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VGsim: scalable viral genealogy simulator for global pandemic

By Vladimir Shchur, Vadim Spirin, Victor Pokrovskii, Dmitry Sirotkin, Evgeni Burovski, Nicola De Maio, Russel Corbett-Detig

Posted 27 Apr 2021
medRxiv DOI: 10.1101/2021.04.21.21255891

As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from most regions in the world. More than one million viral sequences are publicly available as of April 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification of new variants with transmissibility and immunity evasion advantages, and allowing the investigation of viral spread. To validate new methods and to verify results obtained from these vast datasets, one needs an efficient simulator able to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses this problem. The simulation process is split into two phases. During the forward run the algorithm generates a chain of events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape. The code is freely available at https://github.com/Genomics-HSE/VGsim.

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