Genetic heterogeneity of Russian, Estonian and Finnish field rabies viruses

[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.

The phylodynamics of the rabies virus in the Russian Federation

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.

Monitoring of rabies in wild animals in the Kirov region after oral immunization

This work presents the results of the molecular genetic research on genomes of field isolates of the rabies virus circulating in the territory of the Kirov region in order to analyze the phylogenetic relationship between the wild isolate genomes and to determine the possible reversion of the vaccine strain of the rabies virus used in the oral vaccine to virulent variant. We studied 24 brain samples from wild carnivores shot after oral immunization of the area with Rabivak-O/333. A bait with the vaccine provided by the Veterinary Service of the Kirov was also studied. All samples were found to be positive for the presence of the rabies virus as established by FAT and RT-PCR techniques. Phylogenetic analysis of N genome fragments of the rabies virus showed that the field isolates from the Kirov regions were genetically close to the field isolates from Buryatia 2012. Analysis of G genome fragments showed that the Kirov field isolates were close to the isolates from Lipetsk (2011), as well as to the Ukrainian isolates (2006 and 2010). Molecular genetic analysis of the gene fragments N and G for the field isolates and fragments of the genome of the rabies virus vaccine did not reveal any reversion to the virulent vaccine strain.

Rabies in the Baltic States: Decoding a Process of Control and Elimination

Rabies is a fatal zoonosis that still causes nearly 70, 000 human deaths every year. In Europe, the oral rabies vaccination (ORV) of red foxes (Vulpes vulpes) was developed in the late 1970s and has demonstrated its effectiveness in the eradication of the disease in Western and some Central European countries. Following the accession of the three Baltic countries--Estonia, Latvia and Lithuania--to the European Union in 2004, subsequent financial support has allowed the implementation of regular ORV campaigns since 2005-2006. This paper reviews ten years of surveillance efforts and ORV campaigns in these countries resulting in the near eradication of the disease. The various factors that may have influenced the results of vaccination monitoring were assessed using generalized linear models (GLMs) on bait uptake and on herd immunity. As shown in previous studies, juveniles had lower bait uptake level than adults. For the first time, raccoon dogs (Nyctereutes procyonoides) were shown to have significantly lower bait uptake proportion compared with red foxes. This result suggests potentially altered ORV effectiveness in this invasive species compared to the red foxes. An extensive phylogenetic analysis demonstrated that the North-East European (NEE) rabies phylogroup is endemic in all three Baltic countries. Although successive oral vaccination campaigns have substantially reduced the number of detected rabies cases, sporadic detection of the C lineage (European part of Russian phylogroup) underlines the risk of reintroduction via westward spread from bordering countries. Vaccine induced cases were also reported for the first time in non-target species (Martes martes and Meles meles).

Spatio-temporal Use of Oral Rabies Vaccines in Fox Rabies Elimination Programmes in Europe

In Europe, the elimination of wildlife rabies using oral rabies vaccination [ORV] of foxes for more than 30 years has been a success story. Since a comprehensive review on the scope of the different oral rabies vaccine baits distributed across Europe has not been available yet, we evaluated the use of different vaccine baits over the entire period of ORV [1978–2014]. Our findings provide valuable insights into the complexity of ORV programs in terms of vaccine related issues. More than 10 oral vaccines against rabies were used over the past four decades. Depending on many factors, the extent to which oral rabies virus vaccines were used varied considerably resulting in huge differences in the number of vaccine doses disseminated in ORV campaigns as well as in large spatial and temporal overlaps. Although vaccine virus strains derived from the SAD rabies virus isolate were the most widely used, the success of ORV campaigns in Europe cannot be assigned to a single oral rabies virus vaccine alone. Rather, the successful elimination of fox rabies is the result of an interaction of different key components of ORV campaigns, i.e. vaccine strain, vaccine bait and strategy of distribution.

Oral rabies vaccination [ORV] is the pre-eminent example of successful vaccination of wildlife populations which has resulted in virtual elimination of fox-mediated rabies from large parts of Western and Central Europe. This achievement is unprecedented in history. Attractive species-specific baits, efficient vaccination strategy, and highly potent and safe oral rabies vaccines have been instrumental for the success. Numerous oral rabies vaccines for wildlife have been developed over the past four decades. However, information on the use of those vaccines in operational ORV programs in Europe that exists has until now not been fully publicly accessible. Here, we provide the first comprehensive review of the spatio-temporal use of oral rabies vaccines over the entire period of ORV [1978–2014]. Although ‘first generation’ vaccine virus strains derived from the SAD rabies isolate are the most widely used, the results do not support significant differences in efficacy of these strains under field conditions nor can success of ORV be attributed solely to one vaccine type. In contrast, vaccination strategy is of major importance. Our analyses could help in the development of adequate rabies control strategies by documenting the importance of vaccination strategy, in which oral rabies vaccines are only one contributing component among other parameters.

Complete genome sequences of three rabies viruses isolated from rabid raccoon dogs and a cow in Korea

The complete genomes of three rabies viruses (BD0406CC, BV9901PJ, and 08F40) of two raccoon dogs (Nyctereutes procyonoides koreensis) and a cow were determined. The genomic organization is typical of rabies viruses, and the open reading frames of the N, P, M, G, and L genes are 1,353, 894, 609, 1,575, and 6,384 bases in length, respectively. The full genome length of the three strains was 11,928 nucleotides, and the sequence similarity between the rabies viruses at the nucleotide level was 98.5-99.5%. Sequence comparisons indicated that these rabies viruses belong to the "Arctic and Arctic-like" group, with high homology to the Eurasian cluster. All Korean strains were clustered with the Mongolia strains, which belong to Arctic-like 1 clade. The 08F40 and BD0406CC strains were constructed with rabies virus strains isolated in Gangwon province. The BV9901PJ strain was closely related to strains isolated in Gyeonggi province in Korea. Three strains were more dependent upon geographical distribution and time period than host species. Complete genome sequencing of different host-origin rabies viruses will provide information that should contribute to understanding the transmission cycle and genetic variability of rabies from different hosts.

Complete genome sequences of four virulent rabies virus strains isolated from rabid animals in Russia

Rabies virus (RABV) strains Rus(Lipetsk)-8052f, Rus(Lipetsk)-8053c, Rus(Lipetsk)-8054f, and Rus(Lipetsk)-8057f were isolated from foxes (Vulpes vulpes) and a cat (Felis catus) in the Lipetsk region of Russia in 2011. Close relationships between these strains and the members of the "Cosmopolitan" group from Russia (98% homology) and from Europe (95% homology) were estimated.

Molecular characterization of China rabies virus vaccine strain

BACKGROUND

Rabies virus (RV), the agent of rabies, can cause a severe encephalomyelitis in several species of mammals, including humans. As a human rabies vaccine strain employed in China, the genetic knowledge of the aG strain has not been fully studied. The main goal of the present study is to amplify the whole genome of aG strain, and genetic relationships between other vaccine strains and wild strains were analyzed.

RESULTS

The entire genome of human rabies virus vaccine strain aG employed in China was sequenced; this is the second rabies virus vaccine strain from China to be fully characterized. The overall organization and the length of the genome were similar to that of other lyssaviruses. The length of aG strain was 11925nt, comprising a leader sequence of 58nt, nucleoprotein (N) gene of 1353nt, phosphoprotein (P) gene of 894 nt, matrix protein (M) gene of 609nt, glycoprotein (G) gene of 1575nt, RNA-dependent RNA polymerase (RdRp,L) gene of 6384nt, and a trailer region of 70 nt. There was TGAAAAAAA (TGA7) consensus sequence in the end of each gene, except AGA7 at the end of G gene. There was AACAYYYCT consensus start signal at the beginning of each gene.

CONCLUSIONS

In this report, we analyzed the full genome of China human rabies vaccine strain aG. Our studies indicated that the genome of aG retained the basic characteristics of RV. At gene level, N was the most conserved among the five coding genes, indicating this gene is the most appropriate for quantitative genotype definition. The phylogenetic analysis of the N indicated the aG strain clustered most closely with Japanese and Russian rabies vaccine strains, suggesting that they may share the same ancestor; also, the aG strain did not share high homology with wild strains isolated from China, making it may not be the best vaccine strain, more research is needed to elucidate the genetic relationship among the RV circulating in China.

International interlaboratory trials on rabies diagnosis: an overview of results and variation in reference diagnosis techniques (fluorescent antibody test, rabies tissue culture infection test, mouse inoculation test) and molecular biology techniques

Interlaboratory trials on rabies diagnosis were organised in 2009 and in 2010 by the European Union Reference Laboratory (EURL) for rabies. In 2009, two panels of virus samples were sent to participating laboratories to compare results on reference diagnosis techniques and on RT-PCR. A single panel was sent in 2010 to test FAT (fluorescent antibody test), RTCIT (rabies tissue culture infection test) and RT-PCR techniques. The virus panels included the RABV, EBLV-1, EBLV-2 and ABLV strains. Results revealed that laboratories produced the highest proportion of concordant results using RT-PCR (90.5%) and FAT (87.1%), followed by RTCIT (70.0%) and MIT (35.0%) in 2009 and in FAT (85.0%) and RT-PCR (80.6%) followed by RTCIT (77.3%) in 2010. Errors were only observed in bat strains (i.e. none in the RABV strain) for the RT-PCR or FAT techniques, highlighting the need to improve diagnosis most specifically in such strains. RT-PCR was the technique showing the lowest rate of false negative results in either trial year, while RTCIT and MIT (performed in 2009 only) were the techniques with the lowest proportion of false positive results. Nevertheless, the FAT technique represented a good compromise with both satisfactory sensitivity and specificity, as only a few false positive (1.6% in 2009, 5.8% in 2010) and false negative results (1.6% in both 2009 and 2010) were detected. The analysis of technical questionnaires describing the protocols used by participating laboratories revealed variation in the methods used that may induce inconsistencies in the results. In this study, the number of readers for FAT slide examination was identified as a factor affecting significantly the results of laboratories, suggesting that two independent readers are necessary for routine rabies diagnosis. Our findings highlight the need for all rabies diagnostic laboratories to improve harmonisation of procedures.

Evolutionary dynamics of rabies viruses highlights the importance of China rabies transmission in Asia

Rabies in Asia is emerging as a serious public health issue. To explore the possible origin, phylogenetic relationships, and evolutionary dynamics of Asian Rabies viruses (RABV), we examined 200 complete nucleoprotein (N) gene sequences from RABV isolates in the region. Phylogeny supported the classification of Asian RABVs into five distinct clusters in lyssavirus genotype 1. Our geospatial and temporal analyses demonstrated that China appears to be the prime source of Asian RABVs. Understanding of rabies transmission and associated human activities, such as dog translocation, can help rabies control and elimination in Asia through collaborative efforts or programs.

Characterization of Russian rabies virus vaccine strain RV-97

The RV-97 rabies virus vaccine strain is widely used in Russia as a component of the live attenuated oral anti-rabies vaccine "Sinrab". This vaccine has also been used in some other countries, such as Kazakhstan, Belarus, and Ukraine. Entire genome sequencing is an effective tool for studying the genetic properties of virus strains. In this study, a simple technique for obtaining the entire genome sequence of the rabies virus was used. The entire genome sequence and the deduced amino acid sequences of the major viral proteins were compared with those of other rabies vaccine virus strains. The RV-97 strain forms a separate phylogenetic branch and seems to be phylogenetically more related to the group of Japanese vaccine strains. It also contains several unique amino acid changes in known immunodominant sites of G and P proteins.