Evidence-based national policies are essential to curb local COVID-19 infections
Genetic sequencing of SARS-CoV-2 and population mobility data in Bangladesh have shed light on the spread of the virus during the first wave.
The research is the result of a consortium comprised of the Wellcome Sanger Institute, University of Bath, and Bangladesh-based Institutes, including the Institute of Epidemiology, Disease Control and Research (IEDCR), icddr,b (formerly International Centre for Diarrhoeal Disease Research) and Institute for Developing Science and Health Initiatives (ideSHi), plus other local and international institutions.
The paper, published on the 8th September 2021 in Nature Microbiology, details the analysis of the genome sequencing data of 391 SARS-CoV-2 samples collected in Bangladesh between March and July 2020, in combination with anonymised population mobility data collected from Facebook and three mobile operators. This analysis allowed the researchers to see the evolution of the virus, track the different times and locations where new lineages of SARS-CoV-2 appeared, and enabled the authors to work directly with the government on the detection of variants of concern (Alpha and Beta) in Bangladesh.
The study is the first of its kind and shows the unique advantage of combining mobility and genomic data to help untangle what is going on during an infectious disease outbreak. This information is crucial as it can later be used to shape policies and interventions as the situation progresses. Insights from this project could be implemented in other countries to ensure that SARS-CoV-2 is tracked as accurately as possible and informed decisions can be made.
SARS-CoV-2 is an RNA virus and as such its genetic code is prone to errors each time it replicates. It is currently estimated that the virus mutates at a rate of 2.5 nucleotides (the A, C, G and T of genetic code) per month. Reading – or sequencing – the genetic code of the virus can provide valuable information on its biology and transmission. It allows researchers to create ‘family trees’ – known as phylogenetic trees – that show how samples relate to each other. When a virus replicates and gathers multiple mutations that change how it acts, it is known as a lineage or variant of the original strain.
This new research analysed 391 Bangladeshi SARS-CoV-2 samples, 67 of these were sequenced from positive samples taken at in country testing facilities between March and July 2020, while the other 324 were Bangladeshi samples taken from GISAID (Global Initiative on Sharing All Influenza Data). A further 68,000 GISAID global genomes were also used in the analysis to build the phylogenetic trees.
They found that 85 per cent of virus samples fell into three dominant variants, namely B.1.1, B.1.1.25, and B.1.36. Variant B.1.1 accounted for 19 per cent of samples, while B.1.1.25 accounted for 58 per cent. Variant B.1.36 accounted for 8 per cent of the overall sequences and was predominant in southern Bangladesh with 64 per cent of these found in the Chattogram division.
To investigate the factors that led to country-wide spread of these three dominant variants, the consortium examined the history of events that unfolded before the first wave of COVID-19. Bangladesh reported the first COVID-19 case on 8 March 2020. To contain the spread of the virus, the Government of Bangladesh announced a national public holiday with stay-at-home order on 23 March 2020, which was effective from 26 March to 4 April and later incrementally extended until 30 May 2020.
However, the population mobility data collected from Facebook and three mobile phone operators showed an important link between population movement and the spread of SARS-CoV-2. It indicated a mass migration out of Dhaka to all areas of the country on 23-26 March 2020. Together, these mobility data are consistent with the transmission of SARS-CoV-2 out of Dhaka to the rest of the country during the first wave. Combining population mobility and genomics data revealed a direct link between the transmission of three dominant variants and the spread of the disease across the country during the first wave.
Later on, the consortium sequenced another 85 SARS-CoV-2 samples in April 2021 collected between November 2020 and April 2021. Of these, 30 were variant B.1.1.25 (35 per cent), 13 were variant of concern Alpha (B.1.1.7, 15 per cent), 40 were variant of concern Beta (B.1.351, 47 per cent), 1 was variant B.1.1.315, and 1 was variant B.1.525. Their analysis of the first wave and the revealed country-wide spread through inter-city travel led the authors to work directly with the government on the detection of variants of concern, Alpha and Beta in Bangladesh.
The government of Bangladesh responded accordingly and implemented interventions that would limit spread of the virus through the same channels as observed during the first wave, such as restrictions on inter-city travel.
“It was a privilege to be involved in such a pioneering genomic epidemiology study led by Bangladesh. By combining different data streams from genomic and mobility data, we were able to provide new resolution to how SARS-CoV-2 spread in Bangladesh. This study showcases the incredible capacity for genome sequencing that has been built in Bangladesh that will continue to be used during the ongoing COVID-19 pandemic but also in future outbreaks of other pathogens.”
Dr Lauren Cowley, co-first author and Research Staff at the University of Bath
“Our consortium has provided many invaluable insights that helped the decision-makers to devise essential real-time policy decisions. These include the provision of mandatory quarantine and isolation of travellers arriving from countries where the variant of concern was dominating, imposing lockdown measures and restricting inter-city movements of people, banning all international flights from high-risk countries to Bangladesh. It is important that we continue to generate evidence to aid our policymakers to contain the spread of the virus successfully.”
Professor Tahmina Shirin, senior author and Director at the Institute of Epidemiology, Disease Control and Research (IEDCR), Bangladesh
“As more mutations accumulate in the SARS-CoV-2’s genetic code, there would be more variants of which some could have the strength to breakthrough natural or vaccine-induced immunity. This is already evident, Bangladesh has experienced the second wave with the Beta variant and is currently battling the third wave with the Delta variant. Real-time genomic surveillance is critical to understand the efficacy of these vaccines and to devise relevant strategies for Bangladesh and beyond.”
Dr Firdausi Qadri, senior author and Senior Scientist at icddr,b
“Our teams have worked together productively for many years studying many different infectious diseases. We have shared expertise, experiences, students, and training. This study was built on those shared experiences and a lot of hard work. It is a great example of what can be achieved when scientists work collectively with public health professionals towards a collective goal.”
Professor Nicholas Thomson, senior author and Head of the Parasites and Microbes Programme and Group Leader at the Wellcome Sanger Institute
More information
Publication:
L. Cowley, M. Afrad, S. Rahman, Md. Mahfuz-Al-Mamun, et al. (2021) Genomics, social media, and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh. Nature Microbiology. DOI: 10.1038/s41564-021-00955-3
Funding:
This research was funded by Government of Bangladesh, Bill and Melinda Gates Foundation, and Wellcome.
