Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 33001029.
- Also identified by DOI 10.7554/eLife.59633 and PMC identifier 7655111.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize <i>ORF3d</i>, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of <i>ORF3d</i> translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of <i>Severe acute respiratory syndrome-related coronavirus</i>), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). <i>ORF3d</i> has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene <i>ORF3b</i>, leading to confusion. Our results liken <i>ORF3d</i> to other accessory genes in emerging viruses and highlight the importance of OLGs.
Medical subject headings
- Betacoronavirus
- Coronavirus Infections
- Evolution, Molecular
- Genes, Overlapping
- Genes, Viral
- Host Specificity
- Open Reading Frames
- Pandemics
- Pneumonia, Viral
- Viral Proteins