Статья

Spread of endemic SARS-CoV-2 lineages in Russia

G. Klink, K. Safina, S. Garushyants, M. M, E. Nabieva, K. Ab, D. Lioznov, G. Bazykin,
2021

In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) or P.1 (501Y.V3), none have been sampled in Russia before January 2021. Instead, since summer 2020, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). In February-March 2021, these lineages reached frequencies of 26.9% (95% C.I.: 23.1%-31.1%) and 32.8% (95% C.I.28.6%-37.2%) respectively in Russia. Their frequency has increased in different parts of Russia. Together with the fact that these lineages carry several spike mutations of interest, this suggests that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1, although there is no direct data on change in transmissibility. Comparison of frequency dynamics of lineages carrying subsets of characteristic mutations of B.1.1.317 and B.1.1.397+ suggests that, if indeed some of these mutations affect transmissibility, the transmission advantage of B.1.1.317 may be conferred by the (S:D138Y+S:S477N+S:A845S) combination; while the advantage of B.1.1.397+ may be conferred by the S:M153T change. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, and two lineages prospectively named B.1.1.v1 and B.1.1.v2, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:{Delta}140-142, S:{Delta}144 or S:{Delta}136-144), and nsp6:{Delta}106-108 (also known as ORF1a:{Delta}3675-3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.v1 and B.1.1.v2, 15.2% (95% C.I.: 7.6%-28.2%). The combinations of mutations observed in B.1.1.317, B.1.1.397+, AT.1, B.1.1.v1 and B.1.1.v2 together with frequency increase of these lineages make them candidate variants of interest.

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  • 1. Version of Record от 2021-05-27

Метаданные

Об авторах
  • G. Klink
    Russian Academy of Sciences
  • K. Safina
    Skolkovo Institute of Science and Technology
  • S. Garushyants
    Russian Academy of Sciences
  • M. M
    Skolkovo Institute of Science and Technology
  • E. Nabieva
    Skolkovo Institute of Science and Technology
  • K. Ab
    Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia;
  • D. Lioznov
    Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia;
  • G. Bazykin
    Skolkovo Institute of Science and Technology
Предметная рубрика
  • COVID-19
Тип документа
  • preprint
Источник
  • lens