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

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.

Fig. 1. Phylogenetic analysis of 391 Bangladesh SARS-CoV-2 genomes March–July 2020.

a, Maximum-likelihood phylogenetic analysis of 391 viruses sampled from Bangladesh (black) on a background of 68,870 publicly available GISAID global sequences in collapsed clades. Collapsed clades are coloured by the predominant region/country that they were sampled in (blue, Europe; red, United States; green, India; pink, Middle East). International arrival frequencies from those regions between 18 February 2020 and 18 March 2020 are displayed in a bar chart and shown in the same colours. b, Maximum-likelihood Bayesian time-scaled phylogenetic analysis generated using BEAST (v.1.10.4); clades, internal nodes and migration events are annotated.

Fig. 2. Lineage dynamics of 391 Bangladesh SARS-CoV-2 genomes March–July 2020.

a, Proportional bar plot of Pango lineage diversity in Bangladesh between March and July 2020. b, Steam graph of the lineage dynamics between March and July 2020. c, Bubble plot of the representation of Pango lineages across eight divisions of Bangladesh.

Fig. 3. Population mobility dynamics in Bangladesh 2020.

a, The percentage change in the Facebook user population over time for each district in Bangladesh (grey lines) compared with a baseline average. Specific districts are highlighted; the Dhaka district is shown in red. The dashed vertical lines indicate notable events. b, The distribution of trips from Dhaka by distance (km) travelled for each month and during Eid (29–31 July) based on call detail records data from three mobile phone operators. c, The number of subscribers travelling to and from Narayanganj.

Fig. 4. Bangladesh genomes in the context of a Nextstrain time-scaled global phylogeny.

a, Nextstrain time-scaled phylogeny of 1,489 representative global sequences of SARS-CoV-2 sampled from GISAID on 20 April 2021. Pango lineages labelled on clades, and Bangladesh sequences (n = 166) are highlighted at the tips, coloured by lineage membership. b, Map of Bangladesh with pie chart representations of Pango lineage representation in each locality.