SARS‐COV‐2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages

  1. Alex Ranieri Jerônimo Lima
  2. Gabriela Ribeiro
  3. Vincent Louis Viala
  4. Loyze Paola Oliveira de Lima
  5. Antonio Jorge Martins
  6. Claudia Renata dos Santos Barros
  7. Elaine Cristina Marqueze
  8. Jardelina de Souza Todao Bernardino
  9. Debora Botequio Moretti
  10. Evandra Strazza Rodrigues
  11. Elaine Vieira Santos
  12. Ricardo Augusto Brassaloti
  13. Raquel de Lello Rocha Campos Cassano
  14. Pilar Drummond Sampaio Corrêa Mariani
  15. Luan Gaspar Clemente
  16. Patricia Akemi Assato
  17. Felipe Allan da Silva da Costa
  18. Mirele Daiana Poleti
  19. Jessika Cristina Chagas Lesbon
  20. Elisangela Chicaroni Mattos
  21. Cecilia Artico Banho
  22. Lívia Sacchetto
  23. Marília Mazzi Moraes
  24. Melissa Palmieri
  25. Maiara Martininghi
  26. Luiz Artur Vieira Caldeira
  27. Fabiana Erica Vilanova da  Silva
  28. Rejane Maria Tommasini Grotto
  29. Jayme A. Souza‐Neto
  30. Marta Giovanetti
  31. Luiz Carlos Junior Alcantara
  32. Maurício Lacerda Nogueira
  33. Heidge Fukumasu
  34. Luiz Lehmann Coutinho
  35. Simone Kashima
  36. Raul Machado Neto
  37. Dimas Tadeu Covas
  38. Svetoslav Nanev Slavov
  39. Sandra Coccuzzo Sampaio
  40. Maria Carolina Elias

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Abstract

Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely‐Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS‐CoV‐2 variants which can impact the ongoing SARS‐CoV‐2 vaccination and public health policies.

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  1. Version published to 10.1002/jmv.27674
  2. ScreenIT

    SciScore for 10.1101/2021.11.29.21266819: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Trimming was performed using Trimmomatic (4) version 0.3.9 in order to select the sequences with the best quality.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    We mapped the trimmed sequences against the SARS-CoV-2 reference (Genbank RefSeq NC_045512.2) using BWA (5) software and samtools for read indexing.
    RefSeq
    suggested: (RefSeq, RRID:SCR_003496)
    BWA
    suggested: (BWA, RRID:SCR_010910)
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The mapped files were submitted to refinement using Pilon (7) to obtain the correct indels and insertions.
    Pilon
    suggested: (Pilon , RRID:SCR_014731)

    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.

  3. Version published to 10.1101/2021.11.29.21266819v1 on medRxiv