SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers.

ABSTRACT: While most of the spontaneous mutations in the viral genome have no functional, diagnostic, or clinical consequences, some have. In February 2021, we noticed in Southern Finland coronavirus disease 2019 cases where two commercial polymerase chain reaction (PCR) analyses failed to recognize the used N gene target but recognized the other target gene of severe acute respiratory syndrome coronavirus 2. Complete viral genome sequence analysis of the strains revealed several mutations that were not found at that time in public databases. A short 3 bp deletion and three subsequent single nucleotide polymorphisms in the N gene were found exactly at the site where an early published and widely used N gene-based PCR primer is located, explaining the negative results in the N gene PCR. Later the var

SUBMITTER: Laine P 

PROVIDER: S-EPMC8661661 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature