Spread of endemic SARS-CoV-2 lineages in Russia before April 2021
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Abstract
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.
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SciScore for 10.1101/2021.05.25.21257695: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Wilson score intervals were estimated using Hmisc R package46, and results were visualised with the ggplot2 package47 of R language48. ggplot2suggested: (ggplot2, RRID:SCR_014601)To estimate positive selection, we employed MEME and FEL models implemented in the HyPhy package10,11. HyPhysuggested: (HyPhy, RRID:SCR_016162)The tree for the selection analysis was built upon the whole-genome alignment of Russian sequences with the RAxML package v.8.0.26 (model GTRCAT)53. RAxMLsuggested: (RAxML, RRID:SCR_006086)Results from OddPub: We did not detect open data. We also did not detect open code. …
SciScore for 10.1101/2021.05.25.21257695: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Wilson score intervals were estimated using Hmisc R package46, and results were visualised with the ggplot2 package47 of R language48. ggplot2suggested: (ggplot2, RRID:SCR_014601)To estimate positive selection, we employed MEME and FEL models implemented in the HyPhy package10,11. HyPhysuggested: (HyPhy, RRID:SCR_016162)The tree for the selection analysis was built upon the whole-genome alignment of Russian sequences with the RAxML package v.8.0.26 (model GTRCAT)53. RAxMLsuggested: (RAxML, RRID:SCR_006086)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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