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

Lauren A. Cowley, Mokibul Hassan Afrad, Sadia Isfat Ara Rahman, Md Mahfuz Al Mamun, Taylor Chin, Ayesha Mahmud, Mohammed Ziaur Rahman, Mallick Masum Billah, Manjur Hossain Khan, Sharmin Sultana, Tilovatul Khondaker, Stephen Baker, Nandita Banik, Ahmed Nawsher Alam, Kaiissar Mannoor, Sayera Banu, Anir Chowdhury, Meerjady Sabrina Flora, Nicholas R. Thomson, Caroline O. BuckeeFirdausi Qadri, Tahmina Shirin

Research output: Contribution to journalArticlepeer-review

10 Citations (SciVal)

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.

Original languageEnglish
Pages (from-to)1271-1278
Number of pages10
JournalNature Microbiology
Volume6
Issue number10
Early online date8 Sept 2021
DOIs
Publication statusPublished - 31 Oct 2021

Bibliographical note

Funding Information:
We dedicate this work to Professor Dr Salehin Qadri for all his effort and support in making this study, and studies like this, possible. The Bill and Melinda Gates foundation, Wellcome Trust (grant 206194) and the Government of Bangladesh supported the in-country sequencing of SARS-CoV-2 Bangladesh samples. We would like to acknowledge Sally Forrest for her efforts in shipping reagents during the pandemic, which enabled the sequencing detailed in this report. We would also like to acknowledge diagnostic testing staff at IEDCR and ideSHI who provided initial diagnostics of SARS-CoV-2 samples. icddr,b is grateful to the Governments of Bangladesh, Canada, Sweden and the UK for providing core/unrestricted support.

Data availability
All sequencing data used in this study are available on GISAID, as described in the Supplementary Information and in the GISAID acknowledgements (Supplementary Data 1). Sequencing reads generated in this study have been made available on the NCBI Sequence Read Archive service (BioProject ID: PRJNA737194).

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Applied Microbiology and Biotechnology
  • Genetics
  • Microbiology (medical)
  • Cell Biology

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