High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021

  1. Ueric José Borges de Souza
  2. Raíssa Nunes dos Santos
  3. Fabrício Souza Campos
  4. Karine Lima Lourenço
  5. Flavio Guimarães da Fonseca
  6. Fernando Rosado Spilki
  7. Corona-ômica.BR/MCTI Network

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Abstract

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5′ and two in 3′ UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough “space” for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the “hotspots” in the generation of new variants.

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  1. Version published to 10.3390/v13091806
  2. ScreenIT

    SciScore for 10.1101/2021.07.10.451922: (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
    SentencesResources
    The SAM files from the alignments were sorted, converted to BAM and indexed using Samtools V1.9 (Li et al., 2009).
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The Variant Effect Predictor (VEP) was used to assess functional effects of detected variants on SARS-CoV-2 transcripts (McLaren et al., 2016). 2.3) Dynamics of SARS-CoV clades: Genomic surveillance of SARS-CoV-2 across Brazilian regions was performed using the Nextstrain (https://nextstrain.org/ncov), an open-source program which generates updated phylogeny with interactive visualization of publicly available SARS-CoV-2 genomes.
    Variant Effect Predictor
    suggested: None
    Because of the large number of sequenced genomes, we conduct a subsampling of Brazilian genomes from GISAID by using Nextstrain’s bioinformatics toolkit, that includes python3 scripts for preparing GISAID data for processing by Augur.
    python3
    suggested: None

    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.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2021.07.10.451922v1 on bioRxiv