Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants

  1. Alessandra Pavan Lamarca
  2. Luiz G. P. de Almeida
  3. Ronaldo da Silva Francisco
  4. Liliane Cavalcante
  5. Otávio Brustolini
  6. Alexandra L. Gerber
  7. Ana Paula de C. Guimarães
  8. Thiago Henrique de Oliveira
  9. Érica Ramos dos Santos Nascimento
  10. Cintia Policarpo
  11. Isabelle Vasconcellos de Souza
  12. Erika Martins de Carvalho
  13. Mario Sergio Ribeiro
  14. Silvia Carvalho
  15. Flávio Dias da Silva
  16. Marcio Henrique de Oliveira Garcia
  17. Leandro Magalhães de Souza
  18. Cristiane Gomes Da Silva
  19. Caio Luiz Pereira Ribeiro
  20. Andréa Cony Cavalcanti
  21. Claudia Maria Braga de Mello
  22. Amilcar Tanuri
  23. Ana Tereza R. de Vasconcelos

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Abstract

During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.

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  1. Version published to 10.1099/mgen.0.000859 on Access Microbiology
  2. ScreenIT

    SciScore for 10.1101/2022.01.17.22269136: (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
    Epidemiological analyses: Daily number of confirmed COVID-19 cases, deaths and people vaccinated were obtained from the National Immunization Program (Programa Nacional de Imunização, PNI), esus-VE and SIVEP-Gripe databases through the COVID-19 portal (https://www.saude.rj.gov.br/informacao-sus/dados-sus/2020/11/covid-19) maintained by the Secretary of Health of the state of Rio de Janeiro.
    National Immunization Program
    suggested: (Centers for Disease Control and Prevention, RRID:SCR_012976)
    All newly sequenced and assembled genomes are publicly available at GISAID (Table S1) and SRA-NCBI (BioProject PRJNA774631) databases..
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    These sequences were independently aligned to the WH01 (EPI ISL 406798) sequence from Wuhan, China using MAFFT v.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The outgroup (WH01) was then removed and root-to-tip distances were calculated using TempEst.
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    To accomplish this, we used the BEAST software and the Relaxed Random Walk model with Cauchy’s distribution on coordinates randomly selected within each sample’s collection city.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Dispersal routes were extracted from the consensus tree using the seraphim package and plotted using the ggplot2 package, both in R software.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)

    Results from OddPub: Thank you for sharing your data.

    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 10.1101/2022.01.17.22269136v1 on medRxiv