Isolation of SARS-CoV-2 strains carrying a nucleotide mutation, leading to a stop codon in the ORF 6 protein

Emerg Microbes Infect. 2021 Dec;10(1):252-255. doi: 10.1080/22221751.2021.1884003.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was isolated from the oro/pharyngeal swabs of two Italian COVID-19 patients, physicians in a COVID-19 division hospital, with different courses of the disease. The complete genome sequences show that the two isolates belong to the B1.1 lineage, but contain a nucleotide mutation in the ORF6, leading to a stop codon and to the deletion of 6 amino acids in the C terminus. This deletion was unique, compared to the currently available sequences deposited in the GISAID and GenBank database. It did not affect the in vitro viral replication, neither the neutralizing activities of the patients' antibodies. Based on homology analysis with other Coronaviruses, the two isolated lacked the ORF6 aminoacidic portion responsible for the inhibition of the antiviral Interferon (IFN)-based host response. IFN seems to have a dual role of in SARS-CoV-2 infected patients: not only antiviral activity, but also a detrimental role in case of excessive production. A deletion in the SARS-CoV-2 ORF6 protein might have a specific, still unknown role in the viral pathogenesis.

Keywords: COVID-19 pathogenesis; ORF6; SARS-CoV-2; interferon; stop codon.

Publication types

  • Case Reports
  • Letter

MeSH terms

  • COVID-19 / diagnosis
  • COVID-19 / virology*
  • Codon, Terminator / genetics*
  • Female
  • Humans
  • Male
  • Middle Aged
  • Point Mutation*
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / growth & development
  • SARS-CoV-2 / isolation & purification
  • Viral Proteins / genetics*

Substances

  • Codon, Terminator
  • ORF6 protein, SARS-CoV-2
  • Viral Proteins

Grants and funding

This project was partially supported by MIUR, grant PRIN 2017 to PF, by Università degli Studi di Milano, grant PSR 2018, by Italian Ministry of Health, grant COVID-2020-12371849 to SD, and by MIUR, grant Progetto Eccellenza, and by departmental “Linea 2 – Azione A 2019” to IE.