We are implementing a qPCR-based SARS-CoV-2 diagnostics pipeline at the Institut Pasteur of Madagascar, based on IGI's blueprint. We will use next-generation sequencing to look at viral RNA sequences in positive samples. This data will then be used to develop epidemiological, phylodynamic models of the spread of SARS-CoV-2 across Madagascar.

We are particularly interested in estimating the timing of origin of the virus to the island, the underreporting rate of positive case counts, and patterns of connectivity that will inform public health interventions targeted at reducing transmission from the capital city to the rest of the country.