The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein
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Abstract
Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. Importantly, we detected the community transmission of different P.1 lineages bearing NTD indels ∆69-70 (which can impact several SARS-CoV-2 diagnostic protocols), ∆144 and ins214ANRN, and a new VOI N.10 derived from the B.1.1.33 lineage carrying three NTD deletions (∆141–144, ∆211, and ∆256–258). These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil generates new viral lineages that might be more resistant to antibody neutralization than parental variants of concern.
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SciScore for 10.1101/2021.03.19.21253946: (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 Additionally, the same reads were imported in a different pipeline 35 based on Bowtie2 and bcftools 36 mapping and consensus generation allowing us to further confirm the indels for all samples sequenced in this study. Bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Maximum Likelihood Phylogenetic Analyses: SARS-COV-2 sequences here obtained were aligned with high quality (<1% of N) and complete (>29 kb) lineages B.1.1.28, P.1, P2 and B.1.1.33 sequences that were available in EpiCoV database in the GISAID (https://www.gisaid.org/) at March 1st, 2021 and subjected to maximum-likelihood (ML) … SciScore for 10.1101/2021.03.19.21253946: (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 Additionally, the same reads were imported in a different pipeline 35 based on Bowtie2 and bcftools 36 mapping and consensus generation allowing us to further confirm the indels for all samples sequenced in this study. Bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Maximum Likelihood Phylogenetic Analyses: SARS-COV-2 sequences here obtained were aligned with high quality (<1% of N) and complete (>29 kb) lineages B.1.1.28, P.1, P2 and B.1.1.33 sequences that were available in EpiCoV database in the GISAID (https://www.gisaid.org/) at March 1st, 2021 and subjected to maximum-likelihood (ML) phylogenetic analysis using IQ-TREE v2.1.2 38. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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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