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

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 approa...

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Bibliographic Details
Published in:Journal of general virology 2020-10, Vol.101 (10), p.1085-1089
Main Author: Firth, Andrew E
Format: Article
Language:English
Subjects:
Amino Acid Sequence - genetics
Betacoronavirus - genetics
Coronavirus Infections - virology
COVID-19
Genes, Overlapping - genetics
Humans
Pandemics
Phylogeny
Pneumonia, Viral - virology
Reading Frames - genetics
SARS-CoV-2
Sequence Alignment
Short Communication
Viral Regulatory and Accessory Proteins - genetics
Viroporin Proteins
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Summary: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.
ISSN:0022-1317
1465-2099
DOI:10.1099/jgv.0.001469