Covariance predicts conserved protein residue interactions important for the emergence and continued evolution of SARS-CoV-2 as a human pathogen
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Abstract
SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs. Differences in nucleotide and protein sequence composition within related β-coronaviruses are often used to better understand CoV evolution, host adaptation, and their emergence as human pathogens. Here we report the comprehensive analysis of amino acid residue changes that have occurred in lineage B β-coronaviruses that show covariance with each other. This analysis revealed patterns of covariance within conserved viral proteins that potentially define conserved interactions within and between core proteins encoded by SARS-CoV-2 related β-coronaviruses. We identified not only individual pairs but also networks of amino acid residues that exhibited statistically high frequencies of covariance with each other using an independent pair model followed by a tandem model approach. Using 149 different CoV genomes that vary in their relatedness, we identified networks of unique combinations of alleles that can be incrementally traced genome by genome within different phylogenic lineages. Remarkably, covariant residues and their respective regions most abundantly represented are implicated in the emergence of SARS-CoV-2 and are also enriched in dominant SARS-CoV-2 variants.
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SciScore for 10.1101/2022.01.13.476204: (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 Protein sequences for NSP1 through NSP16, Spike, ORF3a, E, M, and N were concatenated and then aligned using MAFFT the G-INS-i accuracy setting71. MAFFTsuggested: (MAFFT, RRID:SCR_011811)This relative score is provided as metadata in the Gephi Force mapping file. Gephisuggested: (Gephi, RRID:SCR_004293)Prediction of interacting residues and mapping of residues in Spike trimer structure: The Arpeggio program was used to calculate inter and intramolecular interactions between residues in the 7JJI. Arpeggiosuggested: (Arpeggio, RRID:SCR_010876)Residues in Spike were mapped onto the PDB … SciScore for 10.1101/2022.01.13.476204: (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 Protein sequences for NSP1 through NSP16, Spike, ORF3a, E, M, and N were concatenated and then aligned using MAFFT the G-INS-i accuracy setting71. MAFFTsuggested: (MAFFT, RRID:SCR_011811)This relative score is provided as metadata in the Gephi Force mapping file. Gephisuggested: (Gephi, RRID:SCR_004293)Prediction of interacting residues and mapping of residues in Spike trimer structure: The Arpeggio program was used to calculate inter and intramolecular interactions between residues in the 7JJI. Arpeggiosuggested: (Arpeggio, RRID:SCR_010876)Residues in Spike were mapped onto the PDB structure for Spike (7JJI.pdb) using PyMol (v.2.3.4)58,75,76. PyMolsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
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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