High-coverage SARS-CoV-2 genome sequences acquired by target capture sequencing.
J Med Virol
; 92(10): 2221-2226, 2020 10.
Article
en En
| MEDLINE
| ID: mdl-32492196
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.
Palabras clave
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
ADN de Cadena Simple
/
Sondas de ADN
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Genoma Viral
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Secuenciación Completa del Genoma
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SARS-CoV-2
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COVID-19
Tipo de estudio:
Diagnostic_studies
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Guideline
Límite:
Humans
Idioma:
En
Revista:
J Med Virol
Año:
2020
Tipo del documento:
Article
País de afiliación:
China