Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design.

ABSTRACT:

Background

As the rapidly evolving characteristic of SARS-CoV-2 could result in false negative diagnosis, the use of as much sequence data as possible is key to the identification of conserved viral sequences. However, multiple alignment of massive genome sequences is computationally intensive.

Objective

To extract conserved sequences from SARS-CoV-2 genomes for the design of diagnostic PCR primers using a bioinformatics approach that can handle massive genomic sequences efficiently.

Methods

A total of 230,163 full-length viral genomes were retrieved from the NCBI SARS-CoV-2 Resources and GISAID EpiCoV database. This number was reduced to 14.11% following removal of 5'-/3'-untranslated regions and sequence dereplication. Fast, reference-based, multiple sequence alignm

SUBMITTER: Jeong H 

PROVIDER: S-EPMC9160177 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature