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.

基因组学与人口流动数据相结合，用于绘制高收入国家 SARS-CoV-2 的输入和空间传播图，从而能够实施当地控制措施。在这里，为了在国家层面追踪 SARS-CoV-2 谱系在孟加拉国的传播，我们使用基因组学、Facebook 的“善用数据”和来自三个移动电话运营商的数据分析了爆发轨迹和变异出现。我们对 67 个 SARS-CoV-2 样本（由孟加拉国 IEDCR 于 2020 年 3 月至 7 月期间收集）的完整基因组进行了测序，并将这些数据与 324 个公开的全球共享所有流感数据倡议 (GISAID) SARS-CoV-2 基因组相结合当时来自孟加拉国。我们发现，在 2020 年中期，大多数 (85%) 的测序分离株是 Pango 谱系 B.1.1.25 (58%)、B.1.1 (19%) 或 B.1.36 (8%)。贝叶斯时间尺度系统发育分析预测，SARS-CoV-2 于 2 月中旬从国外首次出现在孟加拉国，2020 年 3 月 8 日报告了首例 2019 年冠状病毒病 (COVID-19) 病例。 2020 年 3 月，三个离散的血统在孟加拉国扩展和无性繁殖。孟加拉国病毒多样性的变化模式，结合流动性数据显示，3 月底人们从城市大规模迁移到农村地区，随后是达卡（孟加拉国首都）和其他地区之间的频繁旅行。国家，传播了三种主要的病毒谱系。对另外 85 个基因组的进一步分析（2020 年 11 月至 2021 年 4 月）发现，已经发生了受关注变体 Beta（B.1.351）的输入，并且 Beta 在达卡已占主导地位。