SARS-CoV-2 originated from SARS-CoV-1-related Bat-CoVs through Pan-CoVs rather than from SARS-CoV-2-related Bat-CoVs
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Abstract
The emergence of the novel SARS-CoV-2 in 2019 sparked a dispute concerning its origin. Here, we report that the SARS-CoV-2 originated through pangolin-coronavirus (Pan-CoVs) from the SARS-CoV-related-bat-coronaviruses (SARS-CoV-1-rB-CoVs) rather than from SARS-CoV-2-related-bat-coronaviruses (SARS-CoV-2-rB-CoVs), in contrast to the previous thought. Further, our analyses strongly suggest that the Pan-CoVs evolved from the SARS-CoV-1-rB-CoVs without recombination. Further, our results suggest that the SARS-CoV-1-rB-CoVs’ perhaps jumped into the pangolin, which forced the viruses to mutate and adapt to the new host, and resulted in the origin of Pan-CoVs. Surprisingly, the Pan-CoVs formed an evolutionary intermediate between SARS-CoV-2 and SARS-CoV-2-rB-CoVs at the spike gene. Our findings also suggest that the Pan-CoV/GX and Pan-CoV/Guangdong lineages recombined to form the SARS-CoV-2 spike gene. We also found evidence that the SARS-CoV-2-rB-CoVs spike gene evolved via recombination between Pan-CoV/Guangdong and SARS-CoV-1-rB-CoVs. Overall, our findings suggest that the SARS-CoV-2 emerged from SARS-CoV-1-rB-CoVs through host jumping.
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SciScore for 10.1101/2021.09.06.459210: (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
Software and Algorithms Sentences Resources II. Net Between Group Mean Distance (NBGMD) analysis: The NBGMD were measured using MEGA7 tool and the Kimura 2-parameter model, with a gamma distribution (shape parameter=5) used as a model to measure rate variation among sites, a bootstrap test (1000 replicates) was used to estimate the Standard error and all ambiguous sites for each sequence pair were removed from the analysis. MEGA7suggested: NoneSimPlot analysis: SimPlot 3.5.1 was used to calculate the percent identity between the query and reference sequences. SimPlotsuggested: NoneResults from OddPub: We did not detect open data. We …
SciScore for 10.1101/2021.09.06.459210: (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
Software and Algorithms Sentences Resources II. Net Between Group Mean Distance (NBGMD) analysis: The NBGMD were measured using MEGA7 tool and the Kimura 2-parameter model, with a gamma distribution (shape parameter=5) used as a model to measure rate variation among sites, a bootstrap test (1000 replicates) was used to estimate the Standard error and all ambiguous sites for each sequence pair were removed from the analysis. MEGA7suggested: NoneSimPlot analysis: SimPlot 3.5.1 was used to calculate the percent identity between the query and reference sequences. SimPlotsuggested: NoneResults 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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