ABSTRACT
Background. The ongoing pandemic of the novel coronavirus infection (COVID-19) draws attention to the significance of molecular and genetic monitoring of the SARS-CoV-2 spread among the population of the Russian Federation. The aim of the study was to analyze the dynamics of circulation of SARS-CoV-2 genetic variants in Russia. Materials and methods. The analysis of the circulation dynamics for SARS-CoV-2 genetic variants in Russia was carried out, covering the period from 28/12/2020 to 26/6/2022. The analysis included the data from Rospotrebnadzor Report No. 970 "Information about Infectious Diseases in Individuals with Suspected Novel Coronavirus Infection" and the Virus Genome Aggregator of Russia (VGARus). The presence of SARS-CoV-2 RNA was confirmed by the real-time reverse transcription polymerase chain reaction. The primer panels developed at the Central Research Institute of Epidemiology were used for amplification of genomic fragments and the subsequent sequencing. Results and discussion. Using the Russian VGARus platform developed by the Central Research Institute of Epidemiology, we received the data on mutational variability of SARS-CoV-2. By monitoring the circulation of SARS-CoV-2 genetic variants in Russia from 28/12/2020 to 26/6/2022, we found that Delta and Omicron genetic variants prevailed at different stages of the epidemic. Conclusion. The data of molecular and genetic studies are an essential component of epidemiological surveillance, being critically important for making executive decisions aimed at prevention of further spread of SARS-CoV-2 and laying the groundwork for creating new vaccines. © 2022, Central Research Institute for Epidemiology. All rights reserved.
ABSTRACT
The COVID-19 pandemic which began in March 2020 has again drawn attention to the problem of treating primary viral pneumonia (PVP), wherein damage to the tissues of the lower respiratory tract including functionally important alveolocytes occurs as a result of cell infection by pathogens of the Virae Kingdom. Whereas treatment of bacterial pneumonia is based on the basic approach related to the use of antibiotics (which effectiveness needs to be verified more often than ever due to the “curse of the resistance effect” - that, however, does not cancel the essence of the basic approach), efficient PVP treatment is feasible only in case of available etiotropic, but catastrophically few, drugs. Such drugs in case of the influenza A virus (Articulavirales: Orthomyxoviridae, Alphainfluenzavirus) have been known since the second part of the XXth century. However, no consensus was achieved among clinicians regarding particularly dangerous human coronaviruses (Nidovirales: Coronaviridae, Betacoronavirus) which threat has driven the world epidemiology in the XXIst century: SARS-CoV (subgenus Sarbecovirus), MERS-CoV (Merbecovirus), SARS-CoV-2 (Sarbecovirus). And we should be prepared to the fact that increase in population density and scaling up of anthropogenic impact on ecosystems elevates a probability of overcoming interspecies barriers by natural focal viruses and their penetration into the human population with adverse epidemic consequences. Therefore, PVP therapy should be developed systematically in the nearest future. Antimicrobial peptides (AMP) as the components of non-specific innate immunity against a wide range of infectious pathogens: bacteria (Bacteria), microscopic fungi (Fungi) and viruses (Virae) may serve as a platform for developing such system. Our review justifies a way to select such platform and provides well-known examples of successfully used AMP in treatment of PVP and related pathological conditions.
ABSTRACT
Due to the current epidemiological situation caused by the pandemic of COVID-19 the study of virus diversity in bats as a potential source of zoonotic diseases is crucially important. Our previous study based on genus specific PCR-using Coronaviridaespecific primers and following high throughput sequencing revealed the presence of several types of coronaviruses. In this study we performed the whole genome sequencing for the samples which were positive for Coronaviridae in order to get more information about viral communities in bat fecal samples. Fecal samples from bat species (Pippistrellus nathusii, Nyctalus noctula, Myotis brandtii, Myotis daubentonii) were collected in 2015 in the Moscow region and stored in RNA later. RNA extraction using Viral RNA Mini Kit (Qiaqen), library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) and HTS on Illumina Hiseq platform was performed. Metagenomic data was obtained using FastQC, trimmomatic 0.38 and SPAdes 3.13 for genome assembly, taxonomy of resulting contigs was identified by the BLASTn.For 8 bat fecal samples positive for Coronaviridae we performed the whole genome sequencing and metagenomic analysis. In one sample we detected the complete genome (37915 bp) with 74,66% nucleic identity to Mastadenovirus sp. isolate WA3301 from a Nyctalus noctula, in the other sample from Pippistrellus nathusii we found the complete genome sequence with 82% nucleotide identity to Bat alphacoronavirus isolate BtCoV/020-16/M.dau/FIN/2016 (28.245 bp).Whereas, as we've reported the presence of Alphacoronavirus before, this is the first time when we detect the whole genome of Mastadenovirus. The fact that the material was obtained from bats which nest next to human and domestic animals our findings might give better understanding the potential risk of the cross-species transmission and virus migration in bats from Moscow Region.
ABSTRACT
The first case of COVID-19 was diagnosed in St. Petersburg on March 2, 2020;the period of increase in the incidence lasted for 10 weeks, the maximum rates were recorded in mid-May, and subsequently there was a statistically significant decrease in the incidence. Objective: to determine the level and structure of community immunity to SARS-CoV-2 among the population of St. Petersburg during the period of intensive spread of COVID-19. Materials and methods. Selection of volunteers for the study was carried out through interviewing and randomization. The exclusion criterion was active COVID-19 infection at the time of the survey. 2713 people aged 1 to 70 years and above were examined for the presence of specific antibodies to SARS-CoV-2. Antibodies were detected by enzyme immunoassay. Results and discussion. Studies have shown that in St. Petersburg, in the active phase of COVID-19 epidemic, there was a moderate seroprevalence to SARS-CoV-2, which amounted to 26 %, against the background of a high frequency (84.5 %) of asymptomatic infection in seropositive individuals who did not have a history of COVID-19 disease, positive PCR result and ARI symptoms on the day of examination. The maximum indicators of herd immunity were established in children 1–6 years old (31.1 %), 7–13 years old (37.7 %) and people over 70 years old (30.4 %). Differences in the level of seroprevalence in the age groups of 18–49 years are statistically significant. The highest level of seroprevalence was found among the unemployed (29.7 %), healthcare workers (27.1 %), education sector (26.4 %) and business sector personnel (25 %). In convalescents, COVID-19 antibodies are produced in 75 % of cases. In individuals with positive result of PCR analysis carried out earlier, antibodies are detected in 70 % of the cases. The results of the study of herd immunity to SARS-CoV-2 are essential to forecast the development of the epidemiological situation, as well as to plan measures for specific and non-specific prevention of COVID-19. © 2020 Russian Research Anti-Plague Institute. All rights reserved.
ABSTRACT
The first case of COVID-19 was registered in the Leningrad Region on March 13, 2020. The period of increasing intensity of the epidemic process lasted 8 weeks. One month after reaching the maximum incidence rate, a study was organized to determine seroprevalence to COVID-19 among the population of the Region. Objective of the study was to determine the level and structure of community immunity to SARS-CoV-2 virus in the population of the Leningrad Region in the period of intensive COVID-19 transmission. Materials and methods. The work was carried out within the framework of the Rospotrebnadzor project on assessment of community immunity to the SARS-CoV-2 virus in the population of the Russian Federation. The content of antibodies to SARS-CoV-2 was determined applying ELISA using a kit for the analysis of human serum or blood plasma for the presence of specific IgG to the nucleocapsid of the SARS-CoV-2 virus, manufactured by the State Scientific Center of Applied Microbiology and Biotechnology (Obolensk) in accordance with the instructions for use. Results and discussion. The study has showed that the herd immunity of the population of the Leningrad Region was 20.7 %. The maximum level has been established in children 1–6 years old (42.3 %) and people over 70 years old (29.0 %). The highest level of seropositivity, except for children and older people, was found among the unemployed (25.1 %). The lowest level of seroprevalence was detected in civil servants (12.8 %) and military personnel (16.7 %). It has been shown that the risk of infection increases by 1.5 times in case of contacts with COVID-19 patients. After exposure to COVID-19 virus, antibodies are produced in 82.1 % of the cases. In individuals with a positive PCR test result obtained earlier, antibodies are detected in 82.8 % of cases. The share of asymptomatic forms among seropositive residents of the Leningrad Region was 86.9 %. The results of assessing the herd immunity to SARS-CoV-2 in the population of the Leningrad Region indicate that during the period of intensive COVID-19 transmission, an average level of seroprevalence was formed. A significant proportion of asymptomatic forms of infection characterizes the high intensity of the latently developing epidemic process. The results obtained should be taken into account when organizing preventive measures, including vaccination, and predicting morbidity rates. © 2020 Russian Research Anti-Plague Institute. All rights reserved.