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

Carla Mavian; Simone Marini; Mattia Prosperi; Marco Salemi

Available genome sequences are rapidly growing. SARS-CoV-2 full genome dataset is now showing less than 40% of unresolved quartets in the center: 38.6% unresolved quartets on March 18 th (794 genome sequences) ( Figure S1c ) and 32.3% on March 25 th (1,660 genome sequences) ( Figure S1d ). This indicates that the amount of phylogenetic information is now potentially usable to define phylogenetic relationships among strains. Plotting mean genetic distance of each sequence from the root of a phylogeny versus the sequence sampling time allows to testing for significant linear correlation, which is necessary for the calibration of a reliable molecular clock (13) ( Figure S3 ). As expected in genomes obtained over a very short period of time (~ three months) since the beginning of the outbreak, correlation in the current data is fairly week (Table S3 ). However, Bayesian analysis (14) , which infers phylogenetic and phylogeographic patterns from a posterior distribution of trees, might facilitate comparisons about different evolutionary scenarios, help in retrieving the correct topology, and estimate an accurate evolutionary rate using relaxed clock methods (15) . Reconstructing the phylogenetic relationships of the same European Subclade A discussed above with sequence available on March 18 th 2020 showed a much more complex snapshot of SARS-CoV-2 spreading ( Figure S4 ). Taking a closer look at the Sublade A reveals that even with more genomes available, inference is bias by over-sampling of some countries and under-sampling of others ( Figure S4 ). Yet, even with more genomes available, inference is bias by over-sampling of some countries and under-sampling of others . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 ( Figure S4 ). Recently, methods were developed to estimate, for each pair of viral sequences from two infected individuals, how many intermediates there are in the putative transmission chain connecting them, using a transmission matrix (16) . The analysis of SARS-CoV-2 genomes shows that numerous links among samples are still missing ( Figure S5 ). In such a scenario, it is not advisable to extrapolate conclusions on the origin and dissemination of strains.