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

Genomic surveillance combined with population mobility data was used to track the emergence, importation, and spread of SARS-CoV-2 lineages in Bangladesh. The authors sequenced 67 complete SARS-CoV-2 genomes collected by IEDCR between March and July 2020 and integrated them with 324 publicly available GISAID genomes from Bangladesh, alongside Facebook Data for Good and mobile phone operator mobility data. Most isolates belonged to three lineages (notably B.1.1.25/B.1.125, B.1.1, and B.1.36). Time-scaled phylogenetics indicates viral introduction from abroad in mid-February 2020, with three discrete lineages circulating by early March. Rapid dissemination of these lineages coincided with mass migration from Dhaka to rural areas during late March. Analysis of an additional 85 genomes (Nov 2020–Apr 2021) revealed importation and subsequent dominance of the Beta (B.1.351) variant, predominantly in Dhaka. Findings informed Bangladeshi policy to limit within-country travel to control spread.

Lauren A. Cowley, Mokibur Hassan Afrad, Sadia Iftak 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, Kaiissaar Mannoor, Sayera Banu, Anir Chowdhury, Meerajdy Sabrina Flora, Nicholas R. Thomson, Caroline O. Buckee, Firdausi Qadri, Tahmina Shirin