Abstract
Using available phylogeographical data of 3585 SARS–CoV–2 genomes we attempt at providing a global picture of the virus’s dynamics in terms of directly interpretable parameters. To this end we fit a hidden state multistate speciation and extinction model to a pre-estimated phylogenetic tree with information on the place of sampling of each strain. We find that even with such coarse–grained data the dominating transition rates exhibit weak similarities with the most popular, continent–level aggregated, airline passenger flight routes.
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Availability of Data and Materials
The R scripts, RevBayes scripts, MCMC chains, along with the used phylogenetic tree, geographical classification, inside and between regions air passenger volume fractions are available at https://github.com/KHDS-mod/COVID-19-HiSSE and https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-185867. An already constructed phylogenetic tree and strain (i.e. leaf) data were downloaded from NextStrain (https://nextstrain.org/ncov/global) on 26\(^{\textrm{th}}\) April 2020. This data set contains 3585 genomes sampled between December 2019 and April 2020. A full acknowledgments table of the research groups and authors from the whole world generating the sequence data, from which NextStrain’s phylogenetic tree is constructed, is provided in the nextstrain_ncov_global_authors.tsv file in COVID-19-HiSSE repository. The geographic distribution of COVID–19 case fatalities worldwide (presented in Tab. 1) were downloaded from European Centre for Disease Prevention and Control (https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide ECDC) on 11\(^{\textrm{th}}\) May 2020. We took a subset of the case fatalities for 26\(^{\textrm{th}}\) April 2020 corresponding to NextStrain’s sequences. The region of North America includes the following countries: Canada, Mexico, Panama, USA. The region of South America includes the following countries: Brazil, Chile, Colombia, Ecuador, Peru, Uruguay. The 5 deaths from Georgia were subtracted from Europe and added to Asia, because Georgia is classified as Asia in the NextStrain data. In addition, there are 7 deaths not classified in any of the regions by ECDC. These are labelled as “Cases on an international conveyance Japan” and seem to correspond to deaths on cruise ships. We excluded these completely. The air passenger data have been obtained through the commercial provider SABRE [18]. Data are consolidated for the years 2019 and 2020.
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Acknowledgements
We thank Fredrik Ronquist for very valuable comments. K.B.’s research is supported by Vetenskapsrådets Grant 2017–04951 and partially by an ELLIIT Call C grant. H.K.’s research is partially supported by Vetenskapsrådets Grant 2017–04951.
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Kiang, H.C., Bartoszek, K., Sakowski, S., Iacus, S.M., Vespe, M. (2022). Summarizing Global SARS-CoV-2 Geographical Spread by Phylogenetic Multitype Branching Models. In: Chicco, D., et al. Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2021. Lecture Notes in Computer Science(), vol 13483. Springer, Cham. https://doi.org/10.1007/978-3-031-20837-9_14
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