Genomic surveillance of SARS-CoV-2 and nationwide capacity building across Bangladesh

Our proof-of-concept study used MinION (Oxford Nanopore Technology), "Lab in a suitcase" to generate genomic data that we combined with mobility data mobile phone operators to provide an early picture of the dynamics of the COVID-19 epidemic in Bangladesh. We showed evidence of repeated introductions by returning migrant workers and international travelers leading to the emergence and rapid country-wide dissemination of SARS-CoV-2 lineages or variants. Bangladesh urgently needs an integrated genomics network suitable to identify and track known or novel variants. Our proposal is to establish a country-wide network for SARS-CoV-2 genomic surveillance. We will do this by extending the number of MinION-based sequencing platforms to seven federated sites linked to the Ministry of Health and Family Welfare, representing facilities in different administrative areas (6 of 8) comprising Bangladesh. The advantage of these devices is their portability and ease of use, and the flexibility of the platform beyond SARS-CoV-2 in the context of future epidemics. We will use the expertise we have developed to train researchers, adopting a "train the trainer" model of capacity building, in sequencing, bioinformatics, and epidemiological modeling, such that we are able to respond to COVID-19 as it evolves, as well as to future pathogen threats.