The phylodynamics of the rabies virus in the Russian Federation

Phylogenetic Characterization of Rabies Virus Field Isolates Collected from Animals in European Russian Regions in 2009-2022

Rabies is a fatal disease of mammals that poses a high zoonotic risk to humans as well. The distribution of rabies is mainly driven by host animal migration and human-mediated dispersion. To contribute to the global understanding of the rabies virus (RABV) molecular epidemiology, 94 RABV field isolates collected from animals in 13 European Russian regions were phylogenetically characterized using the nearly full-size N gene nucleotide sequences. According to phylogenetic inferences, all isolates belonged to one of the two established phylogenetic groups, either group C (n = 54) or group D (n = 40), which are part of the clade Cosmopolitan of RABVs. Some representatives of group C collected from regions located far apart from each other had a remarkably high level of nucleotide identity. The possibility of the contribution of local bat species to the distribution of RABVs was discussed. Interestingly, over the years, the fraction of group D isolates has been constantly decreasing compared with that of group C isolates. The phylogenetic insights generated herein might have an important contribution to the control and surveillance of animal rabies epidemiology in the region.

[Lethal cases of lyssavirus encephalitis in humans after contact with bats in the Russian Far East in 2019-2021]

INTRODUCTION

On the territory of Russia four species of lyssaviruses (genus Lyssavirus) were identified, three of them caused human deaths.

THE AIM OF WORK

to characterize fatal cases in humans after contacts with bats in the Far East in 20182021 and to perform typing of isolated pathogens.

MATERIALS AND METHODS

Lyssavirus infection was confirmed in samples of sectional material from people who died in the Amur Region in 2019, in the Primorsky Krai in 2019 and 2021. Diagnostics was performed by fluorescent antibody test (FAT) and RT-PCR using diagnostic kits of domestic production. Viruses were isolated in a bioassay. The nucleoprotein sequences were analyzed after 1st passage. The analysis of phylogenetic relationships and the construction of a dendrogram were performed using the MEGA7 software.

RESULTS

The viruses that caused the fatal cases in humans in the Amur Region and Primorsky Krai share more than 90% identity to Lyssavirus irkut detected in Russia and China. Together they form a separate monophyletic cluster with 100% bootstrap support.

CONCLUSION

On the territory of Russia, monitoring of bat populations for infection with lyssaviruses is relevant. The material of people who died from encephalomyelitis of unknown etiology within 1015 days from the onset of the disease must be examined for lyssavirus infection. It is necessary to develop PCR assays that employ genus-specific primers. The use of molecular biological methods is promising for improving the diagnosis of rabies and epidemiological surveillance, as well as increasing the efficiency of the system of biological safety of the population of the Russian Federation.

RABIES IN ARCTIC FOX (VULPES LAGOPUS) AND REINDEER (RANGIFER TARANDUS PLATYRHYNCHUS) DURING AN OUTBREAK ON SVALBARD, NORWAY, 2011-12

Rabies is an important zoonotic disease with high fatality rates in animals and humans. In the Arctic, the Arctic fox (Vulpes lagopus) is regarded as the principal reservoir, but there is considerable debate about how the disease persists at the low population densities that are typical for this species. We describe an outbreak of rabies among Arctic foxes and Svalbard reindeer (Rangifer tarandus platyrhynchus) during 2011-12 on the remote Arctic archipelago of Svalbard, an area with a very low and relatively stable Arctic fox density. The aim of the research was to increase knowledge of Arctic rabies in this ecosystem and in the presumed spillover host, the Svalbard reindeer. Phylogenetic analysis of rabies virus (RABV) RNA isolates from Arctic fox and reindeer was performed, and clinical observations and histologic and immunohistochemical findings in reindeer were described. An ongoing capture-mark-recapture project allowed collection of serum samples from clinically healthy reindeer from the affected population for detection of rabies virus-neutralizing antibodies. The outbreak was caused by at least two different variants belonging to the RABV Arctic-2 and Arctic-3 clades, which suggests that rabies was introduced to Svalbard on at least two different occasions. The RABV variants found in Arctic fox and reindeer were similar within locations, suggesting that Arctic foxes and reindeer acquired the infection from the same source(s). The histopathologic and immunohistochemical findings in 10 reindeer were consistent with descriptions in other species infected with RABV of non-Arctic lineages. Evidence of RABV was detected in both brain and salivary gland samples. None of 158 examined serum samples from clinically healthy reindeer had virus-neutralizing antibodies against RABV.

Hotspots in a cold land-reported cases of rabies in wildlife and livestock in Mongolia from 2012-2018

The epidemiological profile of rabies virus within Mongolia remains poorly characterized despite 21,302 domestic animal cases being reported between 1970-2005. This lack of knowledge is particularly concerning given that roughly 26% of the population lives a pastoral herding lifestyle and livestock production contributes up to 18% of Mongolia's total gross domestic product (GDP). The gaps in knowledge of the rabies disease ecology within Mongolia combined with the lack of routine vaccination of domestic animals and wildlife poses a significant threat to the more than 60 million heads of livestock within Mongolia. Animal rabies case data from the General Authority for Veterinary Services and National Center for Zoonotic Diseases were used in this study. Each data point included year of report, an animal descriptor, geographic coordinates and the aimag (province) of origin. A total of 2,359 animal rabies cases were reported between 2012-2018. Cattle were the most commonly reported animal overall (861 cases), followed by goats (268), sheep (251) and dogs (221) within the domestic animal category. Red foxes were responsible for most reported wildlife cases (317) followed by wolves (151). Most rabid animals were reported in the Khuvsgul, Uvurkhangai and Govi-Altai aimags, and a positive correlation was found between livestock numbers per soum and the number of rabies cases reported. Rabies poses a significant threat to the Mongolian economy and the health of human and animal populations within Mongolia. The close association of the nomadic pastoralists with both domestic animals and wildlife represents a significant threat for disease emergence and necessitates studies that describe the ecology of rabies, which may threaten these populations.

Diversity of rabies virus detected in Inner Mongolia, China, 2019-2021

Rabies is a serious public health issue in China, with over 95% of human infections transmitted by dogs. As part of a routine surveillance carried out in the Inner Mongolia Autonomous Region (IMAR) between 2019 and 2021, 80 of 95 suspected rabies cases in domestic animals (dogs, livestock) and wild carnivores (foxes, badgers, a raccoon dog) were confirmed as rabies virus (RABV) positive. Phylogenetic analysis of RABVs of the 80 cases based on complete N genes showed that 97.5% (78/80) of the virus strains belonged to the Cosmopolitan (steppe-type) clade, with one in each of Arctic-related (AL2) and Asian (SEA1) clades. The data show that infected foxes have become a major transmission source of rabies in China, second only to dogs, and play a pivotal role in animal rabies epizootics in the north and northwest of the country. The recent spread of fox rabies to other animal species presents an increasing threat to public health and emphasizes the importance of animal rabies surveillance.

Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses

Rabies is a globally prevalent viral zoonosis that causes 59,000 deaths per year and has important economic consequences. Most virus spread is associated with the migration of its primary hosts. Anthropogenic dissemination, mainly via the transportation of rabid dogs, shaped virus ecology a few hundred years ago and is responsible for several current outbreaks. A systematic analysis of aberrant long-distance events in the steppe and Arctic-like groups of rabies virus was performed using statistical (Bayesian) phylogeography and plots of genetic vs. geographic distances. The two approaches produced similar results but had some significant differences and complemented each other. No phylogeographic analysis could be performed for the Arctic group because polar foxes transfer the virus across the whole circumpolar region at high velocity, and there was no correlation between genetic and geographic distances in this virus group. In the Arctic-like group and the steppe subgroup of the cosmopolitan group, a significant number of known sequences (15-20%) was associated with rapid long-distance transfers, which mainly occurred within Eurasia. Some of these events have been described previously, while others have not been documented. Most of the recent long-distance transfers apparently did not result in establishing the introduced virus, but a few had important implications for the phylogeographic history of rabies. Thus, human-mediated long-distance transmission of the rabies virus remains a significant threat that needs to be addressed.

[Comparative molecular and genetic characterization of rabies viruses (Rabies lyssavirus, Lyssavirus, Rhabdoviridae) circulated in the Russian Federation in 1985-2016.]

INTRODUCTION

Rabies caused by the neurotropic virus of the genus Lyssavirus, Rhabdoviridae family, which infects all warm-blooded vertebrates including human beings. The homology level of the amino acid sequences for Lyssaviruses nucleoprotein reaches 78-93%. Aim - study the genetic diversity and molecular epidemiology of Lyssaviruses circulated in the Russian Federation in 1985-2016.

MATERIAL AND METHODS

54 isolates of rabies virus isolated from animals, and 2 isolates from humans, 4 vaccine strains of rabies virus: RV-97, ERA, Shchelkovo 51, ERAG333 used in phylogenetic study. Phylogenetic analysis was performed using Genbank data on genome fragments of 73 rabies virus isolates and 9 EBLV-1 isolates. DNASTAR V.3.12, Bio Edit 7.0.4.1 and MEGA v.10.0.5, Primer Premier 5 programs have been used.

RESULTS

Comparative molecular genetic analysis of genomes fragments of 130 Lissaviruses, isolated on the territory of the RF, Ukraine in 1985-2016, vaccine strains of rabies virus, showed their distribution by geographical feature. Comparison of the nucleoprotein fragments of the rabies virus isolates with vaccine strains revealed 4 marker mutations: V56I (Eurasian group), L/V95W (Central group), D101N/S/T, and N/G106D. Phylogenetic analysis of the isolate «Juli», isolated from a human bitten by a bat proved his belonging to the European Bat lyssavirus-1a.

DISCUSSION

Study of the molecular epidemiology of rabies within the Russian Federation allows for the genotyping of the viruses and helps to study the hidden mechanisms of rabies infection in animal and human populations, and to characterize vaccine strains, including during oral vaccination.

CONCLUSION

Further study of the molecular epidemiology of rabies within the Russian Federation and the countries bordering it is important.

Fox rabies outbreaks in the republic of Buryatia: Connections with neighbouring areas of Russia, Mongolia and China

The Republic of Buryatia (RB) is located southeast of Lake Baikal and shares a long border with Mongolia. This region of Russia was rabies-free from 1982 to 2010. The first outbreak of fox rabies in RB was identified in 2011, about 30 km from the Russian-Mongolian border. We assessed the possible pathways to further spread the 'steppe' phylogenetic lineage of the rabies virus near the northeastern limits of its known distribution. All rabies cases were located 30-210 km north of the Russia-Mongolia border, with a distance of up to 320 km from each other. Rabies has spread to the north across steppe landscapes and river valleys, with foxes being the main natural hosts of the infection. All RABV isolates from RB belong to the 'steppe' phylogenetic lineage, and three major phylogenic groups could be separated. Group 1 contains sequences from RB, Mongolia, China (Inner Mongolia), and bordering regions of Russia. Group 2 is formed by isolates from other regions of Eastern Siberia, which have no borders with RB and foreign countries. Group 3 contains samples from Western Siberia with endemic fox rabies since the 1950s. The most probable cause of fox rabies epizooty in the RB was multiple drift of the RABV across the Russian-Mongolian border. Our data show that after 2010, fox rabies affected new areas in Central Asia and extended to the north and northeast. Affected areas are similar to the Mongolian-type steppes in their zoogeographical aspect. Closely related genetic lineages of RABV are circulating in RB, Mongolia and the nearest areas of China. International cooperation is necessary to prevent the spread of rabies in the bordering territories of these countries.

Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis?

Tick-borne encephalitis (TBE) is one of the most important viral zoonosis transmitted by the bite of infected ticks. In this study, all tick-borne encephalitis virus (TBEV) E gene sequences available in GenBank as of June 2019 with known date of isolation (n = 551) were analyzed. Simulation studies showed that a sample bias could significantly affect earlier studies, because small TBEV datasets (n = 50) produced non-overlapping intervals for evolutionary rate estimates. An apparent lack of a temporal signal in TBEV, in general, was found, precluding molecular clock analysis of all TBEV subtypes in one dataset. Within all subtypes and most of the smaller groups in these subtypes, there was evidence of many medium- and long-distance virus transfers. These multiple random events may play a key role in the virus spreading. For some groups, virus diversity within one territory was similar to diversity over the whole geographic range. This is best exemplified by the virus diversity observed in Switzerland or Czech Republic. These two countries yielded most of the known European subtype Eu3 subgroup sequences, and the diversity of viruses found within each of these small countries is comparable to that of the whole Eu3 subgroup, which is prevalent all over Central and Eastern Europe. Most of the deep tree nodes within all three established TBEV subtypes dated less than 300 years back. This could be explained by the recent emergence of most of the known TBEV diversity. Results of bioinformatics analysis presented here, together with multiple field findings, suggest that TBEV may be regarded as an emerging disease.

Inner Mongolia: A Potential Portal for the Spread of Rabies to Western China

In recent years, the number of human rabies cases in China has decreased annually. However, some western provinces with no human cases for more than 10 years have begun to report rabies cases, and all of the rabies lineages that circulated in western China were found in Inner Mongolia as well. In this study, we generated a phylogenetic tree with all the Inner Mongolia rabies strains available in GenBank and our laboratory, as well as strains from western China and representative viruses from neighboring countries, based on the N gene sequence. Furthermore, the possible relationships underlying the spread of the virus within Inner Mongolia and neighboring regions were analyzed. Three of six rabies lineages of China (China I-VI) were shown to exist in Inner Mongolia, and a spatial cluster analysis supported that the China I lineage, the dominant cluster of China, likely spread to Ningxia from Inner Mongolia. Wild raccoon dog rabies (China IV/Arctic-like-2) may have spread to Inner Mongolia from Russia and likely continued to spread to Qinghai and Tibet. The red fox lineage (China III/Cosmopolitan), which likely spread from Russia and Mongolia, has been shown to circulate in Inner Mongolia and was a serious threat to Xinjiang, which is adjacent to Inner Mongolia. Thus, Inner Mongolia likely became a location where national and international rabies viruses collected and developed into a potential portal for the spread of rabies to western China. To effectively control the spread of rabies in China, both prevention and control of dog and wild animal rabies in Inner Mongolia should be a top priority.

Recombination in the rabies virus and other lyssaviruses

Recombination is a common event in RNA viruses; however, in the rabies virus there have been only a few reports of isolated recombination events. Comprehensive analysis found traces of recent recombination events within Arctic, Arctic-like and Africa 1b rabies virus groups, as well as recombination between distinct lyssaviruses. Recombination breakpoints were not linked to gene boundaries and could be detected all over the genome. However, there was no evidence that recombination is an important factor in the genetic variability of the rabies virus. It is therefore likely that recombination in the rabies virus is limited by ecological factors (e.g., rare co-circulation of distinguishable lineages and a narrow window for productive coinfection in most carnivore hosts), rather than molecular barriers (e.g., incompatibility of genome fragments).