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High-coverage SARS-CoV-2 genome sequences acquired by target capture sequencing.
Wen, Shaoqing; Sun, Chang; Zheng, Huanying; Wang, Lingxiang; Zhang, Huan; Zou, Lirong; Liu, Zhe; Du, Panxin; Xu, Xuding; Liang, Lijun; Peng, Xiaofang; Zhang, Wei; Wu, Jie; Yang, Jiyuan; Lei, Bo; Zeng, Guangyi; Ke, Changwen; Chen, Fang; Zhang, Xiao.
  • Wen S; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.
  • Sun C; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Zheng H; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Wang L; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Zhang H; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Zou L; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Liu Z; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Du P; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Xu X; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Liang L; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Peng X; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Zhang W; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Wu J; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Yang J; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Lei B; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Zeng G; Institute of Archaeological Science, School of Life Sciences, Fudan University, Shanghai, China.
  • Ke C; MGI Shenzhen, BGI Shenzhen, Shenzhen, China.
  • Chen F; Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
  • Zhang X; MGI Shenzhen, BGI Shenzhen, Shenzhen, China.
J Med Virol ; 92(10): 2221-2226, 2020 10.
Article in English | MEDLINE | ID: covidwho-505569
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 502 120 nt single-stranded DNA 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 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. 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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA, Single-Stranded / DNA Probes / Genome, Viral / Whole Genome Sequencing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: J Med Virol Year: 2020 Document Type: Article Affiliation country: Jmv.26116

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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA, Single-Stranded / DNA Probes / Genome, Viral / Whole Genome Sequencing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study / Randomized controlled trials Limits: Humans Language: English Journal: J Med Virol Year: 2020 Document Type: Article Affiliation country: Jmv.26116