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

Andrey B. Komissarov, Ksenia R. Safina, Sofya K. Garushyants, Artem V. Fadeev, Mariia V. Sergeeva, Anna A. Ivanova, Daria M. Danilenko, Dmitry Lioznov, Olga V. Shneider, Nikita Shvyrev, Vadim Spirin, Dmitry Glyzin, Vladimir Shchur and Georgii A. Bazykin ()
Additional contact information
Andrey B. Komissarov: Smorodintsev Research Institute of Influenza
Ksenia R. Safina: Skolkovo Institute of Science and Technology (Skoltech)
Sofya K. Garushyants: A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences
Artem V. Fadeev: Smorodintsev Research Institute of Influenza
Mariia V. Sergeeva: Smorodintsev Research Institute of Influenza
Anna A. Ivanova: Smorodintsev Research Institute of Influenza
Daria M. Danilenko: Smorodintsev Research Institute of Influenza
Dmitry Lioznov: Smorodintsev Research Institute of Influenza
Olga V. Shneider: Vreden Russian Research Institute of Traumatology and Orthopaedics
Nikita Shvyrev: National Research University Higher School of Economics
Vadim Spirin: National Research University Higher School of Economics
Dmitry Glyzin: National Research University Higher School of Economics
Vladimir Shchur: National Research University Higher School of Economics
Georgii A. Bazykin: Skolkovo Institute of Science and Technology (Skoltech)

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract 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].

Date: 2021
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/s41467-020-20880-z Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20880-z

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-20880-z

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().