A genetic element in the SARS-CoV-2 genome is shared with multiple insect species
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Abstract
SARS-CoV-2 is a member of the subgenus Sarbecovirus and thus contains the genetic element s2m. We have extensively mined nucleotide data in GenBank in order to obtain a comprehensive list of s2m sequences both in the four virus families where s2m has previously been described and in other groups of organisms. Surprisingly, there seems to be a xenologue of s2m in a large number of insect species. The function of s2m is unknown, but our data show a very high degree of sequence conservation both in insects and in viruses and that the version of s2m found in SARS-CoV-2 has unique features, not seen in any other virus or insect strains.
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SciScore for 10.1101/2020.06.29.177030: (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 To characterize the specific genotype of s2m found in SARS-CoV-2, BLASTN (Altschul, et al. 1990) was used to search the entire virus section of GenBank using all s2m sequence genotypes reported in the literature (n = 97) (Jonassen, et al. 1998; Robertson, et al. 2005; Tengs, et al. 2013; Tengs and Jonassen 2016) as query sequences. BLASTNsuggested: (BLASTN, RRID:SCR_001598)For the phylogenetic analyses, sequences were aligned using the Clustal W algorithm (Thompson, et al. 1994) … SciScore for 10.1101/2020.06.29.177030: (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 To characterize the specific genotype of s2m found in SARS-CoV-2, BLASTN (Altschul, et al. 1990) was used to search the entire virus section of GenBank using all s2m sequence genotypes reported in the literature (n = 97) (Jonassen, et al. 1998; Robertson, et al. 2005; Tengs, et al. 2013; Tengs and Jonassen 2016) as query sequences. BLASTNsuggested: (BLASTN, RRID:SCR_001598)For the phylogenetic analyses, sequences were aligned using the Clustal W algorithm (Thompson, et al. 1994) and maximum likelihood analysis were performed using MEGA X (Kumar, et al. 2018). MEGAsuggested: (Mega BLAST, RRID:SCR_011920)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.
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