Dataset Information

The phylodynamics of the rabies virus in the Russian Federation.

ABSTRACT: Near complete rabies virus N gene sequences (1,110 nt) were determined for 82 isolates obtained from different regions of Russia between 2008 and 2016. These sequences were analyzed together with 108 representative GenBank sequences from 1977-2016 using the Bayesian coalescent approach. The timing of the major evolutionary events was estimated. Most of the isolates represented the steppe rabies virus group C, which was found over a vast geographic region from Central Russia to Mongolia and split into three groups (C0-C2) with discrete geographic prevalence. A single strain of the steppe rabies virus lineage was isolated in the far eastern part of Russia (Primorsky Krai), likely as a result of a recent anthropogenic introduction. For the first time the polar rabies virus group A2, previously reported in Alaska, was described in the northern part of European Russia and at the Franz Josef Land. Phylogenetic analysis suggested that all currently circulating rabies virus groups in the Russian Federation were introduced within the few last centuries, with most of the groups spreading in the 20th century. The dating of evolutionary events was highly concordant with the historical epidemiological data.

SUBMITTER: Deviatkin AA

PROVIDER: S-EPMC5321407 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The phylodynamics of the rabies virus in the Russian Federation.

Deviatkin Andrei A AA Lukashev Alexander N AN Poleshchuk Elena M EM Dedkov Vladimir G VG Tkachev Sergey E SE Sidorov Gennadiy N GN Karganova Galina G GG Galkina Irina V IV Shchelkanov Mikhail Yu MY Shipulin German A GA

PloS one 20170222 2

Near complete rabies virus N gene sequences (1,110 nt) were determined for 82 isolates obtained from different regions of Russia between 2008 and 2016. These sequences were analyzed together with 108 representative GenBank sequences from 1977-2016 using the Bayesian coalescent approach. The timing of the major evolutionary events was estimated. Most of the isolates represented the steppe rabies virus group C, which was found over a vast geographic region from Central Russia to Mongolia and split ...[more]

PMID: 28225771

Similar Datasets

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.

Project description:Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increasingly, whole-genome information is being used to uncover these patterns, but the limits of phylogenetic resolution that can be achieved with this are unclear. Here, whole-genome variation was used to uncover fine-scale population structure in endemic canine rabies virus circulating in Tanzania. This is the first whole-genome population study of rabies virus and the first comprehensive phylogenetic analysis of rabies virus in East Africa, providing important insights into rabies transmission in an endemic system. In addition, sub-continental scale patterns of population structure were identified using partial gene data and used to determine population structure at larger spatial scales in Africa. While rabies virus has a defined spatial structure at large scales, increasingly frequent levels of admixture were observed at regional and local levels. Discrete phylogeographic analysis revealed long-distance dispersal within Tanzania, which could be attributed to human-mediated movement, and we found evidence of multiple persistent, co-circulating lineages at a very local scale in a single district, despite on-going mass dog vaccination campaigns. This may reflect the wider endemic circulation of these lineages over several decades alongside increased admixture due to human-mediated introductions. These data indicate that successful rabies control in Tanzania could be established at a national level, since most dispersal appears to be restricted within the confines of country borders but some coordination with neighbouring countries may be required to limit transboundary movements. Evidence of complex patterns of rabies circulation within Tanzania necessitates the use of whole-genome sequencing to delineate finer scale population structure that can that can guide interventions, such as the spatial scale and design of dog vaccination campaigns and dog movement controls to achieve and maintain freedom from disease.

Project description:The situation with cardiovascular (CV) burden in Russian population is alerting, and becomes of interest due to high CV mortality, and shorter lifespan if compare with the Western society amid the absence of the established monitoring or screening system for major CV risk factors. The purpose of this systematic epidemiological update was to explore CV burden in Russia. The study represents pooled results with a systematic epidemiological review of the national mass screening, selected randomized clinical trials and statistical datasets of the national public health CV institutions exploring the trends of the CV burden in all 83 regions of Russia. We overviewed data from a number of the available Russian-speaking national data sources of 2001-2014, and NANOM-FIM trial (NCT01270139) as the only available real-world population study. The CV diseases in Russia accounted for 54.9% of all deaths in 2011-2014. The death rate was 13.3 per 1,000 citizens with CV mortality of 653.9 per 100,000. The life expectancy achieves 64.3 years for male and 76.1 years for female. The mean age of pts in trial was 51.6 years (77.2% males). A total of 175 Russian PCI centers implemented 205,902 angio a year, and 75,378 PCI achieving 531 PCI per 1,000,000 with placement of 101,451 stents (1.37 stents per PCI; 48,057 DES). The smoking (17.3% of screened with a 2,786 cigarettes a year; 70.6% in trial), excessive alcohol consumption (1.8% of screened with a 11.6 L per year; 50.6% in trial), unhealthy Russian diet (abundance of carbohydrates/sugar, saturated and trans fats in 24.3% of screened), psychosocial factors (20%) and physical inactivity (19.6% of screened) remain the major modifiable risk factors. They, in turn, affect such risk factors as dyslipidemia (86.7% in trial), obesity (16.7% of screened; BMI in trial was 28.4), and hypertension (40.8% suffered; 86.1% in trial). CV mortality was not directly associated with a level of poverty (r=0.26, P=0.02) or socio-economic development (P>0.05) in regions. The documented 27% 10-year decline of CV mortality was interpreted as a success of the national policy. Mortality statistics show the stark reality of a high CV burden in Russia. New national program and aggressive emerging efforts are required to tackle CV diseases in Russia.

Dataset Information

The phylodynamics of the rabies virus in the Russian Federation.

Publications

The phylodynamics of the rabies virus in the Russian Federation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets