Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020

Matsvay, Alina D.; Klink, Galya V.; Safina, Ksenia R; Nabieva, Elena; Garushyants, Sofya K.; Biba, Dmitry; Bazykin, Georgii A.; Mikhaylov, Ivan M.; Say, Anna; Zakamornaya, Anastasiya I.; Khakhina, Anastasiya O.; Лисица, Т. С.; Ayginin, Andrey A.; Абрамов, И. С.; Bogdan, Sergey A.; Kolbutova, Kseniya B.; Oleynikova, Daria U.; Avdeenko, Tatiana F.; Шипулин, Г А; Yudin, S. M.; Skvortsova, Veronika

doi:10.1101/2021.03.31.21254115

Cited by 11 publications

(11 citation statements)

References 14 publications

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“…Similar studies have been reported from a plethora of countries around the world including the UK, Ireland, Russia, India, Qatar etc. [26,[33][34][35][36]. These studies provide valuable information on the routes of importation of new strains and the emergence of critical mutations that change key parameters such as transmissibility or virulence, as was recently highlighted by the discovery of the B.1.617 variant and its B.1.617.2 sub-lineage in India [37], which led to a surge of SARS-CoV-2 infections in Delhi.…”

Section: Resultsmentioning

confidence: 98%

Molecular epidemiology of SARS-CoV-2 in Cyprus

et al. 2021

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Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.

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Section: Resultsmentioning

confidence: 98%

Molecular epidemiology of SARS-CoV-2 in Cyprus

et al. 2021

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“…Since the beginning of the pandemic, the distribution of genetic lineages in the Russian Federation has notably changed [ 20 , 21 , 22 ]. In March 2020, the diversity was limited to a few genetic lineages, of which B.1 and B.1.1 were dominant (35.5% and 46.3% respectively).…”

Section: Resultsmentioning

confidence: 99%

Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants

et al. 2021

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Since the beginning of the 2021 year, all the main six vaccines against COVID-19 have been used in mass vaccination companies around the world. Virus neutralization and epidemiological efficacy drop obtained for several vaccines against the B.1.1.7, B.1.351 P.1, and B.1.617 genotypes are of concern. There is a growing number of reports on mutations in receptor-binding domain (RBD) increasing the transmissibility of the virus and escaping the neutralizing effect of antibodies. The Sputnik V vaccine is currently approved for use in more than 66 countries but its activity against variants of concern (VOC) is not extensively studied yet. Virus-neutralizing activity (VNA) of sera obtained from people vaccinated with Sputnik V in relation to internationally relevant genetic lineages B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3 and Moscow endemic variants B.1.1.141 (T385I) and B.1.1.317 (S477N, A522S) with mutations in the RBD domain has been assessed. The data obtained indicate no significant differences in VNA against B.1.1.7, B.1.617.3 and local genetic lineages B.1.1.141 (T385I), B.1.1.317 (S477N, A522S) with RBD mutations. For the B.1.351, P.1, and B.1.617.2 statistically significant 3.1-, 2.8-, and 2.5-fold, respectively, VNA reduction was observed. Notably, this decrease is lower than that reported in publications for other vaccines. However, a direct comparative study is necessary for a conclusion. Thus, sera from “Sputnik V”-vaccinated retain neutralizing activity against VOC B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3 as well as local genetic lineages B.1.1.141 and B.1.1.317 circulating in Moscow.

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“…Our procedure for detection of imports is conservative in that it does not allow repeated imports along the same phylogenetic lineage. It generally yields fewer imports than an alternative approach using Treetime [ 35 ], but the imports detected using maximum parsimony are nearly always also supported by Treetime [ 36 ]. The imports inferred under this definition matched well the clusters of Russian sequences observed in phylogenies.…”

Section: Resultsmentioning

confidence: 99%

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

Klink

Safina

Nabieva

et al. 2021

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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.

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Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020

Cited by 11 publications

References 14 publications

Molecular epidemiology of SARS-CoV-2 in Cyprus

Molecular epidemiology of SARS-CoV-2 in Cyprus

Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants

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

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