The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City

  1. Alberto Cedro-Tanda
  2. Laura Gómez-Romero
  3. Nicolás Alcaraz
  4. Guillermo de Anda-Jauregui
  5. Fernando Peñaloza
  6. Bernardo Moreno
  7. Marco A. Escobar-Arrazola
  8. Oscar A. Ramirez-Vega
  9. Paulina Munguia-Garza
  10. Francisco Garcia-Cardenas
  11. Mireya Cisneros-Villanueva
  12. Jose L. Moreno-Camacho
  13. Jorge Rodriguez-Gallegos
  14. Marco A. Luna-Ruiz Esparza
  15. Miguel A. Fernández Rojas
  16. Alfredo Mendoza-Vargas
  17. Juan Pablo Reyes-Grajeda
  18. Abraham Campos-Romero
  19. Ofelia Angulo
  20. Rosaura Ruiz
  21. Claudia Sheinbaum-Pardo
  22. José Sifuentes-Osornio
  23. David Kershenobich
  24. Alfredo Hidalgo-Miranda
  25. Luis A. Herrera

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Abstract

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33–2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32–4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.

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  1. Version published to 10.3390/v13112182
  2. Version published to 10.1101/2021.09.07.21262911v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.09.07.21262911: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: The study was approved by the ethics and research committees of the Instituto Nacional de Medicina Genómica (CEI/1479/20 and CEI 2020/21).
    Field Sample Permit: Effective reproduction number estimation for variants B.1.1.222 and B.1.1.519: We grouped all sequenced samples based on the epidemiological week as the date of sample collection.
    Consent: Verbal consent and identification were the first steps when calling each subject included in the final analysis.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequencing was performed on the MinION platform, and the final library (15 ng) was loaded onto the flow cell R.9 according to the manufacturer’s instructions.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    A final consensus FASTA file was generated by first marking positions not covered by at least 20 reads from either group as low coverage and building a pre-consensus FASTA with BCFtools consensus, which was subsequently aligned against the reference sequence using muscle (v.3.8.1551).
    BCFtools
    suggested: (SAMtools/BCFtools, RRID:SCR_005227)
    Phylogenetic Analysis: The sequences were aligned with MAFFT (version 7.475) using the FFT-NS-2 algorithm20,21.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A maximum-likelihood phylogeny was calculated with FastTree (version 2.1.11) compiled with the double precision tag using a generalized time-reversible model (GTR)22,23.
    FastTree
    suggested: (FastTree, RRID:SCR_015501)

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2021.09.07.21262911v1 on medRxiv