Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay
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Abstract
Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020–February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay’s capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest.
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SciScore for 10.1101/2021.07.27.21261150: (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 Genome sequencing: Sequencing libraries were prepared according to the classic ARTIC protocol described by Quick J. [10,11] or the SARS-CoV2 genome sequencing protocol (1200bp amplicon “midnight” primer set, using Nanopore Rapid kit) described by Freed N. and Silander O. [12,13] with minor modifications (Table S1). Quick Jsuggested: NoneConsensus genomes were generated using the poreCov pipeline [15–24] and Nanopolish was used for consensus generation. Nanopolishsuggested: (Nanopolish, RRID:SCR_016157)Alignment was performed with MAFFT v7.471 [28]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Ma… SciScore for 10.1101/2021.07.27.21261150: (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 Genome sequencing: Sequencing libraries were prepared according to the classic ARTIC protocol described by Quick J. [10,11] or the SARS-CoV2 genome sequencing protocol (1200bp amplicon “midnight” primer set, using Nanopore Rapid kit) described by Freed N. and Silander O. [12,13] with minor modifications (Table S1). Quick Jsuggested: NoneConsensus genomes were generated using the poreCov pipeline [15–24] and Nanopolish was used for consensus generation. Nanopolishsuggested: (Nanopolish, RRID:SCR_016157)Alignment was performed with MAFFT v7.471 [28]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Maximum likelihood (ML) phylogenetic analysis of the 1,796 B.1.1.28 sequences was performed with IQ-TREE version 1.6.12 under the model GTR+F+R3 of nucleotide substitution selected by the built-in ModelFinder option [29]. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Phylogenetic trees were estimated in BEAST v1.10 [35] using the GTR+F+I nucleotide substitution model, the non-parametric Bayesian skyline model as the coalescent tree prior [36], a strict molecular clock model with a uniform substitution rate prior (8-10 ×10−4 substitutions/site/year) and a reversible discrete phylogeographic model (using Uruguayan departments as epidemic locations) [37] with a continuous-time Markov chain (CTMC) rate reference prior [38]. BEASTsuggested: (BEAST, RRID:SCR_010228)MCMC chains were run for 100 million generations and convergence (Effective Sample Size > 200) in parameter estimates was assessed using Tracer v1.7 [39]. Tracersuggested: (Tracer, RRID:SCR_019121)Maximum clade credibility (MCC) tree was summarized with TreeAnnotator v1.10 [40] and visualized using FigTree v1.4.4 [41]. TreeAnnotatorsuggested: (BEAST2, RRID:SCR_017307)FigTreesuggested: (FigTree, RRID:SCR_008515)Additional visualizations were implemented in the R environment with treeio and ggtree Bioconductor packages [42]. Bioconductorsuggested: (Bioconductor, RRID:SCR_006442)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.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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