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- Title
High‐coverage SARS‐CoV‐2 genome sequences acquired by target capture sequencing.
- Authors
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
- 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.
- Subjects
SARS-CoV-2; NUCLEOTIDE sequencing; SINGLE-stranded DNA; COVID-19; SARS virus; VIRAL shedding; ACCESSIBLE design of public spaces
- Publication
Journal of Medical Virology, 2020, Vol 92, Issue 10, p2221
- ISSN
0146-6615
- Publication type
Article
- DOI
10.1002/jmv.26116