Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh

  1. Lauren A. Cowley
  2. Mokibul Hassan Afrad
  3. Sadia Isfat Ara Rahman
  4. Md Mahfuz Al Mamun
  5. Taylor Chin
  6. Ayesha Mahmud
  7. Mohammed Ziaur Rahman
  8. Mallick Masum Billah
  9. Manjur Hossain Khan
  10. Sharmin Sultana
  11. Tilovatul Khondaker
  12. Stephen Baker
  13. Nandita Banik
  14. Ahmed Nawsher Alam
  15. Kaiissar Mannoor
  16. Sayera Banu
  17. Anir Chowdhury
  18. Meerjady Sabrina Flora
  19. Nicholas R. Thomson
  20. Caroline O. Buckee
  21. Firdausi Qadri
  22. Tahmina Shirin

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Abstract

Genomics, combined with population mobility data, used to map importation and spatial spread of SARS-CoV-2 in high-income countries has enabled the implementation of local control measures. Here, to track the spread of SARS-CoV-2 lineages in Bangladesh at the national level, we analysed outbreak trajectory and variant emergence using genomics, Facebook ‘Data for Good’ and data from three mobile phone operators. We sequenced the complete genomes of 67 SARS-CoV-2 samples (collected by the IEDCR in Bangladesh between March and July 2020) and combined these data with 324 publicly available Global Initiative on Sharing All Influenza Data (GISAID) SARS-CoV-2 genomes from Bangladesh at that time. We found that most (85%) of the sequenced isolates were Pango lineage B.1.1.25 (58%), B.1.1 (19%) or B.1.36 (8%) in early-mid 2020. Bayesian time-scaled phylogenetic analysis predicted that SARS-CoV-2 first emerged during mid-February in Bangladesh, from abroad, with the first case of coronavirus disease 2019 (COVID-19) reported on 8 March 2020. At the end of March 2020, three discrete lineages expanded and spread clonally across Bangladesh. The shifting pattern of viral diversity in Bangladesh, combined with the mobility data, revealed that the mass migration of people from cities to rural areas at the end of March, followed by frequent travel between Dhaka (the capital of Bangladesh) and the rest of the country, disseminated three dominant viral lineages. Further analysis of an additional 85 genomes (November 2020 to April 2021) found that importation of variant of concern Beta (B.1.351) had occurred and that Beta had become dominant in Dhaka. Our interpretation that population mobility out of Dhaka, and travel from urban hotspots to rural areas, disseminated lineages in Bangladesh in the first wave continues to inform government policies to control national case numbers by limiting within-country travel.

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  1. Version published to 10.1038/s41564-021-00955-3
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    SciScore for 10.1101/2021.01.05.21249196: (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
    With the full set of Bangladesh sequences, we used a time-aware coalescent Bayesian exponential growth model available in BEAST (v 1.10.4).
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The resulting phylogenies were visualized with a maximum clade credibility tree in FigTree, v1.4.4.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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: We detected the following sentences addressing limitations in the study:
    There are a number of limitations to our study that should be considered in the context of the results. The number of sequences sampled represented a small fraction of the documented number of positive cases at the time in Bangladesh (0·1%); the sample was selected to be a country-wide representative given limited resources for genome sequencing and consequently, the introduced viral diversity may also have been underestimated. However, the mutation rate of SARS-CoV-2 is slow (our estimate from Bangladeshi samples is 0·7 x 10−3 subs/site/year and latest global estimates are similar at 0·8 x 10−3 subs/site/year) so it would be expected that multiple studies sampling widely across all areas of Bangladesh would sample the limited diversity of lineages present in a country isolated by a ban on international arrivals. Despite these limitations, the study is the first of its kind and exemplifies the unique advantage of combining mobility and genomic data to untangle outbreak dynamics during an outbreak. Here we provide support for a more comprehensive country-wide study of the epidemiology and spread of SARS-CoV-2, with the integration of population mobility data, in settings like Bangladesh. Recent evidence of variants of interest emerging in the UK and South Africa have heightened calls for systematic genomic surveillance in more countries globally18. None of the variants of interest have yet been identified in Bangladesh (as of 4/1/21) but increased vigilance and surveillance is...

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 16. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

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  3. Version published to 10.1101/2021.01.05.21249196 on medRxiv