Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic

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 ORF3d, 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 ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d 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 ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.

SARS-CoV-2 Variants Reveal Features Critical for Replication in Primary Human Cells

“…Nevertheless, the Orf3a Q57H variant was acquired shortly after introduction into humans, and is not found in early SARS-CoV-2 sequences or in related bat coronaviruses [44], potentially suggesting positive-selection of this residue similar to S D614G. Notably, the mutation leading to the Orf3a Q57H variant also changes the sequence of two other putative (and poorly characterized) overlapping reading frame products, Orf3c and Orf3d [45, 46]. Further studies, including reverse genetics experiments, will be required to determine whether these variants are functionally linked to one another, and how each variant may mechanistically determine this phenotype.…”

Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

“…Q57 is responsible for the formation of hydrophilic constrictions in the transmembrane helix 1 (TM-1). However, the substitution at this residue with histidine has been shown to have no changes in functional dynamics of membrane channel and evolutionary origins of SARS-CoV-2 [ 37 , 62 ]. For the remaining two substitutions, the change or influence in oligomerization or membrane channel function (intra- and extracellular) remains unknown.…”

SARS-CoV-2 vaccines in advanced clinical trials: Where do we stand?

“…In SARS-CoV-1, select accessory proteins have been shown to influence the pathogenicity and virulence of the virus by modulating the cytokine response, Type I interferon signaling pathways, and cellular apoptosis [ 36 , 37 ]. As our understanding of SARS-CoV-2 evolves – specifically concerning the nomenclature of orthologous accessory genes and overlapping genes discovered within ORFs [ 38 ] – we anticipate that new genes and proteins may yet be discovered. Of note, accessory proteins encoded by open reading frame (ORF) 3a [ 39 ] and ORF7a [ 40 ] were found on SARS-CoV-1 viral particles, but have yet to be validated for SARS-CoV-2.…”