SARS-CoV-2 and ORF3a: Non-Synonymous Mutations and Polyproline Regions
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Abstract
The effect of the rapid accumulation of non-synonymous mutations on the pathogenesis of SARS-CoV-2 is not yet known. To predict the impact of non-synonymous mutations and polyproline regions identified in ORF3a on the formation of B-cell epitopes and their role in evading the immune response, nucleotide and protein sequences of 537 available SARS-CoV-2 genomes were analyzed for the presence of non-synonymous mutations and polyproline regions. Mutations were correlated with changes in epitope formation. A total of 19 different non-synonymous amino acids substitutions were detected in ORF3a among 537 SARS-CoV-2 strains. G251V was the most common and identified in 9.9% (n=53) of the strains and was predicted to lead to the loss of a B-cell like epitope in ORF3a. Polyproline regions were detected in two strains (EPI_ISL_410486, France and EPI_ISL_407079, Finland) and affected epitopes formation. The accumulation of non-synonymous mutations and detected polyproline regions in ORF3a of SARS-CoV-2 could be driving the evasion of the host immune response thus favoring viral spread. Rapid mutations accumulating in ORF3a should be closely monitored throughout the COVID-19 pandemic.
Importance
At the surge of the COVID-19 pandemic and after three months of the identification of SARS-CoV-2 as the disease-causing pathogen, nucleic acid changes due to host-pathogen interactions are insightful into the evolution of this virus. In this paper, we have identified a set of non-synonymous mutations in ORF3a and predicted their impact on B-cell like epitope formation. The accumulation of non-synonymous mutations in ORF3a could be driving protein changes that mediate immune evasion and favoring viral spread.
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SciScore for 10.1101/2020.03.27.012013: (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 All sequences were uniformly annotated using Prokka v 1.1.3 (4). Prokkasuggested: (Prokka, RRID:SCR_014732)Protein Structure prediction: Sequences were aligned using MUSCLE v3.8.31 (6). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)PROVEAN was used to predict the functional effects of amino acid substitutions (7). PROVEANsuggested: (PROVEAN, RRID:SCR_002182)ExPASy and PROSPER were used for motif scanning and protease site prediction, respectively (8, 9). ExPASysuggested: NoneResults …
SciScore for 10.1101/2020.03.27.012013: (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 All sequences were uniformly annotated using Prokka v 1.1.3 (4). Prokkasuggested: (Prokka, RRID:SCR_014732)Protein Structure prediction: Sequences were aligned using MUSCLE v3.8.31 (6). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)PROVEAN was used to predict the functional effects of amino acid substitutions (7). PROVEANsuggested: (PROVEAN, RRID:SCR_002182)ExPASy and PROSPER were used for motif scanning and protease site prediction, respectively (8, 9). ExPASysuggested: NoneResults 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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