, Huahui Ren, Peidi Song, Wenchen Wang, Daxi Xiao, Minfeng Xu, Xun Yang, Guifang Zhong, Huanzi Zhu, Shida Cai, Jielun Liang, Tianzhu
source	Medline; PMC; WHO
abstract	BACKGROUND: COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e., sequencing samples with low viral load often results in insufficient viral reads for analyses. METHODS: We applied a novel multiplex PCR amplicon (amplicon)-based and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of SARS-CoV-2 from serials dilutions of a cultured isolate, and eight clinical samples covering a range of sample types and viral loads. We also examined and compared the sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. RESULTS: We demonstrated that both amplicon and capture methods efficiently enriched SARS-CoV-2 content from clinical samples, while the enrichment efficiency of amplicon outran that of capture in more challenging samples. We found that capture was not as accurate as meta and amplicon in identifying between-sample variations, whereas amplicon method was not as accurate as the other two in investigating within-sample variations, suggesting amplicon sequencing was not suitable for studying virus-host interactions and viral transmission that heavily rely on intra-host dynamics. We illustrated that meta uncovered rich genetic information in the clinical samples besides SARS-CoV-2, providing references for clinical diagnostics and therapeutics. Taken all factors above and cost-effectiveness into consideration, we proposed guidance for how to choose sequencing strategy for SARS-CoV-2 under different situations. CONCLUSIONS: This is, to the best of our knowledge, the first work systematically investigating inter- and intra-individual variations of SARS-CoV-2 using amplicon- and capture-based whole-genome sequencing, as well as the first comparative study among multiple approaches. Our work offers practical solutions for genome sequencing and analyses of SARS-CoV-2 and other emerging viruses.
has issue date	2020-06-30(xsd:dateTime)
bibo:doi	10.1186/s13073-020-00751-4
bibo:pmid	32605661
has license	cc-by
sha1sum (hex)	e0081f898e3036edd3ba0f2b92ebbba17e050ec5
schema:url	https://doi.org/10.1186/s13073-020-00751-4
resource representing a document's title	Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
has PubMed Central identifier	PMC7325194
has PubMed identifier	32605661
schema:publication	Genome Med
resource representing a document's body	covid:e0081f898e3036edd3ba0f2b92ebbba17e050ec5#body_text
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