Inter- and intra-community mapping of SARS-CoV-2 spread by combining whole-genome sequencing, phylogeographical analysis and movement traces

Since the introduction of SARS-CoV-2, the virus has been spreading very rapidly and has caused severe respiratory pathology around the world. A pandemic ensued within a short time. The virus originated from a zoonotic event, where likely a bat or even a pangolin was carrying the virus and infected a human by animal-to-human transmission. This means that the virus is still seeking an optimal fit with its new host, the human. This is, for example, illustrated by a still suboptimal binding between the human ACE2-receptor and the receptor-binding domain of the viral spike protein. This evolutionary pressure drives mutations
that allows us to closely follow the evolution of the virus. Our research question in this project proposal is how does this new coronavirus spread among the population both at micro level (e.g. in a school, or hospital) and at macro level (nationwide)? We propose to study the spatial distribution of Belgian SARS- CoV-2 clusters by a combination of full-length sequencing and phylodynamic analysis to assess how the spatio-temporal distribution of Belgian clusters evolved during the lockdown in March and April, during the release of these measures in May and June, and from the past summer period (June to August). Furthermore, we aim to investigate new positive cases during the next 12 months in a near real-time fashion to describe the evolution of the circulation dynamics through time and assess the impact of COVID19 measures on spatial transmission over time.