Ongoing global and regional adaptive evolution of SARS-CoV-2
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Abstract
Understanding the ongoing evolution of SARS-CoV-2 is essential to control and ultimately end the pandemic. We analyzed more than 300,000 SARS-CoV-2 genomes available as of January 2021 and demonstrate adaptive evolution of the virus that affects, primarily, multiple sites in the spike and nucleocapsid protein. Selection appears to act on combinations of mutations in these and other SARS-CoV-2 genes. Evolution of the virus is accompanied by ongoing adaptive diversification within and between geographic regions. This diversification could substantially prolong the pandemic and the vaccination campaign, in which variant-specific vaccines are likely to be required.
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SciScore for 10.1101/2020.10.12.336644: (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 Sequences sourced from non-human hosts were manually identified from the metadata and those excluded at the previous step were added to the alignment using MAFFT, (again specifying -- keeplength). MAFFTsuggested: (MAFFT, RRID:SCR_011811)A second iteration of FastTree was initiated on the second alignment to produce an intermediate tree. FastTreesuggested: (FastTree, RRID:SCR_015501)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 …SciScore for 10.1101/2020.10.12.336644: (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 Sequences sourced from non-human hosts were manually identified from the metadata and those excluded at the previous step were added to the alignment using MAFFT, (again specifying -- keeplength). MAFFTsuggested: (MAFFT, RRID:SCR_011811)A second iteration of FastTree was initiated on the second alignment to produce an intermediate tree. FastTreesuggested: (FastTree, RRID:SCR_015501)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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