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

Carla Mavian; Simone Marini; Mattia Prosperi; Marco Salemi

Transition/transversions vs. genetic distance plot were calculated using DAMBE6 (19) . Evaluation of the presence of phylogenetic signal satisfying resolved phylogenetic relationships among sequences was carried out with IQ-TREE, allowing the software to search for all possible quartets using the best-fitting nucleotide substitution model (11) . ML tree reconstruction was performed in IQ-TREE based on the best-fit model chosen according to Bayesian Information Criterion (BIC) (20, 21) . Exploration of temporal structure, i.e. presence of molecular clock in the data, was assessed by regression of divergence -root-to-tip genetic distance-against sampling time using TempEst (13) . In this case, absence of a linear trend indicates that the data does not contain temporal signal and that the data is not appropriate for phylogenetic inference using molecular clock models. TransPhylo R package was used to infer transmission matrices of SARS-CoV-2 (16) . The copyright holder for this preprint (which was not peer-reviewed) is the .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 Figure S2 ). Each bidirectional arrow, and corresponding number, connects two tip branches that were switched to generate an alternative tree topology to be tested (see Table 1 , Methods). The copyright holder for this preprint (which was not peer-reviewed) is the .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 Table S1 . Acknowledgment table with full information of genome sequences. Downloaded from GISAID on March 10 th 2020 and provided as Excel file. . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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