Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia

Komissarov, Andrey; Safina, Ksenia R; Garushyants, Sofya K.; Fadeev, Artem; Sergeeva, Mariia; Ivanova, Anna; Danilenko, Daria; Lioznov, Dmitry; Shneider, Olga V.; Shvyrev, Nikita; Spirin, Vadim; Glyzin, Dmitry; Shchur, Vladimir; Bazykin, Georgii A.

doi:10.1038/s41467-020-20880-z

Cited by 69 publications

(73 citation statements)

References 32 publications

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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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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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“…Although the COVID-19 outbreak in Russia started later compared to many neighboring European countries, Russia is currently among the six countries with the highest number of confirmed COVID-19 cases, as of 9 May 2021 [22,23]. Limited data suggest that the seroprevalence of SARS-CoV-2 infection in Russia was approximately 9-10% in May-June 2020 [24], reaching 19.6-31.3% [25][26][27] by the end of the year.…”

Section: Introductionmentioning

confidence: 99%

Seroprevalence of SARS-CoV-2 Antibodies in Symptomatic Individuals Is Higher than in Persons Who Are at Increased Risk Exposure: The Results of the Single-Center, Prospective, Cross-Sectional Study

et al. 2021

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The present study aimed to assess antibody seropositivity prevalence among symptomatic individuals and individuals with a high risk of occupational exposure to SARS-CoV-2. Participants from Chelyabinsk (Russian Federation) who were at an increased risk of exposure to SARS-CoV-2 (high-risk group, n = 1091) and participants who either had symptoms consistent with COVID-19 or were suspected to have experienced COVID-19 in the past (symptomatic group, n = 692) were enrolled between 28 September and 30 December 2020. Blood samples were tested by enzyme-linked immunosorbent assay D-5501 SARS-Cov-2-IgG-EIA-BEST and D-5502 SARS-Cov-2-IgM-EIA-BEST (AO Vector-Best, Novosibirsk, Russia). The overall seropositivity rate was 28.33–28.53%. SARS-CoV-2 antibodies were detected in 17.23% (adjusted prevalence of 17.17–17.29%) of participants in the high-risk and 45.95% (adjusted prevalence of 45.91–46.24%) in the symptomatic group. Higher IgG and IgM titers were observed in women compared to men, as well as in participants in the symptomatic group compared to those in the high-risk group. The results indicate that the seroprevalence among residents in several Russian regions is low (28.38%) and inadequate to provide herd immunity. The lower seroprevalence among participants in the high-risk group may be attributed to the enforcement of healthcare protocols and the use of adequate personal protective equipment.

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“…1 b). A recent genomic study has shown that most of the sampled sequences from Russia in the early stage are nested within other European subclades, which indicates multiple introductions of the virus from Europe [ 9 ]. Our simulation indicated that if travel restrictions were implemented five days earlier, 64.1% of the cases could have been avoided as of 20 May 2020, as shown in Fig.…”

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confidence: 99%