Leptospirosis is a major zoonosis, yet genetic data on Leptospira strains in animal reservoirs in Southern Vietnam are limited. This study aimed to detect and genotype pathogenic Leptospira in synanthropic small mammals. From 2016 to 2020, 856 animals were captured in three regions. Kidneys were screened by qPCR targeting pathogenic Leptospira 16S rRNA, and positive samples were genotyped via secY gene sequencing. The overall prevalence was 7.8%. Rattus norvegicus was the primary host (12.4% infected). Leptospira interrogans predominated (77.6%), followed by L. borgpetersenii (22.4%). Infection risk was significantly associated with the following factors: larger host body size (increased body mass and hindfoot length); capture in Ho Chi Minh City; and the rainy season. The study confirms the stable circulation of highly virulent L. interrogans in urban R. norvegicus populations. The identified risk factors provide a basis for targeted interventions to mitigate human health risks.

Rickettsia spp. are ubiquitous in nature and capable of causing diseases of varying severity. The most extensive group comprises the spotted fever group (SFG) Rickettsiae, the members of which are predominantly transmitted by ticks. The expansion of tick habitats observed in recent decades poses an increasing threat of dissemination of tick-borne infections into regions previously considered non-endemic. The aim of this study was to determine the prevalence of SFG Rickettsiae in ixodid ticks collected in Northwest Russia and to characterize the species diversity of these pathogens within the study area. Questing adult ixodid ticks (n = 4566) were collected from eight regions of Northwest Russia (Arkhangelsk, Kaliningrad, Leningrad, Novgorod, Pskov and Vologda Regions, as well as the Republic of Karelia and St. Petersburg) in 2023 to 2025 (from April to September). The species composition included Ixodes ricinus (n = 1683), Ixodes persulcatus (n = 2404), and Dermacentor reticulatus (n = 479). Genomic DNA was extracted from individual ticks and screened for SFG Rickettsiae using real-time PCR, followed by conventional PCR targeting the gltA, ompA, ompB, and sca4 (gene D) genes. Nucleotide sequences obtained for a subset of positive samples for the various genes were analyzed. The overall prevalence of SFG Rickettsiae was 12.6% (95% CI: 11.7-13.6). Circulation of the following species was detected: Rickettsia helvetica, Rickettsia conorii subsp. raoultii, Candidatus Rickettsia tarasevichiae, Rickettsia monacensis, and Rickettsia felis. The findings indicate considerable species diversity of SFG Rickettsiae in natural foci of Northwest Russia. Rickettsia monacensis was detected in ixodid ticks within the study area for the first time, and R. felis was identified in Russia for the first time.

Abstract Background Tick-borne encephalitis virus (TBEV, Orthoflavivirus encephalitidis) is an arbovirus of the family Flaviviridae. It is the etiological agent of tick-borne encephalitis (TBE), a severe disease affecting the central nervous system. Among arboviral infections, TBE represents the greatest burden in northern Eurasia, both in terms of emerging infection risk and mortality. Globalization and climate change increase the risk of TBEV introduction into nonendemic countries. They may also lead to the emergence of new viral variants featuring increased virulence for humans or altered antigenic characteristics. Hence, sensitive and specific TBEV detection methods are needed not only for diagnostics but also for One Health approach goals (surveillance and identification of viral sources in the environment). Methods Here, we describe a newly developed reverse transcription PCR (RT‒PCR) assay for TBEV detection. The assay was developed and evaluated using armored RNA positive control particles (ARCs). The assay was evaluated using several sample types: (1) a panel of heterologous viral and bacterial RNA/DNA; (2) RNA from TBEV strains isolated in different years in various Russian regions; and (3) RNA from TBEV-positive and TBEV-negative ticks (collected in northwest Russia). Results The limit of detection (LOD) of the assay is 103 copies/mL (20 copies/reaction) of TBEV RNA. The developed demonstrated 100% analytical specificity. The assay was compared with the two most commonly used Russian commercial kits for TBEV diagnostics. Conclusions The results indicate that the developed RT‒PCR assay is a reliable and competitive method for the detection of TBEV RNA, which establishes its value as a tool for diagnosing and monitoring the virus. Graphical Abstract

Aedes aegypti is a primary vector for globally significant arboviruses such as dengue virus (DENV). The mosquito's metavirome, particularly its insect-specific virus (ISV) component, is recognized as a key modulator of arboviral transmission. However, the natural ecology of these interactions in populations remains poorly understood. This study presents the first comparative analysis of the metavirome in wild-caught A. aegypti from Vietnam based on natural DENV infection status. Metaviromic analysis was performed on 69 DENV-positive pools from six central provinces. The results obtained were compared with previously obtained metaviromic data from 7 DENV-negative pools (from the same region). Analysis suggests the presence of a stable 'core metavirome' of 11 ISVs present in both groups. Interestingly, six ISVs were detected only in DENV-negative mosquitoes, which may suggest potential antagonistic interactions requiring further investigation. Conversely, five ISVs were found only in DENV-positive pools, including Aedes partiti-like virus 1 and Aedes anphevirus. The latter may suggest possible synergistic relationships that facilitate arboviral replication. Phylogenetic analysis of prevalent ISVs, such as Phasi Charoen-like phasivirus (PCLV) and Chaq-like virus, revealed patterns of both local circulation and genetic diversity. The findings describe distinct ISV profiles associated with DENV infection in a natural setting, providing a data-driven foundation for hypothesizing specific virus-virus interactions. The data underscores the complexity of the mosquito metavirome. Here, we identified several candidate ISVs for future experimental studies aimed at understanding potential functional impact on arboviral vector competence.

Russia is a country with a high incidence of tick-borne encephalitis (TBE). In northwestern regions of Russia, 110 TBE cases were registered in 2021. The largest numbers of TBE cases were registered in the Arkhangelsk region and St. Petersburg. TBEV seropositivity among healthy individuals, including the unvaccinated population in northwestern Russia, was found in 12.2% of studied samples, indicating active TBEV circulation. The prevalence of TBEV is 2.4% in the two tick species most common in northwestern regions of Russia, Ixodes ricinus and Ixodes persulcatus. However, there is still no comprehensive data on the molecular characterization and phylogenetic analysis of the circulating TBEV strains. The purpose of the study was to determine the prevalence of TBEV and to identify its subtypes in ixodid ticks collected in specific areas of northwestern Russian regions. Phylogenetic analysis of E protein sequences of ten obtained strains showed that they all belong to the Siberian subtype, which were clustered into two groups: the most numerous Baltic group, clusteron 3D; and the Vasilchenko group. However, some unique isolates may form new clusterons.

Mosquitoes are important vectors for various infectious pathogens. More than 200 species of mosquitoes are common in Vietnam, one of the main carriers of viruses that are important for humans is the mosquito of the genus Aedes aegypti. Metavirome sequencing can shed light on the diversity of mosquito-borne viruses classified as insect-specific viruses (ISV). After BLAST analysis using the viral database, contigs were classified as belonging to seventeen ISVs. Ten of them are distributed among five families: Totiviridae; Flaviviridae; Partitiviridae; Phenuiviridae; and Orthomyxoviridae. The other seven species belonged to recently identified RNA viruses whose taxonomic position is undefined in the current classification of the International Committee on Taxonomy of Viruses (ICTV). This is the first study to reveal the diversity of RNA viruses associated with Aedes aegypti mosquitoes in Vietnam, while highlighting the need for further study of ISV in mosquito vectors.

In this report, we document and analyze a case in which the Irkut virus (IRKV) (Mononegavirales: Rhabdoviridae) caused a fatal human case following a bat bite in June 2021. Unfortunately, the available data did not permit a detailed taxonomic classification of the carrier bat (Chiroptera). The event occurred in the southwestern part of the Sikhote-Alin mountain region (Russian Far East) covered by the Ussuri taiga forest. The symptoms of the illness began with the following: fever; pronounced psychomotor and motor agitation; tremor of the lower jaw and tongue; aphasia; dyslexia; and dysphagia. These rapidly developed, leading to a severe and fatal encephalitis. The patient was not vaccinated for rabies and did not receive rabies immunoglobulin. Using brain sections prepared from the deceased, molecular diagnostics were performed: immunofluorescence (polyclonal anti-rabies immunoglobulin) indicating the presence of the lyssavirus antigen; and RT-PCR indicating traces of viral RNA. Sectional material (brain) was used for whole-genome sequencing, resulting in a near-complete sequence of the lyssavirus genome. The obtained genomic sequence was identified as the Irkut virus. A comparative analysis of the new sequence and other currently available IRKV sequences (NCBI) revealed differences. Specifically, amino acid differences between antigenic sites in the isolate and those of the rabies vaccine strain used regionally were noted. The patient history and subsequent analysis confirm human IRKV infection following bat contact. Like other fatal cases of IRKV infection described earlier, this case occurred in the southern part of the Russian Far East. Two have occurred in the southwestern part of the Sikhote-Alin mountain region. This indicates the possible existence of an active, natural viral focus.

The severity of MeV infection has been greatly reduced by the development of a live attenuated vaccine, which has been incorporated into vaccination programs in many countries. However, poor access to health facilities, and above all, the increase in anti-vaccination movements, has prevented the achievement of sufficient vaccination coverage. In outbreak scenarios, a rapid and transportable method can improve differential diagnosis, including removing ambiguity in suspected measles cases, contacts, or a cohort. In response to the need, we have developed a new RT-qPCR-based MeV detection assay. The LOD of the developed assay was determined on different PCR machines and the higher threshold was 1-1.2 103 copies/mL. The joint diagnostic sensitivity of ELISA and RT-PCR (used together) was 100%, and used combinedly, these two methods enable detection of all measles-infected persons, which is extremely important for controlling contagion and spread of infection. During the clinical validation of the assay on 200 clinical samples from measles-suspected cases using ELISA, 157 samples showed a positive result, while 163 positive cases were confirmed by the RT-qPCR assay. The concordance between the two techniques was 93%. According to our results, the real-time RT-PCR approach used in our study is more sensitive and appears to be a more promising method for measles diagnosis during early stages of the disease, likely before the rise of specific IgM antibodies detected by ELISA.

Abstract Background Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. The study aimed to investigate the epidemiology of COVID-19, including whole-genome sequencing of SARS-CoV-2 samples from Southern Vietnam, during the period January 2020 to December 2021 for identification of the main circulating variants. Methods Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2. Results Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases. Conclusions Pandemic dynamics in Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.

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Background. The COVID-19 pandemic has become a substantial global health crisis, unparalleled in world history. Infection dynamics can have specific characteristics in different countries due to social, economic, climatic, or geographic factors. Aim: to study features of SARS-CoV-2 collective immunity among the Armenian population. Materials and methods. A cross-sectional, randomized study of collective immunity was carried out according to a program developed by Rospotrebnadzor and the St. Petersburg Pasteur Institute, taking into account WHO recommendations. The study was approved by the ethics committees of the National Center for Infectious Diseases (Armenia) and the St. Petersburg Pasteur Institute (Russia). A volunteer cohort was formed (N = 6057), randomized by age and region. The studys analysis included: shares and distributions of antibodies (Abs) to nucleocapsid (Nc) antigen (Ag) and receptor binding domain (RBD) S-1 Ag in the cohort; and quantitative determination of these Abs by ELISA. During the survey, a history of vaccination was indicated by 4395 people. Results. Overall seropositivity formed in the whole cohort (by April 14, 2022) was 98.6% (95% CI: 98.198.7). It did not depend on age, place of residence, or occupation. When quantifying Nc and RBD Abs, the proportions of volunteers with Nc Ab levels of 117 BAU/ml and RBD Ab levels of 22.6220 BAU/ml were the smallest, amounting to 6.9% (95% CI: 6.27.5) and 20.4% (95% CI: 19.421.4), respectively. With increasing serum concentrations (Nc 667 BAU/ml, RBD 450 BAU/ml), the proportions of individuals with the corresponding levels were 20.2% for Nc (95% CI: 19.221.3) and 54.2% for RBD (95% CI: 52.955.5). Vaccination coverage was 72.6% (95% CI: 71.573.7). The most frequently used were Sinopharm/BIBP (32.4%), AZD1222 (22.3%), and Gam-COVID-Vac (21%). The remaining vaccines (CoronaVac, mRNA-1273, BNT162b2, CoviVac) were used by 24.3% of vaccinated individuals. When summing vaccines by platform, it was found that: vector vaccines were used in 40.34% (95% CI: 33.5742.39) of cases; whole-virion vaccines were used in 26.83% (95% CI: 24.7632.20); and mRNA vaccines were used in 6.33% (95% CI: 4.848.91). Conclusion. The epidemic situation in Armenia by April 2022 was characterized by a high level of collective immunity, independent of age or regional factors. Vector and whole-virion vaccines have been used most widely.

Background. The course of the COVID-19 epidemic process depends on population immunity which prevents pathogen spread among the population. Aim: to study the evolution of SARS-CoV-2 humoral immunity in the Belarusian population relative to COVID-19 pandemic dynamics. Materials and methods. The work was carried out according to a methodology for assessing population immunity developed by Rospotrebnadzor (Russia) and the Belarusian Ministry of Health with the participation of the St. Petersburg Pasteur Institute (SPPI), taking into account WHO recommendations. The study was approved by the Bioethics Committee of Belarus and the SPPI Bioethics Committee. Participant selection was carried out by questionnaire using a cloud (internet server) service. To monitor population immunity, a cohort of 4,661 people (participating in all stages of seromonitoring) was formed from the overall volunteer group. Volunteers were randomized by age group (1-17, 18-29, 30-39, 40-49, 50-59, 60-69, 70+ years), region, and professional group. For the detection of antibodies (Abs) to nucleocapsid (Nc) and S glycoprotein receptor-binding domain (RBD), corresponding assay systems were used following manufacturer instructions. The study was conducted in 4 stages according to a single scheme. Results. In the 1st stage (pandemic month 15), collective immunity was due mainly to Nc+RBD+ Ab status alone. By the 2nd stage (carried out after 4 months), their share decreased 1.2-fold, while the share of volunteers who had only RBD Abs increased 1.7-fold. In the 3rd and 4th stages (carried out after 9 and 19 months), the share of persons with RBD+Nc‒ compared to the 2nd stage decreased by 3.5%; the proportion of persons with Nc+RBD‒ Abs increased by 1.5-fold. The most important factor in population immunity was vaccination of the population, the coverage of which reached 70% by the 4th stage. Among vaccines, the Sputnik V and Sputnik Light vector designs were used most often. The whole-virion, inactivated BIBP-CorV vaccine was used less often. Conclusion. The evolution of collective SARS-CoV-2 humoral immunity included a set of changes in circulating Ab levels (Nc, RBD). The hybrid immunity formed helped to reduce the incidence to nearly zero.

BACKGROUND:Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. A randomized retrospective study was performed to investigate the epidemiology and genetic diversity of COVID-19. Whole-genome sequencing of 126 SARS-CoV-2 samples collected from Southern Vietnam between January 2020 and December 2021 revealed the main circulating variants and their distribution.METHODS:Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2.RESULTS:Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases.CONCLUSIONS:Pandemic dynamics in Southern Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for over two years of the COVID-19 pandemic and a global health emergency. Genomic surveillance plays a key role in overcoming the ongoing COVID-19 pandemic despite its relative successive waves and the continuous emergence of new variants. Many technological approaches are currently applied for the whole genome sequencing (WGS) of SARS-CoV-2. They differ in key stages of the process, and they feature some differences in genomic coverage, sequencing depth, and in the accuracy of variant-calling options. In this study, three different protocols for SARS-CoV-2 WGS library construction are compared: an amplicon-based protocol with a commercial primer panel; an amplicon-based protocol with a custom panel; and a hybridization capture protocol. Specific differences in sequencing depth and genomic coverage as well as differences in SNP number were found. The custom panel showed suitable results and a predictable output applicable for the epidemiological surveillance of SARS-CoV-2 variants.

Introduction: The COVID-19 pandemic has become a serious challenge for humanity almost everywhere globally. Despite active vaccination around the world, the incidence proportion in different countries varies significantly as of May 2022. The reason may be a combination of demographic, immunological, and epidemiological factors. The purpose of this study was to analyze possible relationships between COVID-19 incidence proportion in the population and the types of SARS-CoV-2 vaccines used in different countries globally, taking into account demographic and epidemiological factors. Materials and methods: An initial database was created of demographic and immunoepidemiological information about the COVID-19 situation in 104 countries collected from published official sources and repository data. The baseline included, for each country, population size and density; SARS-CoV-2 testing coverage; vaccination coverage; incidence proportion; and a list of vaccines that were used, including their relative share among all vaccinations. Subsequently, the initial data set was stratified by population and vaccination coverage. The final data set was subjected to statistical processing both in general and taking into account population testing coverage. Results: After formation of the final data set (including 53 countries), it turned out that reported COVID-19 case numbers correlated most strongly with testing coverage and the proportions of vaccine types used, specifically, mRNA (V1); vector (V2); peptide/protein (V3); and whole-virion/inactivated (V4). Due to the fact that an inverse correlation was found between 'reported COVID-19 case numbers' with V2, V3, and V4, these three vaccine types were also combined into one analytic group, 'non-mRNA group' vaccines (Vnmg). When the relationship between vaccine type and incidence proportion was examined, minimum incidence proportion was noted at V1:Vnmg ratios (%:%) from 0:100 to 30:70. Maximum incidence proportion was seen with V1:Vnmg from 80:20 to 100:0. On the other hand, we have shown that the number of reported COVID-19 cases in different countries largely depends on testing coverage. To offset this factor, countries with low and extremely high levels of testing were excluded from the data set; it was then confirmed that the largest number of reported COVID-19 cases occurred in countries with a dominance of V1 vaccines. The fewest reported cases were seen in countries with a dominance of Vnmg vaccines. Conclusion: In this paper, we have shown for the first time that the level of reported COVID-19 incidence proportion depends not only on SARS-CoV-2 testing and vaccination coverage, which is quite logical, but probably also on the vaccine types used. With the same vaccination level and testing coverage, those countries that predominantly use vector and whole-virion vaccines feature incidence proportion that is significantly lower than countries that predominantly use mRNA vaccines.

Early knowledge about novel emerging viruses and rapid determination of their characteristics are crucial for public health. In this context, development of theoretical approaches to model viral evolution are important. The clusteron approach is a recent bioinformatics tool which analyzes genetic patterns of a specific E protein fragment and provides a hierarchical network structure of the viral population at three levels: subtype, lineage, and clusteron. A clusteron is a group of strains with identical amino acid (E protein fragment) signatures; members are phylogenetically closely related and feature a particular territorial distribution. This paper announces TBEV Analyzer 3.0, an analytical platform for rapidly characterizing tick-borne encephalitis virus (TBEV) strains based on the clusteron approach, workflow optimizations, and simplified parameter settings. Compared with earlier versions of TBEV Analyzer, we provide theoretical and practical enhancements to the platform. Regarding the theoretical aspect, the model of the clusteron structure, which is the core of platform analysis, has been updated by analyzing all suitable TBEV strains available in GenBank, while the practical enhancements aim at improving the platform’s functionality. Here, in addition to expanding the strain sets of prior clusterons, we introduce eleven novel clusterons through our experimental results, predominantly of the European subtype. The obtained results suggest effective application of the proposed platform as an analytical and exploratory tool in TBEV surveillance.

Viral population surveillance is an essential task in public health, especially in preventing pandemics. The Omsk hemorrhagic fever virus (OHFV) is an etiological agent which is close to tick-borne encephalitis virus. Mainly, it is geographically limited to western Siberian regions, including Omsk, Novosibirsk, Kurgan, and Tyumen. Earlier, we presented an online platform, TBEV-Analyzer, for analysis and monitoring of TBEV. That platform relies on a model called clusteron structure, constructed based on phylogenetic networks. Using that experience, we introduce here OHFV Analyzer, an online analytical platform designed for specifically monitoring the Omsk hemorrhagic fever virus. The platform can automatically determine the phylogenetic history of a query strain based on analysis of a specific E protein fragment. In addition, the platform provides the specific amino acid signature of the clusteron to which the query belongs and presents a visualization of it superimposed on the envelope glycoprotein surface. We believe the proposed platform can serve as an exploratory tool for OHFV monitoring while helping to better understand the pathogen's genetic diversity and evolutionary history.

Introduction: Respiratory infections, collectively, are one of the World's most common and serious illness groups. As recent observations have shown, the most severe courses of acute respiratory infection, often leading to death, are due to uncontrolled cytokine production (hypercytokinemia). Methods: The study involved 364 patients with respiratory illness being treated in clinics in St. Petersburg (Russia) in 2018–2019 and 30 healthy controls. Cytokine analysis was carried out in the acute phase of illness (2–3 days from onset of initial symptoms) and in the stage of recovery (days 9–10). The research presented is devoted to the assessment of mRNA expression of specific cytokines (interleukin [IL]-1b, IL-2, IL-4, IL-6, IL-8, IL-10, IL-18, tumor necrosis factor-α [TNF-α], and interferon-λ) and MxA in whole blood leukocytes, by means of real-time polymerase chain reaction. Results: In 70% of patients, bacterial or viral pathogens were identified, with influenza viral infections (types A and B) prevailing. Significant increases in the expression of IL-18, TNF, and IL-10 were observed, relative to controls, only with influenza viral infections. We have shown a difference in IL-6 mRNA expression in patients with bacterial or viral pathogens. No statistically significant difference was found in white blood cells IL-4 expression levels between patients and healthy controls. Conclusion: Investigation of the nuances of systemic cytokine production, in response to specific viral and bacterial pathogens, makes it possible to assess the risks of developing hypercytokinemia during respiratory infection with agents circulating in the human population and to predict the pathogenicity and virulence of circulating threats.

Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia’s second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection.