Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2
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SciScore for 10.1101/2021.09.11.459844: (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 Gene nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 RdRp nsp13 nsp14 nsp15 nsp16 S1 S2 ORF3a E M ORF6 ORF7a ORF7b ORF8 N ORF9b Evol rate 0.1 × 10−3 0.2 × 10−3 1.3 × 10−3 0.8 × 10−3 0.5 × 10−3 3.4 × 10−3 0.3 × 10−3 0.3 × 10−3 0.7 × 10−3 0.1 × 10−3 0.5 × 10−3 0.8 × 10−3 0.3 × 10−3 0.3 × 10−3 0.3 × 10−3 8.4 × 10−3 3.5 × 10−3 1.8 × 10−3 1.6 × 10−3 0.7 × 10−3 0.2 × 10−3 1.5 × 10−3 1.7 × 10−3 16.5 × 10−3 6.10 × 10−3 2.10 × 10−3 5 r 0.05 -0.10 0.30 0.28 -0.09 0.35 -0.42 0.04 0.06 -0.05 0.15 0.20 -0.03 0.15 -0.22 0.46 0.24 -0.06 0.03 0.29 0.01 0.43 0.22 0.19 0.21 0.27 p-value … SciScore for 10.1101/2021.09.11.459844: (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 Gene nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 RdRp nsp13 nsp14 nsp15 nsp16 S1 S2 ORF3a E M ORF6 ORF7a ORF7b ORF8 N ORF9b Evol rate 0.1 × 10−3 0.2 × 10−3 1.3 × 10−3 0.8 × 10−3 0.5 × 10−3 3.4 × 10−3 0.3 × 10−3 0.3 × 10−3 0.7 × 10−3 0.1 × 10−3 0.5 × 10−3 0.8 × 10−3 0.3 × 10−3 0.3 × 10−3 0.3 × 10−3 8.4 × 10−3 3.5 × 10−3 1.8 × 10−3 1.6 × 10−3 0.7 × 10−3 0.2 × 10−3 1.5 × 10−3 1.7 × 10−3 16.5 × 10−3 6.10 × 10−3 2.10 × 10−3 5 r 0.05 -0.10 0.30 0.28 -0.09 0.35 -0.42 0.04 0.06 -0.05 0.15 0.20 -0.03 0.15 -0.22 0.46 0.24 -0.06 0.03 0.29 0.01 0.43 0.22 0.19 0.21 0.27 p-value 0.43 0.89 0.09 0.06 0.84 0.01 1.00 0.44 0.30 0.81 0.26 0.15 0.69 0.23 0.96 <0.005 0.10 0.86 0.39 0.04 0.53 <0.005 0.05 0.19 0.22 0.05 to synonymous sites. Gene nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 RdRp nsp13 nsp14 nsp15 nsp16suggested: NoneSoftware and Algorithms Sentences Resources Time-resolved phylogenies were inferred using Augur 12.0.0 [31], IQ-TREE 2.1.2 [32], and TreeTime 0.8.2 [33]. Augursuggested: NoneIQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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.
Results from scite Reference Check: We found no unreliable references.
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