Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

  1. George Githinji
  2. Zaydah R. de Laurent
  3. Khadija Said Mohammed
  4. Donwilliams O. Omuoyo
  5. Peter M. Macharia
  6. John M. Morobe
  7. Edward Otieno
  8. Samson M. Kinyanjui
  9. Ambrose Agweyu
  10. Eric Maitha
  11. Ben Kitole
  12. Thani Suleiman
  13. Mohamed Mwakinangu
  14. John Nyambu
  15. John Otieno
  16. Barke Salim
  17. Kadondi Kasera
  18. John Kiiru
  19. Rashid Aman
  20. Edwine Barasa
  21. George Warimwe
  22. Philip Bejon
  23. Benjamin Tsofa
  24. Lynette Isabella Ochola-Oyier
  25. D. James Nokes
  26. Charles N. Agoti

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Abstract

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17 th March and 31 st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

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  1. Version published to 10.1038/s41467-021-25137-x
  2. ScreenIT

    SciScore for 10.1101/2020.10.05.20206730: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The whole genome sequencing study protocol was reviewed and approved by the Scientific and Ethics Review Committee (SERU) that sits at the Kenya Medical Research Institute (KEMRI) headquarters in Nairobi (SERU # 4035).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequence alignment and phylogenetics clustering: Multiple sequence alignments were done using MAFFT v7.310.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A time-scaled phylogeny was generated using the BEAST (v1.10.4) Bayesian phylogenetic framework to reconstruct a time-scaled phylogeny from 274 sequences from the Kenyan coast.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The final library was normalized to 15ng prior to loading on a flow-cell and sequencing with a MinION Mk1B device.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    To estimate evolutionary relationships between sequences collected in coastal Kenya, a separate maximum likelihood phylogenetic tree was inferred from an alignment of 274 coastal Kenya sequences in addition to the NC_045512.2 reference sequence using RAxML-NGS v0.9.0) and run with 1000 bootstraps.
    RAxML-NGS
    suggested: None
    MCMC convergence and log files from the runs were inspected using Tracer v1.7.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The detection of a unique lineage (B.1.1.33) in a sample that was collected during mass testing (13-May-2020) in the Mombasa City could be indicative of cryptic transmission within the community in spite of the intervention, but also could be failure to detect this lineage at the port of entry due to sampling limitations. Early COVID-19 control strategies by the Kenyan government were geared towards preventing establishment of community transmission. These policies appear to have been largely successful in that most of the introductions were not associated with subsequent established transmission. Nevertheless, a minority of introductions did go on to establish sustained transmission and give rise to local transmission despite an absence of new virus lineages being imported. This underlines the severe challenge to a strategy aimed at preventing the introduction of virus as any cases escaping the net can potentially establish community spread. A number of samples (n=35) that were analysed in this study were collected at the Kenya-Tanzania border points. In neighbouring Uganda, international truck drivers including those from Kenya were identified as common sources of the infection (Bugembe et al., 2020; Nakkazi, 2020). This led to mass testing of truck drivers in Kenya and a requirement of a “COVID-19 free certificate” before leaving or entering Kenya. The genomic analysis of SARS-CoV-2 cases in Uganda detected lineages similar to those reported in our study (i.e. A, B, B.1, B...

    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.

    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 10.21203/rs.3.rs-93975/v1 on Research Square
  4. Version published to 10.1101/2020.10.05.20206730 on medRxiv