Evidence map›Paper›PMID 34909799›Full record

ArticlemedRxiv : the preprint server for health sciences2021

The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia.

Galya V Klink, Ksenia Safina, Elena Nabieva, Nikita Shvyrev, Sofya Garushyants, Evgeniia Alekseeva, Andrey B Komissarov, Daria M Danilenko, Andrei A Pochtovyi, Elizaveta V Divisenko and 14 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

24 authors.

Galya V KlinkA.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
Ksenia SafinaSkolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.
Elena NabievaSkolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.
Nikita ShvyrevNational Research University Higher School of Economics, Moscow, Russia.
Sofya GarushyantsA.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
Evgeniia AlekseevaSkolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.
Andrey B KomissarovSmorodintsev Research Institute of Influenza, Saint Petersburg, Russia.
Daria M DanilenkoSmorodintsev Research Institute of Influenza, Saint Petersburg, Russia.
Andrei A PochtovyiFederal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia.
Elizaveta V DivisenkoFederal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia.
Lyudmila A VasilchenkoFederal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia.
Elena V ShidlovskayaFederal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia.
Nadezhda A KuznetsovaFederal State Budget Institution "National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia.
Coronavirus Russian Genetics Initiative (CoRGI) Consortium
Andrei E SamoilovFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), Moscow, Russia.
Alexey D NeverovFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), Moscow, Russia.
Anfisa V PopovaFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), Moscow, Russia.
Gennady G FedoninFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), Moscow, Russia.
CRIE Consortium
Vasiliy G AkimkinFederal Budget Institution of Science "Central Research Institute for Epidemiology" of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), Moscow, Russia.
Dmitry LioznovSmorodintsev Research Institute of Influenza, Saint Petersburg, Russia.
Vladimir A GushchinDepartment of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia.
Vladimir ShchurNational Research University Higher School of Economics, Moscow, Russia.
Georgii A BazykinSkolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundDelta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to emergence of multiple sublineages, many of which are well-mixed between countries.

aimHere, we aim to study the emergence and spread of the Delta lineage in Russia.

methodsWe use a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread.

resultsWe show that nearly the entire Delta epidemic in Russia has probably descended from a single import event despite genetic evidence of multiple Delta imports. Indeed, over 90% of Delta samples in Russia are characterized by the nsp2:K81N+ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect.

conclusionThe apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.

Identifiers

PMID34909799
PMCPMC8669866

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.