A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications

Carla Mavian; Simone Marini; Mattia Prosperi; Marco Salemi

As more genome sequences, sampled at different time points and from diverse geographic areas, are daily becoming available, in depth Bayesian phylodynamic and phylogeography analyses of the COVID-19 pandemic may soon be a viable option. As long new data do not increase phylogenetic and temporal signal, results will remain highly questionable. Characterization of transmission events is fundamental to understand the dynamics of any infectious disease. From a public health standpoint, being able to trace transmission at the local level is crucial. Within country identification of active transmission clusters would open the way to more effective public health measures. The most optimal inference of transmission events would have a combination of genetic and epidemiological data for a joint analysis. However, it is not possible, at the moment, to identify transmission clusters within regions, counties, or cities, solely on genetic data, since micro-scale genetic data is not yet available. Indeed, transmission investigations that have been performed so far have been based on contact-tracing, epidemiological and clinical data (17, 18) .