Appearing in Wuhan (China) and quickly spreading across the globe, the novel coronavirus infection quickly became a significant threat to global health. The year 2021 was characterized by both increases and decreases in COVID-19 incidence, and Russia was no exception. In this work, we describe regional features in the Northwestern federal district (FD) of Russia of the pandemic in 2021 based on Rospotrebnadzor statistics and data from SARS-CoV-2 genetic monitoring provided by the Saint Petersburg Pasteur Institute as a part of epidemiological surveillance. The epidemiological situation in the studied region was complicated by the presence of the megacity Saint Petersburg, featuring a high population density and its status as an international transport hub. COVID-19 incidence in the Northwestern FD fluctuated throughout the year, with two characteristic maxima in January and November. An analysis of fluctuations in the age structure, severity of morbidity, mortality rates, and the level of population vaccination in the region during the year is given. Assessment of epidemiological indicators was carried out in relation to changes in locally circulating genetic variants. It was seen that, during 2021, so-called variants of concern (VOC) circulated in the region (Alpha, Beta, Delta, Omicron), with Delta variant strains dominating from June to December. They successively replaced the variants of lines 20A and 20B circulating at the beginning of the year. An epidemiological feature of the northwestern region is the AT.1 variant, which was identified for the first time and later spread throughout the region and beyond its borders. Its share of the regional viral population reached 28.2% in May, and sporadic cases were observed until September. It has been shown that genetic variants of AT.1 lineages distributed in Russia and Northern Europe represent a single phylogenetic group at the base of the 20B branch on the global phylogenetic tree of SARS-CoV-2 strains. The progression of the COVID-19 pandemic occurred against the background of a vaccination campaign. The findings highlight the impact of vaccination on lowering severe COVID-19 case numbers and the mortality rate, despite ongoing changes in circulating SARS-CoV-2 genetic variants.

The COVID-19 pandemic, which began in Wuhan (Hubei, China), has been ongoing for about a year and a half. An unprecedented number of people around the world have been infected with SARS-CoV-2, the etiological agent of COVID-19. Despite the fact that the mortality rate for COVID-19 is relatively low, the total number of deaths has currently already reached more than three million and continues to increase due to high incidence. Since the beginning of the pandemic, a large number of sequences have been obtained and many genetic variants have been identified. Some of them bear significant mutations that affect biological properties of the virus. These genetic variants, currently Variants of Concern (VoC), include the so-called United Kingdom variant (20I/501Y), the Brazilian variant (20J/501Y.V3), and the South African variant (20H/501Y.V2). We describe here a novel SARS-CoV-2 variant with distinct spike protein mutations, first obtained at the end of January 2021 in northwest Russia. Therefore, it is necessary to pay attention to the dynamics of its spread among patients with COVID-19, as well as to study in detail its biological properties.

Enteric viruses are a major cause of waterborne infections due to their high environmental stability and extremely low infectious dose. Current molecular diagnostic methods, while accurate, often depend on thermal cycling and centralized laboratory facilities, limiting their applicability in decentralized or resource-limited settings. In this study, we developed an isothermal biosensor based on a split deoxyribozyme that reconstitutes its catalytic core upon hybridization with a conserved sequence of enteroviral RNA. This activation leads to site-specific cleavage of a fluorogenic substrate, producing a quantifiable fluorescent signal. The system was experimentally validated using both synthetic enteroviral RNA and RNA extracted from environmental water samples. To enhance detection sensitivity, the DNAzyme-based assay was coupled with isothermal RNA amplification. The results demonstrate high selectivity and compatibility with real-world samples, supporting the sensor’s utility for field-deployable viral RNA detection. Overall, this study highlights the potential of the DNAzyme-based platform as a portable, sequence-specific, and amplification-assisted diagnostic tool for environmental surveillance of enteric viruses.

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Background: Coxsackievirus A10 (CV-A10) is currently one of the most common etiological agents of enterovirus infection (EVI). Over the past decade, severe and fatal cases of CV-A10 infection have become more frequent while clinical manifestations of the disease are similar to those of Enterovirus A71 infection. The objective of our study was to characterize circulation of Coxsackievirus A10 in the Russian Federation in 2008–2019 and to study the phylogenetic relationships of strains isolated in Russia and Vietnam. Materials and methods: In 2008–2019, 220 CV-A10 strains were isolated from patients with various clinical manifestations of EVI and from sewage water samples taken in the Russian Federation and then studied using molecular genetic methods. In addition to that, we analyzed 26 CV-A10 strains isolated from patients with hand, foot, and mouth disease (HFMD) and acute flaccid paralysis in South Vietnam in 2018–2019. Results: We established a two-year periodicity of CV-A10 active circulation in Russia. In the structure of clinical forms of CV-A10 infection, herpetic angina prevailed (30.8 %), followed by minor illness (25.25 %), respiratory diseases (15.66 %), exanthema (14.65 %), gastrointestinal disorders (8.08 %), and asymptomatic infections (2.02 %). Symptoms of CNS damage (meningitis, meningoencephalitis) were observed in 3.53 % of cases. Most CV-A10 strains from Vietnam were isolated from patients with CNS affection of varying degrees of severity. During the study period, CV-A10 strains of genotypes C, E, and F3 circulated in the territory of the Russian Federation whereas the strains from South Vietnam were represented by genotypes F3 and F1. The studied strains showed a genetic relationship with those of CV-A10 circulating in different countries. Vietnamese and some Russian strains of the F3 genotype were genetically close to the strains isolated from severe cases. Conclusions: Molecular monitoring of CV-A10 circulation is an important component of the global epidemiological surveillance of EVI.

Aim: Analysis of the morbidity of vaccine-associated paralytic poliomyelitis and acute flaccid paralysis and the results of virological investigation of the patients on 14 territories of the Russian Federation in 1998-2017. Materials and methods: We investigated nearly 3000 stool samples from paralytic patients and contact persons. Isolation and identification of polioviruses were performed according to WHO recommendations with the help of cell lines RD and L20B. We conducted the sequencing of the genome fragments VP3-VP1, VP1-2A and full sequencing of genome region VP1 of 45 poliovirus strains. Results: From 1998 till 2017 1257 cases of acute flaccid paralysis were registered on 14 territories of Russia, 15 cases of which (1,2%) were classified as vaccine-associated paralytic poliomyelitis. From these patients 9 children were non vaccinated and 6 children received from one to four doses of oral poliomyelitis vaccine. The percentage of the detection of polioviruses from the patients and contact persons in different years was not equal and constituted from 3, 4±0,89% to 9, 5±0,79%. All in all from the patients with acute flaccid paralysis and contact persons we isolated 191 polioviruses, 60 of them belonged to type 1, 55 polioviruses were identified as types 2 and 76 as type 3. Some cases of vaccine-associated paralytic poliomyelitis are described in the article; polioviruses were isolated from all these patients. The sequencing of the genome fragments of 45 poliovirus strains showed that the majority of them had the nucleotide substitutions including neurovirulent substitutions. Conclusion:In order to prevent the risk of the appearance of vaccine-associated paralytic poliomyelitis it is necessary to maintain the high quality of surveillance of poliomyelitis and acute flaccid paralysis, to ensure the 95% coverage of children with poliomyelitis vaccine, to minimize the cases of groundless delays of vaccination according to medical recommendations and parents’ refusals to vaccinate children against poliomyelitis and to respect strictly the National calendar of vaccination.