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

Author

Listed:
  • Andrey B. Komissarov

    (Smorodintsev Research Institute of Influenza)

  • Ksenia R. Safina

    (Skolkovo Institute of Science and Technology (Skoltech)
    A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences)

  • 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
    First Pavlov State Medical University)

  • 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)
    A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences)

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].

Suggested Citation

  • 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 & Vadi, 2021. "Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20880-z
    DOI: 10.1038/s41467-020-20880-z
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    Cited by:

    1. Haogao Gu & Ruopeng Xie & Dillon C. Adam & Joseph L.-H. Tsui & Daniel K. Chu & Lydia D. J. Chang & Sammi S. Y. Cheuk & Shreya Gurung & Pavithra Krishnan & Daisy Y. M. Ng & Gigi Y. Z. Liu & Carrie K. C, 2022. "Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Gabriela Lobinska & Ady Pauzner & Arne Traulsen & Yitzhak Pilpel & Martin A. Nowak, 2022. "Evolution of resistance to COVID-19 vaccination with dynamic social distancing," Nature Human Behaviour, Nature, vol. 6(2), pages 193-206, February.

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