Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio
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Abstract
Following the worldwide emergence of the p.Asp614Gly shift in the Spike (S) gene of SARS-CoV-2, there have been few recurring pathogenic shifts occurring during 2020, as assessed by genomic sequencing. This situation has evolved in the last several months with the emergence of several distinct variants (first identified in the United Kingdom and South Africa) that manifest multiple changes in the S gene, particularly p.Asn501Tyr (N501Y), that likely have clinical impact. We report here the emergence in Columbus, Ohio in December 2020 of two novel SARS-CoV-2 clade 20G variants. One variant, that has become the predominant virus found in nasopharyngeal swabs in the December 2020-January 2021 period, harbors S p.Gln677His (Q677H), affecting a consensus QTQTN domain near the S1/S2 furin cleavage site, nucleocapsid (N) p.Asp377Tyr (D377Y) and membrane glycoprotein (M) p.Ala85Ser (A85S) mutations, with additional S mutations in subsets. The other variant present in two samples, contains S N501Y, which is a marker of the UK-B.1.1.7 (clade 20I/501Y.V1) strain, but lacks all other mutations from that virus. The Ohio variant is from a different clade and shares multiple mutations with the clade 20G viruses circulating in the area prior to December 2020. These two SARS-CoV-2 viruses, which we show are also present and evolving currently in several other parts of North America, add to the diversity of S gene shifts occurring worldwide. These and other shifts in this period of the pandemic support multiple independent acquisition of functionally significant and potentially complementing mutations affecting the S QTQTN site (Q675H or Q677H) and certain receptor binding domain mutations (e.g., E484K and N501Y).
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SciScore for 10.1101/2021.01.12.426407: (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 The analysis pipeline included BaseSpace, a custom pipeline using GATK tools and DRAGEN RNA Pathogen Detection software (Illumina) BaseSpacesuggested: (BaseSpace, RRID:SCR_011881)GATKsuggested: (GATK, RRID:SCR_001876)MAFFT alignment files were analyzed for maximum likelihood using RAxML (Stamatakis, 2006) MAFFTsuggested: (MAFFT, RRID:SCR_011811)RAxMLsuggested: (RAxML, RRID:SCR_006086)Prior to formal phylogenetic analyses, both data sets were examined in TempEst version 1.5.3 (Rambaut, 2016) to screen for outliers and assess temporal signal. TempEstsuggested: (TempEst, RRID:SCR_017304)Phylodyn… SciScore for 10.1101/2021.01.12.426407: (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 The analysis pipeline included BaseSpace, a custom pipeline using GATK tools and DRAGEN RNA Pathogen Detection software (Illumina) BaseSpacesuggested: (BaseSpace, RRID:SCR_011881)GATKsuggested: (GATK, RRID:SCR_001876)MAFFT alignment files were analyzed for maximum likelihood using RAxML (Stamatakis, 2006) MAFFTsuggested: (MAFFT, RRID:SCR_011811)RAxMLsuggested: (RAxML, RRID:SCR_006086)Prior to formal phylogenetic analyses, both data sets were examined in TempEst version 1.5.3 (Rambaut, 2016) to screen for outliers and assess temporal signal. TempEstsuggested: (TempEst, RRID:SCR_017304)Phylodynamic analyses were then carried out in BEAST version 1.10.4 (Suchard, 2018) under a strict clock model with coalescent exponential growth and an HKY substitution model with gamma-distributed rates (4 categories) and unlinked parameters for each codon position. BEASTsuggested: (BEAST, RRID:SCR_010228)Tracer version 1.7.1 (Rambaut, 2018) was used to assess convergence. Tracersuggested: (Tracer, RRID:SCR_019121)TreeAnnotater version v1.10.4 (Suchard, 2018) was used to compute the maximum clade credibility (MCC) tree, which was plotted using FigTree version 1.4.4 (Rambaut, 2018). FigTreesuggested: (FigTree, RRID:SCR_008515)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.
- No funding statement was detected.
- No protocol registration statement was detected.
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