A putative new SARS-CoV protein, 3a*, encoded in an ORF overlapping ORF3a
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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.
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SciScore for 10.1101/2020.05.12.088088: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Conservation statistics were then mapped back to NC_045512.2 coordinates for plotting (Fig. 1). Conservationsuggested: (Conservation, RRID:SCR_016064)For the ORF S and 3a analyses (Fig. 3), the ORF S and 3a regions were extracted from all 54 sarbecovirus sequences, translated to amino acids, aligned using MUSCLE (Edgar, 2004), and the amino acid alignments were used to guide codon-respecting nucleotide sequence alignments (EMBOSS tranalign; Rice et al., 2000). MUSCLEsuggested: …SciScore for 10.1101/2020.05.12.088088: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Conservation statistics were then mapped back to NC_045512.2 coordinates for plotting (Fig. 1). Conservationsuggested: (Conservation, RRID:SCR_016064)For the ORF S and 3a analyses (Fig. 3), the ORF S and 3a regions were extracted from all 54 sarbecovirus sequences, translated to amino acids, aligned using MUSCLE (Edgar, 2004), and the amino acid alignments were used to guide codon-respecting nucleotide sequence alignments (EMBOSS tranalign; Rice et al., 2000). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)Molecular mass and isoelectric point were calculated with EMBOSS pepstats (Rice et al., 2000). EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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