tetano
Editor, Senior Moderator
J Med Virol
. 2020 Jun 3.
doi: 10.1002/jmv.26116. Online ahead of print.
High-Coverage SARS-CoV-2 Genome Sequences Acquired by Target Capture Sequencing
Shaoqing Wen[SUP] 1 2 [/SUP], Chang Sun[SUP] 2 [/SUP], Huanying Zheng[SUP] 3 [/SUP], Lingxiang Wang[SUP] 2 [/SUP], Huan Zhang[SUP] 3 [/SUP], Lirong Zou[SUP] 3 [/SUP], Zhe Liu[SUP] 3 [/SUP], Panxin Du[SUP] 2 [/SUP], Xuding Xu[SUP] 2 [/SUP], Lijun Liang[SUP] 3 [/SUP], Xiaofang Peng[SUP] 3 [/SUP], Wei Zhang[SUP] 3 [/SUP], Jie Wu[SUP] 3 [/SUP], Jiyuan Yang[SUP] 2 [/SUP], Bo Lei[SUP] 2 [/SUP], Guangyi Zeng[SUP] 4 [/SUP], Changwen Ke[SUP] 3 [/SUP], Fang Chen[SUP] 4 [/SUP], Xiao Zhang[SUP] 1 5 [/SUP]
Affiliations
Abstract
In this study, we designed a set of SARS-CoV-2 enrichment probes to increase the capacity for sequence-based virus detection and obtain the comprehensive genome sequence at the same time. This universal SARS-CoV-2 enrichment probe set contains 502 120nt ssDNA biotin-labeled probes designed based on all available SARS-CoV-2 viral sequences and it can be used to enrich for SARS-CoV-2 sequences without prior knowledge of type or subtype. Following the CDC health and safety guidelines, marked enrichment was demonstrated in a virus strain sample from a cell culture, three nasopharyngeal swab samples (cycle threshold [Ct] values: 32.36, 36.72, and 38.44) from patients diagnosed with COVID-19 (positive control) and four throat swab samples from patients without COVID-19 (negative controls), respectively. Moreover, based on these high-quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication, and its phylogenetic relationship with other selected high-quality samples from The Genome Variation Map (GVM). Therefore, this universal SARS-CoV-2 enrichment probe system can capture and enrich SARS-CoV-2 viral sequences selectively and effectively in different samples, especially clinical swab samples with a relatively low concentration of viral particles. This article is protected by copyright. All rights reserved.
Keywords: Gene expression; Genetic networks; Genetic variability; Mutation; SARS coronavirus.
. 2020 Jun 3.
doi: 10.1002/jmv.26116. Online ahead of print.
High-Coverage SARS-CoV-2 Genome Sequences Acquired by Target Capture Sequencing
Shaoqing Wen[SUP] 1 2 [/SUP], Chang Sun[SUP] 2 [/SUP], Huanying Zheng[SUP] 3 [/SUP], Lingxiang Wang[SUP] 2 [/SUP], Huan Zhang[SUP] 3 [/SUP], Lirong Zou[SUP] 3 [/SUP], Zhe Liu[SUP] 3 [/SUP], Panxin Du[SUP] 2 [/SUP], Xuding Xu[SUP] 2 [/SUP], Lijun Liang[SUP] 3 [/SUP], Xiaofang Peng[SUP] 3 [/SUP], Wei Zhang[SUP] 3 [/SUP], Jie Wu[SUP] 3 [/SUP], Jiyuan Yang[SUP] 2 [/SUP], Bo Lei[SUP] 2 [/SUP], Guangyi Zeng[SUP] 4 [/SUP], Changwen Ke[SUP] 3 [/SUP], Fang Chen[SUP] 4 [/SUP], Xiao Zhang[SUP] 1 5 [/SUP]
Affiliations
- PMID: 32492196
- DOI: 10.1002/jmv.26116
Abstract
In this study, we designed a set of SARS-CoV-2 enrichment probes to increase the capacity for sequence-based virus detection and obtain the comprehensive genome sequence at the same time. This universal SARS-CoV-2 enrichment probe set contains 502 120nt ssDNA biotin-labeled probes designed based on all available SARS-CoV-2 viral sequences and it can be used to enrich for SARS-CoV-2 sequences without prior knowledge of type or subtype. Following the CDC health and safety guidelines, marked enrichment was demonstrated in a virus strain sample from a cell culture, three nasopharyngeal swab samples (cycle threshold [Ct] values: 32.36, 36.72, and 38.44) from patients diagnosed with COVID-19 (positive control) and four throat swab samples from patients without COVID-19 (negative controls), respectively. Moreover, based on these high-quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication, and its phylogenetic relationship with other selected high-quality samples from The Genome Variation Map (GVM). Therefore, this universal SARS-CoV-2 enrichment probe system can capture and enrich SARS-CoV-2 viral sequences selectively and effectively in different samples, especially clinical swab samples with a relatively low concentration of viral particles. This article is protected by copyright. All rights reserved.
Keywords: Gene expression; Genetic networks; Genetic variability; Mutation; SARS coronavirus.