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

Abstract

Identification of the full complement of genes in 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 and related viruses (subgenus Sarbecovirus), and correlating with the conserved presence of an open reading frame and plausible translation mechanism, we identified a putative new gene, ORF3a*, overlapping ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3a* is indeed translated during infection. ORF3a* is conserved across the subgenus Sarbecovirus, and encodes a 40-41 amino acid predicted transmembrane protein.