Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia

Komissarov, Andrey B.; Safina, Ksenia R.; Garushyants, Sofya K.; Fadeev, Artem V.; Sergeeva, Mariia V.; Ivanova, Anna A.; Danilenko, Daria M.; Lioznov, Dmitry; Shneider, Olga V.; Shvyrev, Nikita; Spirin, Vadim; Glyzin, Dmitry; Shchur, Vladimir; Bazykin, Georgii A.

The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from at least 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions were not from China, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-3) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.0 [1.9, 4.3].