High-coverage SARS-CoV-2 genome sequences acquired by target capture sequencing.
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.
Keywords
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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