The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia.
| العنوان: | The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. |
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| المؤلفون: | Klink GV; A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia., Safina K; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia., Nabieva E; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia., Shvyrev N; National Research University Higher School of Economics, Moscow, Russia., Garushyants S; A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.; Present address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., Alekseeva E; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia., Komissarov AB; Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia., Danilenko DM; Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia., Pochtovyi AA; Federal 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.; Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia., Divisenko EV; Federal 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., Vasilchenko LA; Federal 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., Shidlovskaya EV; Federal 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., Kuznetsova NA; Federal 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., Samoilov AE; Federal 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., Neverov AD; Federal 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., Popova AV; Federal 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., Fedonin GG; Federal 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., Akimkin VG; Federal 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., Lioznov D; Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia.; First Pavlov State Medical University, Saint Petersburg, Russia., Gushchin VA; Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia.; https://corgi.center/en/ (see the list of consortium members in Supplementary File 1)., Shchur V; National Research University Higher School of Economics, Moscow, Russia., Bazykin GA; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.; A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia. |
| مؤلفون مشاركون: | Coronavirus Russian Genetics Initiative (CoRGI) Consortium, CRIE Consortium |
| المصدر: | MedRxiv : the preprint server for health sciences [medRxiv] 2021 Dec 05. Date of Electronic Publication: 2021 Dec 05. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101767986 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: medRxiv Subsets: PubMed not MEDLINE |
| مستخلص: | Background: Delta 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. Aim: Here, we aim to study the emergence and spread of the Delta lineage in Russia. Methods: We use a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread. Results: We 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. Conclusion: The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries. |
| التعليقات: | Update in: Virus Evol. 2022 Mar 05;8(1):veac017. (PMID: 35371558) |
| References: | Cell Rep. 2021 Oct 12;37(2):109825. (PMID: 34614392) Cell Host Microbe. 2022 Apr 13;30(4):545-555.e4. (PMID: 35364015) Syst Biol. 2018 Sep 1;67(5):901-904. (PMID: 29718447) Nature. 2021 Feb;590(7847):544-546. (PMID: 33623168) Science. 2021 Jan 15;371(6526):. (PMID: 33234698) Bioinformatics. 2022 Mar 4;38(6):1735-1737. (PMID: 34954792) Mol Biol Evol. 2020 Jan 1;37(1):295-299. (PMID: 31504749) Cell Mol Immunol. 2021 Nov;18(11):2557-2559. (PMID: 34635807) iScience. 2021 Mar 19;24(3):102187. (PMID: 33615195) PLoS One. 2010 Mar 10;5(3):e9490. (PMID: 20224823) Nat Genet. 2021 Jun;53(6):809-816. (PMID: 33972780) Mol Biol Evol. 2021 Dec 9;38(12):5819-5824. (PMID: 34469548) Nature. 2021 Nov;599(7883):114-119. (PMID: 34488225) Cell Rep. 2021 Jun 1;35(9):109197. (PMID: 34043946) CMAJ. 2021 Oct 25;193(42):E1619-E1625. (PMID: 34610919) Virus Evol. 2018 Jan 08;4(1):vex042. (PMID: 29340210) Wellcome Open Res. 2020 Apr 9;5:67. (PMID: 32685698) Natl Sci Rev. 2020 Sep 24;8(1):nwaa246. (PMID: 34676089) PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. (PMID: 30958812) Mol Biol Evol. 2016 Jun;33(6):1635-8. (PMID: 26921390) Mol Cell. 2021 Jun 17;81(12):2656-2668.e8. (PMID: 33930332) PLoS One. 2023 May 16;18(5):e0285664. (PMID: 37192187) Vopr Virusol. 2021 Sep 18;66(4):269-278. (PMID: 34545719) Nature. 2021 Jul;595(7869):707-712. (PMID: 34098568) Science. 2021 Apr 9;372(6538):. (PMID: 33658326) Nat Commun. 2021 Jan 28;12(1):649. (PMID: 33510171) Nature. 2021 Aug;596(7871):276-280. (PMID: 34237773) Signal Transduct Target Ther. 2021 Sep 27;6(1):349. (PMID: 34580279) Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):228-33. (PMID: 23248286) Int J Infect Dis. 2020 Oct;99:40-46. (PMID: 32721529) Front Bioinform. 2021 Aug 19;1:709533. (PMID: 36303764) |
| تواريخ الأحداث: | Date Created: 20211215 Latest Revision: 20231108 |
| رمز التحديث: | 20231215 |
| مُعرف محوري في PubMed: | PMC8669866 |
| DOI: | 10.1101/2021.12.02.21267168 |
| PMID: | 34909799 |
| قاعدة البيانات: | MEDLINE |
| DOI: | 10.1101/2021.12.02.21267168 |
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