Genomic and mobility data reveal mass population movement as a driver of SARS-CoV-2 dissemination and diversity in Bangladesh

Abstract

AbstractBackgroundNew data streams are being used to track the pandemic of SARS-CoV-2, including genomic data which provides insights into patterns of importation and spatial spread of the virus, as well as population mobility data obtained from mobile phones. Here, we analyse the emergence and outbreak trajectory of SARS-CoV-2 in Bangladesh using these new data streams, and identify mass population movements as a key early event driving the ongoing epidemic.MethodsWe sequenced complete genomes of 67 SARS-CoV-2 samples (March-July 2020) and combined this dataset with 324 genomes from Bangladesh. For phylogenetic context, we also used 68,000 GISAID genomes collected globally. We paired this genomic data with population mobility information from Facebook and three mobile phone operators.FindingsThe majority (85%) of the Bangladeshi sequenced isolates fall into either pangolin lineage B.1.36 (8%), B.1.1 (19%) or B.1.1.25 (58%). Bayesian time-scaled phylogenetic analysis predicted SARS-COV-2 first appeared in mid-February, through international introductions. The first case was reported on March 8th. This pattern of repeated international introduction changed at the end of March when three discrete lineages expanded and spread clonally across Bangladesh. The shifting pattern of viral diversity across Bangladesh is reflected in the mobility data which shows the mass migration of people from cities to rural areas at the end of March, followed by frequent travel between Dhaka and the rest of the country during the following months.InterpretationIn Bangladesh, population mobility out of Dhaka as well as frequent travel from urban hotspots to rural areas resulted in rapid country-wide dissemination of SARS-CoV-2. The strains in Bangladesh reflect the local expansion of global lineages introduced early from international travellers to and from major international travel hubs. Importantly, the Bangladeshi context is consistent with epidemiologic and phylogenetic findings globally. Bangladesh is one of the few countries in the world with a rich history of conducting mass vaccination campaigns under complex circumstances. Combining genomics and these new data streams should allow population movements to be modelled and anticipated rendering Bangladesh extremely well prepared to immunize citizens rapidly. Based on our genomics data and the country’s successful immunization history, vaccines becoming available globally will be suitable for implementation in Bangladesh while ongoing genomic surveillance is conducted to monitor for new variants of the virus.FundingGovernment of Bangladesh, Bill and Melinda Gates Foundation, Wellcome Trust.Research in contextEvidence before this studyThe emergence of SARS-CoV-2, leading to the COVID-19 pandemic, has motivated all countries in the world to obtain high resolution data on the virus. Globally over 300,000 strains have been sequenced and information made available in GISAID. Within the first 100 days of the emergence of SARS-CoV-2, genomic analysis from different countries led to the development of vaccines which have now reached market. Information on the prevailing genotypes of SARS-CoV-2 since introduction is needed in low and middle-income countries (LMICs), including Bangladesh, in order to determine the suitability of therapeutics and vaccines in the pipeline and help vaccine deployment.Added value of this studyWe sequenced SARS-CoV-2 genomes from strains that were prospectively collected during the height of the pandemic and combined these genomic data with mobility data to comprehensively describe i) how repeated international importations of SARS-CoV-2 were ultimately linked to nationwide spread, ii) 85% of strains belonged to the Pangolin lineages B.1.1, B.1.1.25 and B.1.36 and that similar mutation rates were observed as seen globally iii) the switch in genomic dynamics of SARS-CoV-2 coincided with mass migration out of cities to the rest of the country. We have assessed the contributions of population mobility on the maintenance and spread of clonal lineages of SARS-CoV-2. This is the first time these data types have been combined to look at the spread of this virus nationally.Implications of all the available evidenceSARS-CoV-2 genomic diversity and mutation rate in Bangladesh is comparable to strains circulating globally. Notably, the data on the genomic changes of SARS-CoV-2 in Bangladesh is reassuring, suggesting that immunotherapeutic and vaccines being developed globally should also be suitable for this population. Since Bangladesh already has extensive experience of conducting mass vaccination campaigns, such as the rollout of the oral Cholera vaccine, experience of developing and using new data streams will enable efficient and targeted immunization of the population in 2021 with COVID-19 vaccine(s).