Independent acquisition of short insertions at the RIR1 site in the spike N‐terminal domain of the SARS‐CoV‐2 BA.2 lineage
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SciScore for 10.1101/2022.04.11.487924: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources Separate fasta files were created for viral genomes belonging to the following lineages: alpha; beta; gamma; delta; BA.1; BA.1.1; BA.2 (excluding genomes with RIR1 insertions; BA.2+ins(L) and BA.2+ins(LIII) (see Table 1 and Figure 1); sequences not belonging to any VOC from the year 2020 Particular attention was placed in an additional filtering step, which involved the fasta file including the BA.2 sequences bearing RIR1 insertions, aimed at discarding the sequences that may possibly derive … SciScore for 10.1101/2022.04.11.487924: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources Separate fasta files were created for viral genomes belonging to the following lineages: alpha; beta; gamma; delta; BA.1; BA.1.1; BA.2 (excluding genomes with RIR1 insertions; BA.2+ins(L) and BA.2+ins(LIII) (see Table 1 and Figure 1); sequences not belonging to any VOC from the year 2020 Particular attention was placed in an additional filtering step, which involved the fasta file including the BA.2 sequences bearing RIR1 insertions, aimed at discarding the sequences that may possibly derive from low quality assemblies. alpha; beta; gamma; delta; BA.1; BA.1.1; BA.2suggested: NoneSoftware and Algorithms Sentences Resources The Wuhan-Hu-1 strain genome (NCBI accession ID: NC_045512.2) was added as reference sequence All the sampled sequences were merged and aligned with mafft v7.490 (Katoh and Standley, 2013), configured for closely related viral genomes as suggested by the authors. mafftsuggested: (MAFFT, RRID:SCR_011811)The Augur pipeline (Huddleston et al., 2021) was then used to produce the sampling date-refined phylogenetic tree, with the Wuhan-Hu-1 genome set as a reference for rooting. Augursuggested: NoneResults from OddPub: Thank you for sharing your code.
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.
Results from scite Reference Check: We found no unreliable references.
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