Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.

ABSTRACT:

Background

Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings.

Methods

We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021.

Results

In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78

SUBMITTER: Zare Ashrafi F 

PROVIDER: S-EPMC10685895 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature