Impact of SARS-CoV-2 Gamma lineage introduction and COVID-19 vaccination on the epidemiological landscape of a Brazilian city

  1. Cecília Artico Banho
  2. Lívia Sacchetto
  3. Guilherme Rodrigues Fernandes Campos
  4. Cíntia Bittar
  5. Fábio Sossai Possebon
  6. Leila Sabrina Ullmann
  7. Beatriz de Carvalho Marques
  8. Gislaine Ceslestino Dutra da Silva
  9. Marília Mazzi Moraes
  10. Maisa Carla Pereira Parra
  11. Andreia Francesli Negri
  12. Ana Carolina Boldrin
  13. Michela Dias Barcelos
  14. Thayza M. I. L. dos Santos
  15. Bruno H. G. A. Milhim
  16. Leonardo Cecílio Rocha
  17. Fernanda Simões Dourado
  18. Andresa Lopes dos Santos
  19. Victoria Bernardi Ciconi
  20. Caio Patuto
  21. Alice Freitas Versiani
  22. Rafael Alves da Silva
  23. Edoardo Estevam de Oliveira Lobl
  24. Victor Miranda Hernandes
  25. Nathalia Zini
  26. Carolina Colombelli Pacca
  27. Cássia Fernanda Estofolete
  28. Helena Lage Ferreira
  29. Paula Rahal
  30. João Pessoa Araújo
  31. Jamie A. Cohen
  32. Cliff C. Kerr
  33. Benjamin M. Althouse
  34. Nikos Vasilakis
  35. Mauricio Lacerda Nogueira

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Abstract

Background:

The emergence of the Brazilian variant of concern, Gamma lineage (P.1), impacted the epidemiological profile of COVID-19 cases due to its higher transmissibility rate and immune evasion ability.

Methods:

We sequenced 305 SARS-CoV-2 whole-genomes and performed phylogenetic analyses to identify introduction events and the circulating lineages. Additionally, we use epidemiological data of COVID-19 cases, severe cases, and deaths to measure the impact of vaccination coverage and mortality risk.

Results:

Here we show that Gamma introduction in São José do Rio Preto, São Paulo, Brazil, was followed by the displacement of seven circulating SARS-CoV-2 variants and a rapid increase in prevalence two months after its first detection in January 2021. Moreover, Gamma variant is associated with increased mortality risk and severity of COVID-19 cases in younger age groups, which corresponds to the unvaccinated population at the time.

Conclusions:

Our findings highlight the beneficial effects of vaccination indicated by a pronounced reduction of severe cases and deaths in immunized individuals, reinforcing the need for rapid and massive vaccination.

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  1. Version published to 10.1038/s43856-022-00108-5
  2. ScreenIT

    SciScore for 10.1101/2021.07.28.21261228: (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 Committee of Faculdade de Medicina de São José do Rio Preto Institutional Review Board (IRB) (protocol number: CAE# 31588920.0.0000.5415)
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    GeneFinder COVID-19 Plus RealAmp Kit (OSANG Healthcare, KOR) (the manufacturer does not provide sequences of the primers and probe) 34 .
    GeneFinder
    suggested: (GENEFINDER, RRID:SCR_009190)
    OSANG Healthcare
    suggested: None
    Genome assembling and lineage analyses: The quality of FASTQ sequencing data was checked using FastQC software v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and trimming was performed in Geneious Prime v.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    2021.1 (https://www.geneious.com/), using the plugin BBDuk v.
    https://www.geneious.com/
    suggested: (Geneious, RRID:SCR_010519)
    A minimum Phred score of Q30 35 and a minimal read length of 75 base pairs (bp) were used.
    Phred
    suggested: (Phred, RRID:SCR_001017)
    The nucleotide sequences were aligned using MAFFT multiple sequence alignment software version 7.271 38
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Time-scale phylogenetic trees using the Maximum-likelihood (ML) method were reconstructed in IQ-TREE v.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    2.0.3 39, using the best-fit model of nucleotide substitution, according to Bayesian Information Criterion (BIC), inferred by ModelFinder application 40 .
    ModelFinder
    suggested: None
    To investigate the temporal signal from the ML tree, we regressed root-to-tip genetic distances against sample collection dates using TempEst v 1.5.1 (http://tree.bio.ed.ac.uk) 42
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    An ordinary least squares fit was performed using Python 3.8 (https://www.python.org/)
    Python
    suggested: (IPython, RRID:SCR_001658)
    https://www.python.org/
    suggested: (CVXOPT - Python Software for Convex Optimization, RRID:SCR_002918)

    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 10.1101/2021.07.28.21261228 on medRxiv