Spread of endemic SARS-CoV-2 lineages in Russia before April 2021.

Autor: Klink GV; A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia., Safina KR; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia., Garushyants SK; A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia., Moldovan M; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia., Nabieva E; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia., Komissarov AB; Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia., Lioznov D; Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia.; First Pavlov State Medical University, Saint Petersburg, Russia., Bazykin GA; A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2022 Jul 20; Vol. 17 (7), pp. e0270717. Date of Electronic Publication: 2022 Jul 20 (Print Publication: 2022).
DOI: 10.1371/journal.pone.0270717
Abstrakt: In 2021, the COVID-19 pandemic was characterized by global spread of several lineages with evidence for increased transmissibility. Throughout the pandemic, Russia has remained 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 that have spread globally by late 2020, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none have been sampled in Russia before the end of 2020. Instead, between summer 2020 and spring 2021, the epidemic in Russia has been characterized by the spread of two lineages that were rare in most other countries: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). Their frequency has increased concordantly in different parts of Russia. On top of these lineages, in late December 2020, alpha (B.1.1.7) emerged in Russia, reaching a frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, B.1.1.524 and B.1.1.525, 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:Δ140-142, S:Δ144 or S:Δ136-144), and nsp6:Δ106-108 (also known as ORF1a:Δ3675-3677). 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.1.1.524 and B.1.1.525, 15.2% (95% C.I.: 7.6%-28.2%). Although these variants have been displaced by the onset of delta variant in May-June 2021, lineages B.1.1.317, B.1.1.397+, AT.1, B.1.1.524 and B.1.1.525 and the combinations of mutations comprising them that are found in other lineages merit monitoring.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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