Phylodynamics of SARS-CoV-2 transmission in Spain

Diez Fuertes, F.; Iglesias Caballero, M.; Monzon, S.; Jimenez, P.; Varona, S.; Cuesta, I.; Zaballos, A.; Thomson, M. M.; Jimenez, M.; Garcia Perez, J.; Pozo, F.; Perez Olmeda, M.; Alcami, J.; Casas, I.

doi:10.1101/2020.04.20.050039

bioRxiv · 10.1101/2020.04.20.050039

Phylodynamics of SARS-CoV-2 transmission in Spain

Diez Fuertes, F.·Iglesias Caballero, M.·Monzon, S.·Jimenez, P.·Varona, S.·Cuesta, I.·Zaballos, A.·Thomson, M. M.·Jimenez, M.·Garcia Perez, J.·Pozo, F.·Perez Olmeda, M.·Alcami, J.·Casas, I.

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Abstract

ObjectivesSARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe. MethodsMaximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2. ResultsPhylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai. ConclusionsMultiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.

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Diez Fuertes, F., Iglesias Caballero, M., Monzon, S., Jimenez, P., Varona, S., Cuesta, I., Zaballos, A., Thomson, M. M., Jimenez, M., Garcia Perez, J., Pozo, F., Perez Olmeda, M., Alcami, J., Casas, I.. 2020-04-20. Phylodynamics of SARS-CoV-2 transmission in Spain. https://doi.org/10.1101/2020.04.20.050039

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