Whole-Genome Sequencing of Pathogens in Saliva : A Target-Enrichment Approach for SARS-CoV-2.
Methods Mol Biol
; 2327: 119-137, 2021.
Article
in English
| MEDLINE | ID: covidwho-1363726
ABSTRACT
Outbreak analysis and transmission surveillance of viruses can be performed via whole-genome sequencing after viral isolation. Such techniques have recently been applied to characterize and monitor SARS-CoV-2 , the etiological agent of the COVID-19 pandemic. However, the isolation and culture of SARS-CoV-2 is time consuming and requires biosafety level 3 containment, which is not ideal for many resource-constrained settings. An alternate method, bait capture allows target enrichment and sequencing of the entire SARS-CoV-2 genome eliminating the need for viral culture. This method uses a set of hybridization probes known as "baits" that span the genome and provide sensitive, accurate, and minimal off-target hybridization. Baits can be designed to detect any known virus or bacteria in a wide variety of specimen types, including oral secretions. The bait capture method presented herein allows the whole genome of SARS-CoV-2 in saliva to be sequenced without the need to culture and provides an outline of bait design and bioinformatic analysis to guide a bioinformatician.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Saliva
/
Genome, Viral
/
Whole Genome Sequencing
/
SARS-CoV-2
Type of study:
Diagnostic study
/
Etiology study
Limits:
Humans
Language:
English
Journal:
Methods Mol Biol
Journal subject:
Molecular Biology
Year:
2021
Document Type:
Article
Affiliation country:
978-1-0716-1518-8_8
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