Dataset Information

Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022.

ABSTRACT: Analysis of genomic variability of pathogens associated with heightened public health concerns is an opportunity to track transmission routes of the disease and helps to develop more effective vaccines and specific diagnostic tests. We present the findings of a detailed genomic analysis of the genomic variability of the SARS-CoV-2 Omicron variant that spread in Russia between 8 December 2021 and 30 January 2022. We performed phylogenetic analysis of Omicron viral isolates collected in Moscow (n = 589) and downloaded from GISAID (n = 397), and identified that the BA.1 lineage was predominant in Russia during this period. The BA.2 lineage was also identified early in December 2021. We identified three cases of BA.1/BA.2 coinfections and one case of Delta/Omicron coinfection. A comparative genomic analysis of SARS-CoV-2 viral variants that spread in other countries allowed us to identify possible cases of transmission. We also found that some mutations that are quite rare in the Global Omicron dataset have a higher incidence rate, and identified genetic markers that could be associated with ways of Omicron transmission in Russia. We give the genomic variability of single nucleotide variations across the genome and give a characteristic of haplotype variability of Omicron strains in both Russia and around the world, and we also identify them.

SUBMITTER: Chernyaeva EN

PROVIDER: S-EPMC9786029 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022.

Chernyaeva Ekaterina N EN Ayginin Andrey A AA Bulusheva Irina A IA Vinogradov Kirill S KS Stetsenko Ivan F IF Romanova Svetlana V SV Tsypkina Anastasia V AV Matsvay Alina D AD Savochkina Yulia A YA Shipulin German A GA

Pathogens (Basel, Switzerland) 20221202 12

Analysis of genomic variability of pathogens associated with heightened public health concerns is an opportunity to track transmission routes of the disease and helps to develop more effective vaccines and specific diagnostic tests. We present the findings of a detailed genomic analysis of the genomic variability of the SARS-CoV-2 Omicron variant that spread in Russia between 8 December 2021 and 30 January 2022. We performed phylogenetic analysis of Omicron viral isolates collected in Moscow (<i ...[more]

PMID: 36558796

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Project description:BackgroundSevere acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic in young children. Therefore, the true rate of infection is likely underestimated. Few data are available on the rate of infections in young children, and studies on SARS-CoV-2 seroprevalence among children during the omicron wave are limited. We assessed the SARS-CoV-2 infection-induced seroprevalence among children and estimated the associated risk factors for seropositivity.MethodsA longitudinal serological survey was conducted from January 2021 through December 2022. The inclusion criteria were healthy children between 5 and 7 years old and their parents or legal guardians provided written informed consent. Samples were tested for anti-nucleocapsid (N) IgG and anti-receptor binding domain (RBD) IgG using a chemiluminescent microparticle immunoassay (CMIA), and total anti-RBD immunoglobulin (Ig) was detected using an electrochemiluminescence immunoassay (ECLIA). The vaccination and SARS-CoV-2 infection history were collected.ResultsIn all, 457 serum samples were obtained from 241 annually followed-up children in this longitudinal serological survey. Of these, 201 participants provided samples at two serial time points-during the pre-omicron and omicron-dominant wave. Overall, seroprevalence induced by SARS-CoV-2 infection increased from 9.1% (22/241) during the pre-omicron to 48.8% (98/201) during the omicron wave. Amongst seropositive individuals, the infection-induced seropositivity was lower in vaccinated participants with two doses of BNT162b2 than in the unvaccinated participants (26.4% vs. 56%; OR, 0.28; 95%CI: 0.14-0.58). Nevertheless, the ratio of seropositive cases per recalled infection was 1.63 during the omicron dominant wave. The overall seroprevalence induced by infection, vaccination, and hybrid immunity was 77.1% (155/201) between January and December 2022.ConclusionsWe report an increase in infection-induced seroprevalence among children during the omicron wave. These findings highlight that a seroprevalence survey can help determine the true rate of infection, particularly in asymptomatic infection, and optimize public health policies and vaccine strategies in the pediatric population.

Project description:The factors influencing hepatitis E virus (HEV) circulation remain largely unexplored. We investigated HEV seroprevalence in humans and the prevalence of infection in farm pigs and rabbits in different regions of the Russian Federation, as well as the genetic diversity and population dynamics of the HEV. The anti-HEV IgG antibody detection rates in the general population increase significantly with age, from 1.5% in children and adolescents under 20 years old to 4.8% in adults aged between 20 and 59 years old to 16.7% in people aged 60 years and older. HEV seroprevalence varies between regions, with the highest rate observed in Belgorod Region (16.4% compared with the national average of 4.6%), which also has the country's highest pig population. When compared with the archival data, both increases and declines in HEV seroprevalence have been observed within the last 10 years, depending on the study region. Virus shedding has been detected in 19 out of the 21 pig farms surveyed. On one farm, the circulation of the same viral strain for five years was documented. All the human and animal strains belonged to the HEV-3 genotype, with its clade 2 sequences being predominant in pigs. The sequences are from patients, pigs, and sewage from pig farms clustered together, suggesting a zoonotic infection in humans and possible environmental contamination. The HEV-3 population size that was predicted using SkyGrid reconstruction demonstrated exponential growth in the 1970s-1990s, with a subsequent decline followed by a short rise around the year 2010, the pattern being similar to the dynamics of the pig population in the country. The HEV-3 reproduction number (Re) that was predicted using birth-death skyline analysis has fluctuated around 1 over the past 20 years in Russia but is 10 times higher in Belgorod Region. In conclusion, the HEV-3 circulation varies both geographically and temporally, even within a single country. The possible factors contributing to this variability are largely related to the circulation of the virus among farm pigs.

Dataset Information

Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022.

Publications

Genomic Variability of SARS-CoV-2 Omicron Variant Circulating in the Russian Federation during Early December 2021 and Late January 2022.

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