Molecular epidemiology of enzootic rabies in California

Rabies Virus Variants Detected from Cougar (Puma concolor) in Mexico 2000–2021

In 2019, the World Health Organization (WHO) and the Pan-American Health Organization (PAHO) recognized Mexico as a country free of human rabies transmitted by dogs. Nevertheless, the sylvatic cycle remains as a public health concern in the country. Although cougars (Puma concolor) are not reservoirs of any rabies virus variant (RVV), these felines could act as vectors at the top of the food chain, and their relationships with other organisms must be considered important for the regulatory effect on their prey’s populations. In this study, genetic and antigenic characterization was performed on all cougar rabies cases diagnosed at the Rabies Laboratory Network of the Ministry of Health (RLNMH) in Mexico from 2000 to 2021. Samples from other species, a skunk, a horse (Equus caballus) (attacked by a cougar), and a gray fox (Urocyon cineroargenteus), were included as reference. Rabies cases in cougars were restricted to two Northern states of Mexico (Sonora and Chihuahua). Five out of six samples of cougars were RVV7 (Arizona gray fox RVV) and one from Sonora was RVV1. Interestingly, there is no evidence of RVV1 in dogs in the Northern states since the 1990s but skunk species now harbor this RVV1 in this region of the country.

Phylogeography of the current rabies viruses in Indonesia

Rabies is a major fatal zoonotic disease in Indonesia. This study was conducted to determine the recent dynamics of rabies virus (RABV) in various areas and animal species throughout Indonesia. A total of 27 brain samples collected from rabid animals of various species in Bali, Sumatra, Kalimantan, Sulawesi, Java, and Flores in 2008 to 2010 were investigated. The cDNA of the nucleoprotein gene from each sample was generated and amplified by one-step reverse transcription-PCR, after which the products were sequenced and analyzed. The symmetric substitution model of a Bayesian stochastic search variable selection extension of the discrete phylogeographic model of the social network was applied in BEAST ver. 1.7.5 software. The spatial dispersal was visualized in Cartographica using Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. We demonstrated inter-island introduction and reintroduction, and dog was found to be the only source of infection of other animals. Ancestors of Indonesian RABVs originated in Java and its descendants were transmitted to Kalimantan, then further to Sumatra, Flores, and Bali. The Flores descendent was subsequently transmitted to Sulawesi and back to Kalimantan. The viruses found in various animal species were transmitted by the dog.

Lyssaviruses and bats: emergence and zoonotic threat

The continued detection of zoonotic viral infections in bats has led to the microbial fauna of these mammals being studied at a greater level than ever before. Whilst numerous pathogens have been discovered in bat species, infection with lyssaviruses is of particular significance from a zoonotic perspective as, where human infection has been reported, it is invariably fatal. Here we review the detection of lyssaviruses within different bat species and overview what is understood regarding their maintenance and transmission following both experimental and natural infection. We discuss the relevance of these pathogens as zoonotic agents and the threat of newly discovered viruses to human populations.

Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission

One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST) events is the need to analyze a densely sampled outbreak using deep sequencing in order to measure the amount of mutation occurring on a small time scale. In 2009, the California Department of Public Health reported a dramatic increase (350) in the number of gray foxes infected with a rabies virus variant for which striped skunks serve as a reservoir host in Humboldt County. To better understand the evolution of rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt outbreak. For each sample, approximately 11 kb of the 12 kb genome was amplified and sequenced using the Illumina platform. Average coverage was 17,448 and this allowed characterization of the rabies virus population present in each sample at unprecedented depths. Phylogenetic analysis of the consensus sequence data demonstrated that samples clustered according to date (1995 vs. 2009) and geographic location (northern vs. southern). A single amino acid change in the G protein distinguished a subset of northern foxes from a haplotype present in both foxes and skunks, suggesting this mutation may have played a role in the observed increased transmission among foxes in this region. Deep-sequencing data indicated that many genetic changes associated with the CST event occurred prior to 2009 since several nonsynonymous mutations that were present in the consensus sequences of skunk and fox rabies samples obtained from 20032010 were present at the sub-consensus level (as rare variants in the viral population) in skunk and fox samples from 1995. These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change.

Understanding the role of genetic variants within a viral population is a necessary step toward predicting and treating emerging infectious diseases. The high mutation rate of RNA viruses increases the ability of these viruses to adapt to diverse hosts and cause new human and zoonotic diseases. The genetic diversity of a viral population within a host may allow the virus to adapt to a diverse array of selective pressures and enable cross-species transmission events. In 2009 a large outbreak of rabies in Northern California involved a skunk rabies virus variant that efficiently transmitted within a population of gray foxes, suggesting possible adaptation to a novel host species. To better understand the evolution of rabies virus that enabled this host jump, we applied deep-sequencing analysis to rabies virus samples from the outbreak. Deep-sequencing data indicated that many of the genetic changes associated with host jump occurred prior to 2009, and these mutations were present at very low frequencies in viral populations from samples dating back to 1995. These results suggest deep sequencing is useful for characterization of viral populations, and may provide insight to ancestral genomes and role of rare variants in viral emergence.

Bat Rabies

The lyssaviruses are a diverse group of viruses capable of causing rabies, which is an invariably fatal encephalitic disease in both humans and animals. Currently, the lyssavirus genus consists of 12 species with 11 of these distinct species having been isolated from bats. The basis for the apparent geographical segregation of bat lyssavirus infection between the Old and New World is poorly understood. In the New World species of insectivorous, frugivorous, and hematophagous bats, all represent important reservoirs of rabies virus. In contrast, rabies virus has never been detected in Old World bat populations, despite being endemic in terrestrial mammals. Instead, both insectivorous and frugivorous bat species across the Old World appear to act as reservoirs for the non-rabies lyssaviruses. In this chapter, we describe the association of the different lyssaviruses with different bat species across the world, classifying bat species by their feeding behavior.

Epidemiology

This chapter provides an overview of the global epidemiology of rabies, focusing on major changes over the past half-century and highlighting recent discoveries. This chapter also describes the natural and iatrogenic routes of transmission, as well as the risk and necessary actions for the prevention of rabies following an exposure. It reviews the methods for rabies diagnosis and the biologics for prevention, in addition to differences in rabies prophylaxis recommendations among advisory committees. The chapter also considers epidemiology and trends in global human rabies and the dynamics of the corresponding mammalian reservoir hosts for each area. Furthermore, it considers the phylogenetics of rabies virus, other lyssaviruses, and specific rabies virus variants in the context of regional rabies and the potential for novel emergences. Special attention is paid to developed countries, where existing surveillance and diagnostic infrastructure have provided detailed insights into the nature changing patterns in rabies epidemiology-patterns expected to be increasingly relevant to other less-developed nations based on current trends. Special attention is afforded to canine rabies, as dogs remain responsible for over 99% of all human exposures to the virus, including the methods and problems associated with intentional and unintentional movement of dogs at national and international levels. Finally, the chapter discusses the economic burden of rabies in terms of human and infrastructure support.

Novel monoclonal antibodies that bind to wild and fixed rabies virus strains

Ten monoclonal antibodies (MAbs) against rabies virus, including IgG3κ, IgG2aκ, IgMκ, and an IgG2bκ isotype, were produced and characterized using neutralization, ELISA, immunodot-blot, and immunofluorescence assays. MAb 8D11, which recognized rabies virus glycoprotein, was found to neutralize rabies virus in vitro. When submitted to an immunofluorescence assay, seven MAbs showed different reactivity against 35 Brazilian rabies virus isolates. Three MAbs (LIA 02, 3E6, and 9C7) only failed to recognize one or two virus isolates, whereas MAb 6H8 was found to be reactive against all virus isolates tested. MAbs were also evaluated for their immunoreactivity against fixed rabies virus strains present in human and veterinary commercial vaccines. MAbs LIA 02, 6H8, and 9C7 reacted against all vaccine strains, while the remaining MAbs recognized at least 76% of vaccine strains tested. This research provides a set of MAbs with potential application for improving existing or developing new diagnostic tests and immunoassays.

Computational analysis suggests that lyssavirus glycoprotein gene plays a minor role in viral adaptation

The Lyssavirus glycoprotein (G) is a membrane protein responsible for virus entry and protective immune responses. To explore possible roles of the glycoprotein in host shift or adaptation of Lyssavirus, we retrieved 53 full-length glycoprotein gene sequences from NCBI GenBank. The sequences were from different host isolates over a period of 70 years in 21 countries. Computational analyses detected 1 recombinant (AY987478, a dog isolate of CHAND03, genotype 1 in India) with incongruent phylogenetic support. No recombination was detected when AY98748 was excluded in the analyses. We applied different selection models to identify selection pressure on the glycoprotein gene. One codon at amino acid residual 483 was found to be under weak positive selection with marginal probability of 95% by using the maximum likelihood method. We found no significant evidence of positive selection on any site of the glycoprotein gene when the putative recombinant AY987478 was excluded. The computational analyses suggest that the G gene has been under purifying selection and that the evolution of the G gene may not play a significant role in Lyssavirus adaptation.

Molecular characterization of the full-length genome of a rabies virus isolate from India

Rabies is an important public health problem in South East Asia, with cases in this part of the world contributing to about 70% of the global burden. A large number of rabies cases occur in India, however, there is no organized system of surveillance and hence there is a lack of reliable data. Moreover, comprehensive molecular epidemiological studies have not been performed on Indian virus isolates. In this study, we determined the complete nucleotide and deduced amino acid sequence of a primary isolate of rabies virus obtained from the brain of an infected patient. Comparison of the genomic sequence with those of the ten fully sequenced rabies strains available in GenBank showed nucleotide homology ranging from 97% with AY956319 to 81% with AY705373. Amino acid homology of nucleoprotein ranged from 99.7% with AY352493 to 92% with DQ875051. In case of the glycoprotein gene, the homology ranged from 98.8% with AY956319 to 87.2 % with AY705373. An extensive nucleoprotein, glycoprotein, and full-length genome-based phylogenetic analysis was performed along with sequences available from the GenBank. Phylogenetic analysis of the complete genome sequence indicated that this isolate exhibited close homology with the ex Indian strain AY956319.

Transmission dynamics of rabies virus in Thailand: implications for disease control

Background

In Thailand, rabies remains a neglected disease with authorities continuing to rely on human death statistics while ignoring the financial burden resulting from an enormous increase in post-exposure prophylaxis. Past attempts to conduct a mass dog vaccination and sterilization program have been limited to Bangkok city and have not been successful. We have used molecular epidemiology to define geographic localization of rabies virus phylogroups and their pattern of spread in Thailand.

Methods

We analyzed 239 nucleoprotein gene sequences from animal and human brain samples collected from all over Thailand between 1998 and 2002. We then reconstructed a phylogenetic tree correlating these data with geographical information.

Results

All sequences formed a monophyletic tree of 2 distinct phylogroups, TH1 and TH2. Three subgroups were identified in the TH1 subgroup and were distributed in the middle region of the country. Eight subgroups of TH2 viruses were identified widely distributed throughout the country overlapping the TH1 territory. There was a correlation between human-dependent transportation routes and the distribution of virus.

Conclusion

Inter-regional migration paths of the viruses might be correlated with translocation of dogs associated with humans. Interconnecting factors between human socioeconomic and population density might determine the transmission dynamics of virus in a rural-to-urban polarity. The presence of 2 or more rabies virus groups in a location might be indicative of a gene flow, reflecting a translocation of dogs within such region and adjacent areas. Different approaches may be required for rabies control based on the homo- or heterogeneity of the virus. Areas containing homogeneous virus populations should be targeted first. Control of dog movement associated with humans is essential.

Spatial dynamics and molecular ecology of North American rabies

Rabies, caused by a single-stranded RNA virus, is arguably the most important viral zoonotic disease worldwide. Although endemic throughout many regions for millennia, rabies is also undergoing epidemic expansion, often quite rapid, among wildlife populations across regions of Europe and North America. A current rabies epizootic in North America is largely attributable to the accidental introduction of a particularly well-adapted virus variant into a naive raccoon population along the Virginia/West Virginia border in the mid-1970s. We have used the extant database on the spatial and temporal occurrence of rabid raccoons across the eastern United States to construct predictive models of disease spread and have tied patterns of emergence to local environmental variables, genetic heterogeneity, and host specificity. Rabies will continue to be a remarkable model system for exploring basic issues in the temporal and spatial dynamics of expanding infectious diseases and examining ties between disease population ecology and evolutionary genetics at both micro- and macro-evolutionary time scales.

Bat rabies, Texas, 1996-2000

Bats submitted to the Texas Department of Health (1996–2000) were speciated and tested for rabies virus antigen by direct immunofluorescence microscopy. Antigenic analysis of rabies virus–positive specimens was performed with monoclonal antibodies against the nucleoprotein of the virus; atypical or unexpected results were confirmed by genetic analysis of nucleoprotein sequence.

Characterization of rabies virus isolates in Bolivia

In Latin America, rabies is still an important public health problem. Canine rabies, and wild animal rabies, especially transmitted by hematofagous and insectivorous bats, has become an emerging problem in the countries of this region. We received 363 samples with a laboratory-confirmed rabies diagnosis from Bolivia during l997-2001. From these, we could obtain 222 rabies virus isolates by intra-cerebral inoculation in mice. By antigenic characterization we could identify 147 isolates as variant 1, 2 isolates as variant 2, 3 isolates as variant 3, and 1 isolate as variant 5. Phylogenetic analysis of 84 isolates established that they segregated in 3 different branches, corresponding to 3 genetic variants, 78 isolates corresponding to antigenic variant 1 segregated in the same lineage as the antigenic variant 5, 2 isolates corresponding to antigenic variant 2 segregated in another lineage, and 3 isolates from antigenic variant 3 segregated in a different lineage.The genetic variant that mainly circulates in Bolivia is maintained in a cycle whose main reservoir are dogs, but it is not possible to discard the presence of other cycles, in which different species of bats or other wild mammals could be participating.

Genetic characterization of rabies field isolates from Thailand

We sequenced 512 nucleotides in two variable regions of the N gene of 23 rabies isolates from the northeastern part of Thailand by direct sequencing of PCR-amplified products. The sequencing data revealed two new lineages in these rabies isolates. Based on the results of this study together with the findings of our earlier study, the rabies isolates in Thailand were divided into two genogroups, designated as T1 and T2, which were predominantly localized in the northern and northeastern areas, respectively. Each of these two genogroups consisted of four lineages. There was a correlation between these eight lineages and the geographical origins of the isolates. Two lineages belonging to the T2 genogroup from the northeastern area of Thailand were newly identified in this study. The isolates in both genogroups were also prevalent in the central area of Thailand. Each lineage in the T1 and T2 genogroups was found independently in dogs in the upper and lower southern areas of Thailand, respectively. These genetic data and the historical background suggest that rabies viruses belonging to the T2 genogroups were prevalent many years ago in the central and northeastern areas of Thailand and were later transferred to the lower southern parts of Thailand.

Molecular epidemiology of rabies epizootics in Colombia: evidence for human and dog rabies associated with bats

Three urban rabies outbreaks have been reported in Colombia during the last two decades, one of these is occurring in the Caribbean Region (northern Colombia), while the other two occurred almost simultaneously in Arauca (eastern Colombia) and in the Central Region and ended in 1997. In order to derive phylogenetic relationships between rabies viruses isolated in these three areas, 902 nt cDNA fragments encoding the cytoplasmic domain of protein G and a fragment of protein L were obtained by RT-PCR. These amplicons contained the G-L intergenic region and were sequenced to draw phylogenetic trees. Phylogenetic analysis showed three distinct groups of viruses in the study sample. Colombian genetic variant I viruses were isolated in both Arauca and the Central Region. These viruses are apparently extinct in Colombia. Colombian genetic variant II viruses were isolated in the Caribbean Region and are still being transmitted in that area. The third group of viruses consists of viruses isolated from two insectivorous bats, three domestic dogs and a human. According to sequence analysis, the data here indicate that the isolates in this third group are bat rabies virus variants. This finding is the first that associates bats to rabies in Colombian dogs and humans, showing an unsuspected vector threatening animal and public health.

Discrimination between dog-related and vampire bat-related rabies viruses in Brazil by strain-specific reverse transcriptase-polymerase chain reaction and restriction fragment length polymorphism analysis

BACKGROUND

There is a geographical overlap between the two main rabies epidemiological cycles maintained by dogs and vampire bats in Latin America. The geographical and temporal coincidence of rabies outbreaks of respective origins is not unusual in rural areas of Latin America. These circumstances make it difficult to discriminate the intraspecies and interspecies transmission pathways of rabies.

OBJECTIVE

This study was conducted to develop techniques to discriminate dog-related and vampire bat-related rabies virus isolates (DRRV and VRRV, respectively) in Brazil.

STUDY DESIGN

The 1396 nucleotides of the nucleoprotein gene of a total of 27 DRRV and VRRV were sequenced. Strain-specific (SS) primers were developed based on these sequences. Forty-nine rabies virus strains isolated from animals and humans in several parts of Brazil were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) with SS primers. These rabies viruses were also amplified by RT-PCR with general rabies primers and the PCR products were cut by three restriction enzymes, Blp I, Bsu36 I and BspE I.

RESULTS

All the DRRV and VRRV were distinguished by RT-PCR with SS primers. The PCR products obtained from DRRV were cut at one site by Blp I, but not by Bsu36 I. The PCR products obtained from VRRV were cut at one or two sites by Bsu36 I, but not by Blp I. Blp I and Bsu36 I clearly discriminated DRRV and VRRV in restriction fragment length polymorphysim (RFLP) assays. The results of SS RT-PCR and RFLP were consistent.

CONCLUSION

SS RT-PCR and RFLP assays have been developed for determining the origins of rabies virus isolates in Brazil. These assays are simple and rapid, and will be useful for identifying the rabies virus reservoirs of field isolates in Brazil, especially when used together.

A molecular epidemiological study of Australian bat lyssavirus

The genetic diversity of Australian bat lyssavirus (ABL) was investigated by comparing 24 ABL isolate glycoprotein (G) gene nucleotide sequences with those of 37 lyssaviruses representing Lyssavirus genotypes 1-6. Phylogenetic analyses indicated that ABL forms a monophyletic group separate from other lyssaviruses. This group differentiates into two clades: one associated with Pteropus (flying fox) species, the other with the insectivorous bat Saccolaimus flaviventris. Calculation of percentage nucleotide identities between isolates of the two clades revealed up to 18.7 % nucleotide sequence divergence between the two ABL variants. These observations suggest that ABL is a separate lyssavirus species with a similar epidemiology to chiropteran rabies virus (RV), where two distinct ABL variants co-exist in Australia in bat species with dissimilar ecology. Analyses of selection pressures in ABL G gene sequences provided some evidence of weak positive selection within the endodomain at amino acids 499 and 501, although in general the dominant evolutionary process observed was purifying selection. This intimates that, in nature, isolates of ABL, like those of RV, are subject to relatively strong selective constraints, suggesting a stability of host species, cell tropisms and ecological conditions.

Host switching in Lyssavirus history from the Chiroptera to the Carnivora orders

Lyssaviruses are unsegmented RNA viruses causing rabies. Their vectors belong to the Carnivora and Chiroptera orders. We studied 36 carnivoran and 17 chiropteran lyssaviruses representing the main genotypes and variants. We compared their genes encoding the surface glycoprotein, which is responsible for receptor recognition and membrane fusion. The glycoprotein is the main protecting antigen and bears virulence determinants. Point mutation is the main force in lyssavirus evolution, as Sawyer's test and phylogenetic analysis showed no evidence of recombination. Tests of neutrality indicated a neutral model of evolution, also supported by globally high ratios of synonymous substitutions (d(S)) to nonsynonymous substitutions (d(N)) (>7). Relative-rate tests suggested similar rates of evolution for all lyssavirus lineages. Therefore, the absence of recombination and similar evolutionary rates make phylogeny-based conclusions reliable. Phylogenetic reconstruction strongly supported the hypothesis that host switching occurred in the history of lyssaviruses. Indeed, lyssaviruses evolved in chiropters long before the emergence of carnivoran rabies, very likely following spillovers from bats. Using dated isolates, the average rate of evolution was estimated to be roughly 4.3 x 10(-4) d(S)/site/year. Consequently, the emergence of carnivoran rabies from chiropteran lyssaviruses was determined to have occurred 888 to 1,459 years ago. Glycoprotein segments accumulating more d(N) than d(S) were distinctly detected in carnivoran and chiropteran lyssaviruses. They may have contributed to the adaptation of the virus to the two distinct mammal orders. In carnivoran lyssaviruses they overlapped the main antigenic sites, II and III, whereas in chiropteran lyssaviruses they were located in regions of unknown functions.