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

Carla Mavian; Simone Marini; Mattia Prosperi; Marco Salemi

in Germany that appears to be paraphyletic (with strong bootstrap support) to an Italian sequence clustering, in turn, with sequences from Finland, Mexico, Germany and Switzerland. Based on this observation (which was available on NextStrain), a heated discussion circulated on social media about a transmission event from Germany to Italy followed by further spread from Italy the . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.01.020594 doi: bioRxiv preprint other countries. However, in a new tree inferred just one week later, when more than 135 new full genome sequences were made available on GISAID (9) , the direct link between Germany and Italy in Subclade A disappeared due to the additional clustering of previously unsampled sequences from Portugal, Brazil, Wales and Netherland (Figure 2b ). In addition, likelihoods of alternative tree topologies generated arbitrarily switching branches in the tree (arrows in Figure 2b ), implying different dissemination scenarios, were not significantly different (Shimodaira- Hasgawa test, Table S2 ) than the likelihood of the tree inferred from the real data. In other words, it is not possible, with present data, to decide which branching pattern (and, therefore, phylogeographic reconstruction) is the one most likely representing actual dissemination routes among European countries.