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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 variant strain was identified as a member of the B.1.1.318 Pango lineage that had first been found from Nigerian samples collected in January 2021. This strain shares with the Beta variant the S gene E484K mutation linked to impaired vaccine protection, but differs from this variant in several other ways, for example by deletions in the N gene region. Mutations in the N gene causing diagnostic resistance and on the other hand E484K mutation in the causing altered infectivity warrants careful inspection on virus variants that might get underdiagnosed.

SUBMITTER: Laine P

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

REPOSITORIES: biostudies-literature

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

Laine Pia P Nihtilä Hanna H Mustanoja Ella E Lyyski Annina A Ylinen Anne A Hurme Jukka J Paulin Lars L Jokiranta Sakari S Auvinen Petri P Meri Taru T

Journal of medical virology 20211102 3

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 f ...[more]

PMID: 34698407

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

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

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