How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography
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Abstract
SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.
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SciScore for 10.1101/2020.04.26.062406: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. Wuhan-Hu-1suggested: NoneSoftware and Algorithms Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)Bayesian based phylogenetic analysis was performed using BEAST v1.10.4 [15] with strict clock following HKY substitution model and 107 MCMC simulations. BEASTsuggested: (BEAST, RRID:SCR_010228)Demography assessment: Parameters like mismatch distribution test, Harpending’s raggedness index (Rg) and Sum of Squared Deviations … SciScore for 10.1101/2020.04.26.062406: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. Wuhan-Hu-1suggested: NoneSoftware and Algorithms Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)Bayesian based phylogenetic analysis was performed using BEAST v1.10.4 [15] with strict clock following HKY substitution model and 107 MCMC simulations. BEASTsuggested: (BEAST, RRID:SCR_010228)Demography assessment: Parameters like mismatch distribution test, Harpending’s raggedness index (Rg) and Sum of Squared Deviations (SSD) were calculated to test for demographic expansion using Arlequin v3.5 [17]. Arlequinsuggested: (ARLEQUIN, RRID:SCR_009051)Neutrality tests, Tajima’s D [18] and Fu’s Fs [19], to evaluate demographic effects were carried out using DnaSP v6.12 [14]. DnaSPsuggested: (DnaSP, RRID:SCR_003067)We classified nucleotide substitutions (dN/dS ratio) in all sequences, with bat RaTG13, Pangolin- SARSr-CoV, SARS and MERS using synonymous nonsynonymous analysis programme, SNAP v. SNAPsuggested: (SNAP, RRID:SCR_007936)Results 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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SciScore for 10.1101/2020.04.26.062406: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. Wuhan-Hu-1suggested: NoneSoftware and Algorithms Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. MUSCLEsuggested: (MUSCLE, SCR_011812)Demography assessmentParameters like mismatch distribution test, Harpending’s raggedness index (Rg) and Sum of Squared Deviations (SSD) were calculated to test for demographic expansion using Arlequin … SciScore for 10.1101/2020.04.26.062406: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. Wuhan-Hu-1suggested: NoneSoftware and Algorithms Sentences Resources All sequences were aligned using MUSCLE v3.8.31, with the Wuhan-Hu-1 [13]. MUSCLEsuggested: (MUSCLE, SCR_011812)Demography assessmentParameters like mismatch distribution test, Harpending’s raggedness index (Rg) and Sum of Squared Deviations (SSD) were calculated to test for demographic expansion using Arlequin v3.5 [17]. Arlequinsuggested: (ARLEQUIN, SCR_009051)Neutrality tests, Tajima’s D [18] and Fu’s Fs [19], to evaluate demographic effects were carried out using DnaSP v6.12 [14]. DnaSPsuggested: (DnaSP, SCR_003067)To date changes in the effective population size over time, we used Coalescent Bayesian Skyline Plot (BSP) analysis as implemented in BEAST v. BEASTsuggested: (BEAST, SCR_010228)We classified nucleotide substitutions (dN/dS ratio) in all sequences, with bat RaTG13, Pangolin- SARSr-CoV, SARS and MERS using synonymous nonsynonymous analysis programme, SNAP v. SNAPsuggested: (SNAP, SCR_007936)Results from OddPub: Thank you for sharing your data.
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