Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.

ABSTRACT:

Objectives

Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping.

Methods

We established and used a sequencing data analysis workflow that reliably identifies and removes technical artefacts; such artefacts can result i

SUBMITTER: Kubik S 

PROVIDER: S-EPMC8016543 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature