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Volume 101, Issue 10

A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a Open Access

Abstract

Identification of the full complement of genes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high-throughput experimental approaches – such as ribosome profiling – cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV-2 and related viruses (subgenus ) and correlating the results with the conserved presence of an open reading frame (ORF) and a plausible translation mechanism, a putative new gene – ORF3c – was identified. ORF3c overlaps ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3c is indeed translated during infection. ORF3c is conserved across the subgenus , and encodes a 40–41 amino acid predicted transmembrane protein.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 3c , coronavirus , ORF3c , overlapping gene , sarbecovirus and SARS-CoV
Funding
This study was supported by the:
  • H2020 European Research Council (Award 646891)
    • Principle Award Recipient: Andrew Firth
  • Wellcome Trust (Award 106207)
    • Principle Award Recipient: Andrew Firth
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2020-07-15
2024-04-26
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A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a
J. Gen. Virol. 101, 1085 (2020); https://doi.org/10.1099/jgv.0.001469
/content/journal/jgv/10.1099/jgv.0.001469
/content/journal/jgv/10.1099/jgv.0.001469
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