Genotypic and antigenic study of SARS-CoV-2 from an Indian isolate
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Abstract
Coronaviruses (CoVs) are one of the largest groups of positive-sense RNA virus families within the Nidovirales order, which are further classified into four genera: alpha, beta, gamma, and delta. Coronaviruses have an extensive range of natural hosts and are known to be responsible for a broad spectrum of diseases in multiple species. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) that has unleashed a global threat to public health and the economy. Coronaviruses are extensively present in birds and mammals, with horseshoe bats ( Rhinolophus affinis ), being the reservoir for the ongoing SARS-CoV-2 that seems to have resulted from a zoonotic spillover to the human host, causing respiratory infections, lung injury and Acute Respiratory Distress Syndrome(ARDS). About six coronavirus serotypes are linked with the disease in humans, namely HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, SARS-CoV-2, and MERS-CoV. SARS-CoV-2 is the seventh CoV to infect humans. We analyzed the genome sequence of CoV-2 from isolates derived from China as well from India and encountered minute variations in their sequence. A cladogram analysis revealed the predominant strain circulating in India belongs to the A2a clad. We took one such strain (MT012098) and performed a rigorous in-silico genotypic and antigenic analysis to identify its relatedness to other strains. Further, we also performed a detailed prediction for B and T cell epitopes using BepiPred 2.0 server and NetCTL 1.2 server (DTU Bioinformatics), respectively. We hope this information may assist in an effective vaccine designing program against SARS-CoV-2.
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SciScore for 10.1101/2020.06.10.140657: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Blast: Blast P of NCBI was used for Structural protein comparisons between reference strain NC_045512 and Indian Strain MT012098 B cell Epitope prediction: For B cell linear epitopes Bepipred version 2 algorithm was used. MT012098suggested: NoneSoftware and Algorithms Sentences Resources Complete Genome of SARS CoV-2 strains Reference genome NCBI ID, NC_045512, and Indian genome GenBank ID, MT012098, were taken from NCBI website. NCBIsugges…SciScore for 10.1101/2020.06.10.140657: (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. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Blast: Blast P of NCBI was used for Structural protein comparisons between reference strain NC_045512 and Indian Strain MT012098 B cell Epitope prediction: For B cell linear epitopes Bepipred version 2 algorithm was used. MT012098suggested: NoneSoftware and Algorithms Sentences Resources Complete Genome of SARS CoV-2 strains Reference genome NCBI ID, NC_045512, and Indian genome GenBank ID, MT012098, were taken from NCBI website. NCBIsuggested: (NCBI, RRID:SCR_006472)ElliPro (Ellipsoid and Protrusion), is a web-tool that implements a modified version of Thornton’s method(Thorton et al. 1986). Protrusionsuggested: NoneResults from OddPub: Thank you for sharing your data.
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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