Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

Development and validation of an all-in-one rabies virus Bat-Clade genomic sequencing and host identification protocol

Rabies virus (RABV), remains a significant public health concern, with bat-maintained lineages accounting for all currently documented cases in Brazil. Despite the availability of pharmacological prophylaxis for humans and animals, the high genetic diversity of RABV in diverse natural bat hosts and continued circulation in multiple animals pose challenges for effective surveillance. Here, we developed and validated a novel, rapidly deployable amplicon-based sequencing approach for RABV genomic surveillance. This "all-in-one" protocol integrates whole RABV genome sequencing with host species identification through COI gene amplification and sequencing, addressing the challenges posed by RABV's high genetic diversity and complex transmission dynamics. We assessed the protocol's effectiveness by sequencing 25 near-complete RABV genomes from host species across four distinct families (Bovidae, Equidae, Felidae, and Microchiroptera) obtained from the Rabies Control and Surveillance Program from the Rio Grande do Sul State, Southern Brazil. The method achieved an average genome coverage of 91.4 % at a minimum 5x read depth, with a mean depth coverage of 816x across sequenced genomes. The results demonstrated significant Bat-Clade sublineage diversity, which was classified using the MADDOG RABV lineage system. The protocol successfully identified three bat species (Tadarida brasiliensis, Desmodus rotundus, and Myotis nigricans) among the samples, highlighting its capability for precise host identification. This study presents a powerful tool for high-resolution evaluation of RABV genomic features and host identification, enabling more targeted animal and human health interventions. This new approach has the potential to enhance RABV surveillance capabilities, contributing to more effective rabies control strategies within a One Health framework.

Optimization of pan-lyssavirus LN34 assay for streamlined rabies diagnostics by real-time RT-PCR

Reliable, validated diagnostic tests are critical for rabies control in animals and prevention in people. We present a performance assessment and updates to the LN34 real-time RT-PCR assay for rabies diagnosis in postmortem animal brain samples. In two U.S. laboratories during 2017-2022, routine used of the LN34 assay produced excellent diagnostic sensitivity (99.72-100 %) and specificity (99.99-100 %) compared to the direct fluorescence antibody test (DFA). Almost all (>90 %) DFA indeterminate results caused by non-specific or atypical fluorescence were negative by LN34 testing, representing up to 111 cases where unnecessary post-exposure prophylaxis could be avoided. LN34 assay original primer sequences showed low sensitivity for some rare lyssaviruses. Increased primer concentration combined with new primer formulation showed improved performance for impacted lyssaviruses with no loss in performance across diverse rabies virus variants from clinical samples. The updated LN34 and internal control assays were combined into a single-well LN34 multiplexed (LN34M) format, run at half reagent volumes. The LN34M assay showed similar detection of rabies virus to the singleplexed assay with simplified assay set-up, lower cost, and improved quality controls.

Genomic characterization of a dog-mediated rabies outbreak in El Pedregal, Arequipa, Peru

BACKGROUND

Rabies, a re-emerging zoonosis with the highest known human case fatality rate, has been largely absent from Peru, except for endemic circulation in the Puno region on the Bolivian border and re-emergence in Arequipa City in 2015, where it has persisted. In 2021, an outbreak occurred in the rapidly expanding city of El Pedregal near Arequipa, followed by more cases in 2022 after nearly a year of epidemiological silence. While currently under control, questions persist regarding the origin of the El Pedregal outbreak and implications for maintaining rabies control in Peru.

METHODS

We sequenced 25 dog rabies virus (RABV) genomes from the El Pedregal outbreak (n=11) and Arequipa City (n=14) from 2021-2023 using Nanopore sequencing in Peru. Historical genomes from Puno (n=4, 2010-2012) and Arequipa (n=5, 2015-2019), were sequenced using an Illumina approach in the UK. In total, 34 RABV genomes were generated, including archived and newly obtained samples. The genomes were analyzed phylogenetically to understand the outbreak's context and origins.

RESULTS

Phylogenomic analysis identified two genetic clusters in El Pedregal: 2021 cases stemmed from a single introduction unrelated to Arequipa cases, while the 2022 sequence suggested a new introduction from Arequipa rather than persistence. In relation to canine RABV diversity in Latin America, all new sequences belonged to the new minor clade, Cosmopolitan Am5, sharing relatives from Bolivia, Argentina, and Brazil.

CONCLUSION

Genomic insights into the El Pedregal outbreak revealed multiple introductions over a 2-year window. Eco-epidemiological conditions, including migratory worker patterns, suggest human-mediated movement drove introductions. Despite outbreak containment, El Pedregal remains at risk of dog-mediated rabies due to ongoing circulation in Arequipa, Puno, and Bolivia. Human-mediated movement of dogs presents a major risk for rabies re-emergence in Peru, jeopardizing regional dog-mediated rabies control. Additional sequence data is needed for comprehensive phylogenetic analyses.

Spatial Landscape Structure Influences Cross-Species Transmission in a Rabies-like Virus Model

In this study, we simulated biologically realistic agent-based models over neutral landscapes to examine how spatial structure affects the spread of a rabies-like virus in a two-species system. We built landscapes with varying autocorrelation levels and simulated disease dynamics using different transmission rates for intra- and interspecies spread. The results were analysed based on combinations of spatial landscape structures and transmission rates, focusing on the median number of new reservoir and spillover cases. We found that both spatial landscape structures and viral transmission rates are key factors in determining the number of infected simulated agents and the epidemiological week when the highest number of cases occurs. While isolated habitat patches with elevated carrying capacity pose significant risks for viral transmission, they may also slow the spread compared to more connected patches, depending on the modelled scenario. This study highlights the importance of spatial landscape structure and viral transmission rates in cross-species spread. Our findings have implications for disease control strategies and suggest that future research should also focus on how landscape factors interact with pathogen dynamics, especially in those locations where susceptible agents could be more in contact with pathogens with high transmission rates.

Phylogeography Analysis Reveals Rabies Epidemiology, Evolution, and Transmission in the Philippines

Rabies, caused by rabies virus, is a severe public health problem in the Philippines, where animal rabies epidemiology had been extensively investigated, but little is known about the national epidemiologic situations since 2010. Here, we report a 12-year nationwide animal rabies surveillance with systematic phylogenetic analysis, in which 353 whole genomes of rabies viruses collected from animal rabies cases between 2018 and 2022 were obtained. The phylogenetic and spatial-temporal evolutionary analyses showed that rabies viruses in the Philippines were exclusively classified into the SEA4 subclade within the Asian clade, but forming three major geographically specific lineages. Intra-island spread predominates the rabies transmission in three major island regions, while the inter-island transmission, between major island regions, is very limited, likely due to ocean barriers. Overall, our findings have provided the most comprehensive dataset on the infected animal species, geographic distribution, transmission dynamics, genetic diversity of rabies viruses, and transmission risk factors, thus established a basis to support WOAH-endorsed national control program for dog-mediated rabies in the Philippines.

Typing Arctic and Africa-2 clades of rabies virus using clade-defining single nucleotide polymorphisms

Rabies is a deadly neurotropic, zoonotic disease with a mortality rate of 100% after symptoms appear. Rabies virus (RABV) is the primary cause of rabies disease in humans, and it mainly spreads via dog bites in developing countries. Over the course of RABV evolution, multiple RABV variants, called clades, have emerged. However, our understanding of these clades is limited, as the only method to identify a clade is sequencing, followed by phylogeny. In this study, we have developed a rapid, PCR-based method for typing two RABV clades. We utilised highly conserved amino acid changes specific to the Arctic and Africa-2 clades of the rabies virus (RABV). A single nucleotide substitution from adenine to thymine at position 178 within the nucleoprotein gene was found to be clade-specific in the Arctic clade. Similarly, adenine at position 638 is a distinctive marker for the Africa-2 clade. The assay demonstrated high specificity and offers the added benefit of PCR-based amplification, enabling virus detection even when viral titers are low. The assay can identify the Arctic clade and Africa-2 clade without sequencing and is highly specific and sensitive. Furthermore, this method can be adapted to detect other RABV clades and a wide range of viruses.

Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut

In North America, raccoon rabies virus (RRV) is a public health concern due to its potential for rapid spread, maintenance in wildlife, and impact on human and domesticated animal health. RRV is an endemic zoonotic pathogen throughout the eastern USA. In 1991, an outbreak of RRV in Fairfield County, Connecticut, spread through the state and eventually throughout the Northeast and into Canada. Factors that contribute to, or curb, RRV transmission should be explored and quantified to guide targeted rabies control efforts, including the size and location of buffer zones of vaccinated animals. However, population dynamics and potential underlying determinants of rabies virus diversity and circulation in Connecticut have not been fully studied. In this study, we aim to (i) investigate RRV source-sink dynamics between Connecticut and surrounding states and provinces, (ii) explore the impact of the Connecticut River as a natural barrier to transmission, and (iii) characterize the genomic diversity and transmission dynamics in Connecticut. Using RRV whole-genome sequences collected from various host species between 1990 and 2020, we performed comparative genetic and Bayesian phylodynamic analyses at multiple spatial scales. We analyzed 71 whole-genome sequences from Connecticut, including 21 recent RRV specimens collected at the Connecticut Veterinary Medical Diagnostic Laboratory that we sequenced for this study. Our analyses revealed evidence of RRV incursions over the US-Canada border, including bidirectional spread between Quebec and Vermont. Additionally, we highlighted the importance of Connecticut and New York in seeding RRV transmission in eastern North America, including two introduction events from New York to Connecticut that resulted in sustained local transmission. While RRV transmission does occur across the Housatonic and Connecticut Rivers, we demonstrated the distinct presence of spatial structuring in the phylogenetic trees and characterized the directionality of RRV migration. The significantly higher mean transition rates from locations east to west of the Connecticut River, compared to west to east, may be leveraged in directing interventions to fortify these natural barriers. Ultimately, the findings of these international, regional, and state analyses can inform targeted control programs, vaccination efforts, and enhanced surveillance at borders of key viral sources and sinks.

Spatiotemporal dynamics of rabies virus detected in rabid dogs in Cameroon, 2010-2021

Rabies is a viral zoonosis that causes an estimated 60,000 human deaths each year, mainly in Africa and Asia. The etiological agent of rabies, the Rabies Lyssavirus or Rabies Virus (RABV) has been characterized in dog populations in Cameroon, in previous studies. However, the dynamics of RABV maintenance and propagation in dogs are still to be documented in Cameroon. This study thus, aimed at investigating the spatial and temporal dynamics of RABV variants in Cameroon. Long genomic sequences of about 4893 nucleotides, encompassing the N, P, M and G genes as well as part of the G-L intergenic region (Ψ), were determined from 56 RABV strains recovered from dog populations in Cameroon from 2010 to 2021. Temporal and spatial dynamics of RABV circulation in Cameroon were investigated by Bayesian analyses with the BEAST 1.10.4 package from extended RABV genomic sequences data combined with their collection dates and the geographical coordinates of their sampling areas. This revealed a genetic evolution rate of 3.14 × 10-4 substitutions/site/year among Africa-1a and Africa-2 clades of RABV from Cameroon. The most recent common ancestor (MRCA) of the studied strains of the Africa-1a lineage was estimated to have emerged between 1880 and 1906 (95 % HPD; mean 1894), while that of the strains of the Africa-2 clade had a slightly later estimated origin between 1907 and 1928 (95 % HPD, mean 1918). Overall, phylogeographic analyses suggested RABV spread in Cameroon between sub-national regions. Our data provides substantial support to previous findings from similar epidemiological settings, indicating human mediated movements of infected dogs between distant cities may be a key factor in the maintenance of the enzootic cycle of rabies among dogs in Cameroon.

Identification of clade-defining single nucleotide polymorphisms for improved rabies virus surveillance

Background

Rabies is an ancient disease that remains endemic in many countries. It causes many human deaths annually, predominantly in resource-poor countries. Over evolutionary timelines, several rabies virus (RABV) genotypes have stabilised, forming distinct clades. Extensive studies have been conducted on the origin, occurrence and spread of RABV clades. Single nucleotide polymorphisms (SNPs) distribution across the RABV genome and its clades remains largely unknown, highlighting the need for comprehensive whole-genome analyses.

Methods

We accessed whole genome sequences for RABV from public databases and identified SNPs across the whole genome sequences. Then, we annotated these SNPs using an R script, and these SNPs were categorised into different categories; universal, clade-specific, and clade-defining, based on the frequency of occurrence.

Results

In this study, we present the SNPs occurring in the RABV based on whole genome sequences belonging to 8 clades isolated from 7 different host species likely to harbour dog-related rabies. We classified mutations into several classes based on their location within the genome and assessed the effect of SNP mutations on the viral glycoprotein.

Conclusions

The clade-defining mutations have implications for targeted surveillance and classification of clades. Additionally, we investigated the effects of these mutations on the Glycoprotein of the virus. Our findings contribute to expanding knowledge about RABV clade diversity and evolution, which has significant implications for effectively tracking and combatting RABV transmission.

Complete genome sequence of a vampire bat-related rabies virus obtained by metagenomics from a patient with encephalitis of unknown etiology, French Guiana

We report the complete genome sequence of a rabies virus obtained by direct metagenomics from the cerebellum of a gold panner who died of unknown encephalitis in French Guiana. Phylogenetic analysis exhibited a close genetic relationship with vampire bat-related isolates, confirming the second case of human rabies identified in this territory.

Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus

The molecular clock hypothesis assumes that mutations accumulate on an organism's genome at a constant rate over time, but this assumption does not always hold true. While modelling approaches exist to accommodate deviations from a strict molecular clock, assumptions about rate variation may not fully represent the underlying evolutionary processes. There is considerable variability in rabies virus (RABV) incubation periods, ranging from days to over a year, during which viral replication may be reduced. This prompts the question of whether modelling RABV on a per infection generation basis might be more appropriate. We investigate how variable incubation periods affect root-to-tip divergence under per-unit time and per-generation models of mutation. Additionally, we assess how well these models represent root-to-tip divergence in time-stamped RABV sequences. We find that at low substitution rates (<1 substitution per genome per generation) divergence patterns between these models are difficult to distinguish, while above this threshold differences become apparent across a range of sampling rates. Using a Tanzanian RABV dataset, we calculate the mean substitution rate to be 0.17 substitutions per genome per generation. At RABV's substitution rate, the per-generation substitution model is unlikely to represent rabies evolution substantially differently than the molecular clock model when examining contemporary outbreaks; over enough generations for any divergence to accumulate, extreme incubation periods average out. However, measuring substitution rates per-generation holds potential in applications such as inferring transmission trees and predicting lineage emergence.

Holistic application of the one health approach in the prevention and control of rabies: plausible steps towards achieving the 2030 vision in Africa

Rabies remains a significant public health challenge in Africa, primarily burdening impoverished rural communities, with children and young adults being the most vulnerable. Achieving complete elimination in the continent by 2030 requires a coordinated effort hinged on the One Health concept, external support from international organizations like the World Health Organization (WHO) and the national governments of endemic countries. Here, we reviewed the various socio-economic and ecological factors influencing the spatial distribution and molecular epidemiology of the disease. To mitigate the transmission of rabies on a global scale, and specifically in Africa, we proposed a multi-pronged approach including enhanced access to healthcare resources, cultural sensitization and massive health promotion with efforts geared towards promoting responsible dog and pet ownership and population management, effective monitoring, and mitigation of environmental changes.

Genomic Characterization of a Dog-Mediated Rabies Outbreak in El Pedregal, Arequipa, Peru

Background

Rabies, a re-emerging zoonosis with the highest known human case fatality rate, has been largely absent from Peru, except for endemic circulation in the Puno region on the Bolivian border and re-emergence in Arequipa City in 2015, where it has persisted. In 2021, an outbreak occurred in the rapidly expanding city of El Pedregal near Arequipa, followed by more cases in 2022 after nearly a year of epidemiological silence. While currently under control, questions persist regarding the origin of the El Pedregal outbreak and implications for maintaining rabies control in Peru.

Methods

We sequenced 25 dog rabies virus (RABV) genomes from the El Pedregal outbreak (n=11) and Arequipa City (n=14) from 2021-2023 using Nanopore sequencing in Peru. Historical genomes from Puno (n=4, 2010-2012) and Arequipa (n=5, 2015-2019), were sequenced using an Illumina approach in the UK. In total, 34 RABV genomes were analyzed, including archived and newly obtained samples. The genomes were analyzed phylogenetically to understand the outbreak's context and origins.

Results

Phylogenomic analysis identified two genetic clusters in El Pedregal: 2021 cases stemmed from a single introduction unrelated to Arequipa cases, while the 2022 sequence suggested a new introduction from Arequipa rather than persistence. In relation to canine RABV diversity in Latin America, all new sequences belonged to a new minor clade, Cosmopolitan Am5, sharing relatives from Bolivia, Argentina, and Brazil.

Conclusion

Genomic insights into the El Pedregal outbreak revealed multiple introductions over a 2-year window. Eco-epidemiological conditions, including migratory worker patterns, suggest human-mediated movement drove introductions. Despite outbreak containment, El Pedregal remains at risk of dog-mediated rabies due to ongoing circulation in Arequipa, Puno, and Bolivia. Human-mediated movement of dogs presents a major risk for rabies re-emergence in Peru, jeopardizing regional dog-mediated rabies control. Additional sequence data is needed for comprehensive phylogenetic analyses.

Bat Rabies in the Americas: Is Myotis the Main Ancestral Spreader?

The rabies virus (RABV) is the exclusive lyssavirus affecting both wild and domestic mammalian hosts in the Americas, including humans. Additionally, the Americas stand out as the sole region where bat rabies occurs. While carnivore rabies is being increasingly managed across the region, bats are emerging as significant reservoirs of RABV infection for humans and domestic animals. Knowledge of the bat species maintaining rabies and comprehending cross-species transmission (CST) and host shift processes are pivotal for directing surveillance as well as ecological research involving wildlife reservoir hosts. Prior research indicates that bat RABV CST is influenced by host genetic similarity and geographic overlap, reflecting host adaptation. In this study, we compiled and analyzed a comprehensive nucleoprotein gene dataset representing bat-borne RABV diversity in Argentina and the broader Americas using Bayesian phylogenetics. We examined the association between host genus and geography, finding both factors shaping the global phylogenetic structure. Utilizing a phylogeographic approach, we inferred CST and identified key bat hosts driving transmission. Consistent with CST determinants, we observed monophyletic/paraphyletic clustering of most bat genera in the RABV phylogeny, with stronger CST evidence between host genera of the same family. We further discuss Myotis as a potential ancestral spreader of much of RABV diversity.

Reverse genetic approaches allowing the characterization of the rabies virus street strain belonging to the SEA4 subclade

Rabies virus (RABV) is the causative agent of rabies, a lethal neurological disease in mammals. RABV strains can be classified into fixed strains (laboratory strains) and street strains (field/clinical strains), which have different properties including cell tropism and neuroinvasiveness. RABV Toyohashi strain is a street strain isolated in Japan from an imported case which had been bitten by rabid dog in the Philippines. In order to facilitate molecular studies of RABV, we established a reverse genetics (RG) system for the study of the Toyohashi strain. The recombinant virus was obtained from a cDNA clone of Toyohashi strain and exhibited similar growth efficiency as the original virus in cultured cell lines. Both the original and recombinant strains showed similar pathogenicity with high neuroinvasiveness in mice, and the infected mice developed a long and inconsistent incubation period, which is characteristic of street strains. We also generated a recombinant Toyohashi strain expressing viral phosphoprotein (P protein) fused with the fluorescent protein mCherry, and tracked the intracellular dynamics of the viral P protein using live-cell imaging. The presented reverse genetics system for Toyohashi strain will be a useful tool to explore the fundamental molecular mechanisms of the replication of RABV street strains.

Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya

Rabies, a viral disease that causes lethal encephalitis, kills ≈59,000 persons worldwide annually, despite availability of effective countermeasures. Rabies is endemic in Kenya and is mainly transmitted to humans through bites from rabid domestic dogs. We analyzed 164 brain stems collected from rabid animals in western and eastern Kenya and evaluated the phylogenetic relationships of rabies virus (RABV) from the 2 regions. We also analyzed RABV genomes for potential amino acid changes in the vaccine antigenic sites of nucleoprotein and glycoprotein compared with RABV vaccine strains commonly used in Kenya. We found that RABV genomes from eastern Kenya overwhelmingly clustered with the Africa-1b subclade and RABV from western Kenya clustered with Africa-1a. We noted minimal amino acid variances between the wild and vaccine virus strains. These data confirm minimal viral migration between the 2 regions and that rabies endemicity is the result of limited vaccine coverage rather than limited efficacy.

Reemergence of a Big Brown Bat Lyssavirus rabies Variant in Striped Skunks in Flagstaff, Arizona, USA, 2021-2023

Background: Throughout the Americas, Lyssavirus rabies (RV) perpetuates as multiple variants among bat and mesocarnivore species. Interspecific RV spillover occurs on occasion, but clusters and viral host shifts are rare. The spillover and host shift of a big brown bat (Eptesicus fuscus) RV variant Ef-W1 into mesocarnivores was reported previously on several occasions during 2001-2009 in Flagstaff, Arizona, USA, and controlled through rabies vaccination of target wildlife. During autumn 2021, a new cluster of Ef-W1 RV cases infecting striped skunks (Mephitis mephitis) was detected from United States Department of Agriculture enhanced rabies surveillance in Flagstaff. The number of Ef-W1 RV spillover cases within a short timeframe suggested the potential for transmission between skunks and an emerging host shift. Materials and Methods: Whole and partial RV genomic sequencing was performed to evaluate the phylogenetic relationships of the 2021-2023 Ef-W1 cases infecting striped skunks with earlier outbreaks. Additionally, real-time reverse-transcriptase PCR (rtRT-PCR) was used to opportunistically compare viral RNA loads in brain and salivary gland tissues of naturally infected skunks. Results: Genomic RV sequencing revealed that the origin of the 2021-2023 epizootic of Ef-W1 RV was distinct from the multiple outbreaks detected from 2001-2009. Naturally infected skunks with the Ef-W1 RV showed greater viral RNA loads in the brain, but equivalent viral RNA loads in the mandibular salivary glands, compared to an opportunistic sample of skunks naturally infected with a South-Central skunk RV from northern Colorado, USA. Conclusion: Considering a high risk for onward transmission and spread of the Ef-W1 RV in Flagstaff, public outreach, enhanced rabies surveillance, and control efforts, focused on education, sample characterization, and vaccination, have been ongoing since 2021 to mitigate and prevent the spread and establishment of Ef-W1 RV in mesocarnivores.

Rabies control in Bangladesh and prediction of human rabies cases by 2030: a One Health approach

Background

Bangladesh is making progress toward achieving zero dog-mediated rabies deaths by 2030, a global goal set in 2015.

Methods

Drawing from multiple datasets, including patient immunisation record books and mass dog vaccination (MDV) databases, we conducted a comprehensive analysis between 2011 and 2023 to understand the effectiveness of rabies control programmes and predict human rabies cases in Bangladesh by 2030 using time-series forecasting models. We also compared rabies virus sequences from GenBank in Bangladesh and other South Asian countries.

Findings

The estimated dog population in Bangladesh was determined to be 1,668,140, with an average dog population density of 12.83 dogs/km2 (95% CI 11.14-14.53) and a human-to-dog ratio of 86.70 (95% CI 76.60-96.80). The MDV campaign has led to the vaccination of an average of 21,295 dogs (95% CI 18,654-23,935) per district annually out of an estimated 26,065 dogs (95% CI 22,898-29,230). A declining trend in predicted and observed human rabies cases has been identified, suggesting that Bangladesh is poised to make substantial progress towards achieving the 'Zero by 30' goal, provided the current trajectory continues. The phylogenetic analysis shows that rabies viruses in Bangladesh belong to the Arctic-like-1 group, which differs from those in Bhutan despite sharing a common ancestor.

Interpretation

Bangladesh's One Health approach demonstrated that an increase in MDV and anti-rabies vaccine (ARV) resulted in a decline in the relative risk of human rabies cases, indicating that eliminating dog-mediated human rabies could be achievable.

Funding

The study was supported by the Communicable Disease Control (CDC) Division of the Directorate General of Health Services (DGHS) of the People's Republic of Bangladesh.

Descriptive analyses of knowledge, attitudes, and practices regarding rabies transmission and prevention in rural communities near wildlife reserves in Uganda: a One Health cross-sectional study

BACKGROUND

Despite urban (domestic dog) rabies cycles being the main target for rabies elimination by 2030, sylvatic (wildlife) rabies cycles can act as rabies spillovers especially in settlements contiguous to wildlife reserves. Rural communities next to wildlife reserves are characterized by unique socio-demographic and cultural practices including bat consumption, hunting for bushmeat, and non-vaccination of hunting dogs against rabies among others. This study aimed to compare the knowledge, attitudes, and practices (KAPs) related to rabies transmission and prevention in the three districts of Uganda; (1) Nwoya, neighboring Murchison Falls National Park (MFNP) in the north, (2) Kamwenge neighboring Kibaale National Park (KNP), Queen Elizabeth National Park (QENP) and Katonga Game Reserve (KGR) in the west, and (3) Bukedea, neighboring Pian Upe Game Reserve (PUGR) in the east of Uganda.

METHODS

A community-based cross-sectional survey was conducted in settlements contiguous to these wildlife reserves. Using a semi-structured questionnaire, data were collected from 843 households owning dogs and livestock. Data were collected between the months of January and April 2023. Stratified univariate analyses by district were carried out using the Chi-square test for independence and Fisher's exact test to compare KAPs in the three study districts.

RESULTS

The median age of study participants was 42 years (Q1, Q3 = 30, 52) with males comprising the majority (67%, n = 562). The key findings revealed that participants from the Nwoya district in the north (MFNP) had little knowledge about rabies epidemiology (8.5%, n = 25), only 64% (n = 187) of them knew its signs and symptoms such as a rabid dog presenting with aggressiveness and showed negative attitudes towards prevention measures (15.3%, n = 45). Participants in the Kamwenge district-west (KNP, QENP, and KGR) had little knowledge and negative attitude towards wildlife-human interaction pertaining to rabies transmission and prevention especially those with no or primary level of education (20.9%, n = 27) while participants from Bukedea in the east (PUGR) had remarkedly poor practices towards rabies transmission, prevention, and control (37.8%, n = 114).

CONCLUSIONS

Rabies from sylvatic cycles remains a neglected public health threat in rural communities surrounding national parks and game reserves in Uganda. Our study findings highlight key gaps in knowledge, attitudes, and practices related to rabies transmission and prevention among such communities. Communication and action between veterinary services, wildlife authority, public health teams, social science and community leaders through available community platforms is key in addressing rabies among the sympatric at-risk communities in Uganda.

Mechanism of action of phthalazinone derivatives against rabies virus

Rabies, a viral zoonosis, is responsible for almost 59,000 deaths each year, despite the existence of an effective post-exposure prophylaxis. Indeed, rabies causes acute encephalomyelitis, with a case-fatality rate of 100 % after the onset of neurological clinical signs. Therefore, the development of therapies to inhibit the rabies virus (RABV) is crucial. Here, we identified, from a 30,000 compound library screening, phthalazinone derivative compounds as potent inhibitors of RABV infection and more broadly of Lyssavirus and even Mononegavirales infections. Combining in vitro experiments, structural modelling, in silico docking and in vivo assays, we demonstrated that phthalazinone derivatives display a strong inhibition of lyssaviruses infection by acting directly on the replication complex of the virus, and with noticeable effects in delaying the onset of the clinical signs in our mouse model.

Bayesian modeling of post-vaccination serological data suggests that yearly vaccination of dog aged <2 years old is efficient to stop rabies circulation in Cambodia

Rabies control remains challenging in low and middle-income countries, mostly due to lack of financial resources, rapid turnover of dog populations and poor accessibility to dogs. Rabies is endemic in Cambodia, where no national rabies vaccination program is implemented. The objective of this study was to assess the short and long-term vaccination-induced immunity in Cambodian dogs under field conditions, and to propose optimized vaccination strategies. A cohort of 351 dogs was followed at regular time points following primary vaccination only (PV) or PV plus single booster (BV). Fluorescent antibody virus neutralization test (FAVNT) was implemented to determine the neutralizing antibody titer against rabies and an individual titer ≥0·5 IU/mL indicated protection. Bayesian modeling was used to evaluate the individual duration of protection against rabies and the efficacy of two different vaccination strategies. Overall, 61% of dogs had a protective immunity one year after PV. In dogs receiving a BV, this protective immunity remained for up to one year after the BV in 95% of dogs. According to the best Bayesian model, a PV conferred a protective immunity in 82% of dogs (95% CI: 75-91%) for a mean duration of 4.7 years, and BV induced a lifelong protective immunity. Annual PV of dogs less than one year old and systematic BV solely of dogs vaccinated the year before would allow to achieve the 70% World Health Organization recommended threshold to control rabies circulation in a dog population in three to five years of implementation depending on dog population dynamics. This vaccination strategy would save up to about a third of vaccine doses, reducing cost and time efforts of mass dog vaccination campaigns. These results can contribute to optimize rabies control measures in Cambodia moving towards the global goal of ending human death from dog-mediated rabies by 2030.

Genetic analyses of rabies virus glycoprotein and nucleoprotein gene sequences reveal the emergence of multiple lineages in animals in Arkhangai province, a central region of Mongolia

Genetic characterizations of rabies viruses circulating in carnivore and non-carnivore animals were investigated for the first time in Arkhangai province, a central region of Mongolia. Also, glycoprotein gene of the rabies virus was sequenced for the first time in Mongolia. The nucleotide sequences of the glycoprotein and nucleoprotein genes were analysed, revealing the presence of multiple lineages in this area. Of particular concern are the lineages identified in carnivores, which might emerge to spread throughout Mongolia, further facilitating transboundary transmission to neighbouring countries, including China and Russia.

Are rabid raccoons (Procyon lotor) ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes

North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon (Procyon lotor) in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States. Understanding the spatial movement of RV by raccoon populations is important for monitoring and refining strategies supporting the landscape-level control and local elimination of this lethal zoonosis. We developed a high-throughput genotyping panel for raccoons based on hundreds of microhaplotypes to identify population structure and genetic diversity relevant to rabies management programs. Throughout the eastern United States, we identified hierarchical population genetic structure with clusters that were connected through isolation-by-distance. We also illustrate that this genotyping approach can be used to support real-time management priorities by identifying the geographic origin of a rabid raccoon that was collected in an area of the United States that had been raccoon RV-free for 8 years. The results from this study and the utility of the microhaplotype panel and genotyping method will provide managers with information on raccoon ecology that can be incorporated into future management decisions.

Comparing the genetic typing methods for effective surveillance and rabies control in Georgia

A full nucleoprotein gene sequencing of 68 isolates collected from passive rabies surveillance system in Georgia between 2015 and 2016 identified two distinct dog rabies phylogroups, GEO_V1 and GEO_V2, which both belonged to the cosmopolitan dog clade. GEO_V1 was found throughout the country and was further divided into four sub-phylogroups that overlapped geographically; GEO_V2 was found in the southeast region and was closely related to dog rabies in Azerbaijan. A sequence analysis of the full N gene, partial nucleoprotein gene of N-terminal and C-terminal, and the amplicon sequences of pan-lyssavirus RT-qPCR LN34 showed that all four sequencing approaches provided clear genetic typing results of canine rabies and could further differentiate GEO_V1 and GEO_V2. The phylogenetic analysis results vary and were affected by the length of the sequences used. Amplicon sequencing of the LN34 assay positive samples provided a rapid and cost-effective method for rabies genetic typing, which is important for improving rabies surveillance and canine rabies eradication globally.

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.

Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias

Rabies virus (RABV) is a highly pathogenic virus that causes a fatal disease in humans and other mammals, but the mechanism of its evolution, spread, and spillover remains unknown. In this study, we analyzed the codon usage pattern of 2,018 RABV full-length genome sequences from 79 countries collected between 1931 and 2021 to provide an insight into its molecular evolution and unravel its unknown host-adapted pattern. We found that RABV exhibited a weak codon usage bias, with a preference for the codons ending in A (28.10 ± 0.01) or U (26.43 ± 0.02). Moreover, natural selection plays a major role in shaping the codon usage bias of the RABV. Notably, nearly half of the 18 codons in the virus were best matched to the hosts' most abundant isoacceptor tRNAs, which might account for the wide range of RABV hosts. Furthermore, significant differences were observed in the codon usage patterns of RABV for different host species, suggesting that codon usage bias may be influenced by host-specific factors. In conclusion, our study reveals codon usage patterns of RABV that may help in the development of control strategies and effective vaccines and therapies against this deadly virus.

Evolution and distribution of rabies viruses from a panorama view

Rabies kills more than 59,000 people annually, mainly in developing countries. Previous studies on the evolution and distribution of rabies viruses (RABVs) were scattered. Here, we explore the evolution and distribution of this deadly virus from a novel panorama view. Multiple bioinformatic software tools were employed to analyze the phylogenetic diversity, evolution, spatiotemporal, and distribution of RABVs. The analyses were based on 1,202 qualified full-length genomes of RABVs and numerous literatures. Of the 10 distinct phylogenetic clades of RABV that we identified, more frequent intra- and inter-clade recombination occurs in the sequences of Asian-SEA, Arctic, and Cosmopolitan clades isolated from China, while according to existing sequence information, RABV might originate from bats (posterior probability, PP = 0.75, PP = 0.60 inferred from N and L genes, separately) in North America (PP = 0.57, PP = 0.62 inferred from N and L genes, separately). Due to the difference in evolutionary rate of N (2.22 × 10-4 subs/site/year, 95% HPD 1.99-2.47 × 10-4 subs/site/year) and L genes (1.67 × 10-4 subs/site/year, 95% HPD 1.59-1.74 × 10-4 subs/site/year), the root age was 1,406.6 (95% HPD 1,291.2-1,518.2) and 1,122.7 (95% HPD 1,052.4-1,193.9) inferred from N and L genes, separately. Among other findings, Mephitidae plays an important role in the interspecific transmission and communication of RABV, which we found tends to spread to populations genetically proximate to the host. We also identified amino acids under positive selection in different genes of different clades as well as single nucleotide variation sites important for different lineages. IMPORTANCE Rabies virus is widely distributed all over the world, and wild animals are its largest potential reservoir. Our study offers a panorama view about evolution and distribution of rabies viruses and emphasizes the need to monitor the transmission dynamics of animal rabies.

Uncovering the endemic circulation of rabies in Cambodia

In epidemiology, endemicity characterizes sustained pathogen circulation in a geographical area, which involves a circulation that is not being maintained by external introductions. Because it could potentially shape the design of public health interventions, there is an interest in fully uncovering the endemic pattern of a disease. Here, we use a phylogeographic approach to investigate the endemic signature of rabies virus (RABV) circulation in Cambodia. Cambodia is located in one of the most affected regions by rabies in the world, but RABV circulation between and within Southeast Asian countries remains understudied. Our analyses are based on a new comprehensive data set of 199 RABV genomes collected between 2014 and 2017 as well as previously published Southeast Asian RABV sequences. We show that most Cambodian sequences belong to a distinct clade that has been circulating almost exclusively in Cambodia. Our results thus point towards rabies circulation in Cambodia that does not rely on external introductions. We further characterize within-Cambodia RABV circulation by estimating lineage dispersal metrics that appear to be similar to other settings, and by performing landscape phylogeographic analyses to investigate environmental factors impacting the dispersal dynamic of viral lineages. The latter analyses do not lead to the identification of environmental variables that would be associated with the heterogeneity of viral lineage dispersal velocities, which calls for a better understanding of local dog ecology and further investigations of the potential drivers of RABV spread in the region. Overall, our study illustrates how phylogeographic investigations can be performed to assess and characterize viral endemicity in a context of relatively limited data.

Large-scale phylogenetic analysis reveals genetic diversity and geographic distribution of rabies virus in South-East and South Asia

South-East Asia (SEA) and South Asia (SA) are two important geographic regions with the most severe enzootic rabies in the world. In these regions, phylogenetic analysis of rabies virus (RABV) has been conducted only at a country level; the results obtained from different countries are scattered and unequal, with a non-uniform system to name RABV genotypes. Therefore, it is difficult to undertake origin-tracking and compare inter-country RABV evolution and transmission. To avoid the confusion in understanding and to generate a panoramic picture of RABV genetic diversity, distribution, and transmission in SEA and SA, the present study conducted a systematic phylogenetic analysis by combining all sequences representing 2368 RABV strains submitted to GenBank by 14 rabies endemic SEA and SA countries. The results showed that RABVs circulating in two regions were classified into four major clades and many subclades: the Asia clade is circulating only in SEA, the Indian subcontinent, and Arctic-like clades only in SA, while the Cosmopolitan clade has been detected in both regions. The results also showed a wide range of hosts were infected by divergent RABV subclades, with dogs being the major transmission source. However, wildlife rabies was also found to be an important issue with 6 wild carnivore species identified as potential sources of spillover risk for sylvatic rabies to humans, domestic animals, and other wild animals. Current findings indicate that the two regions have separate virus clades circulating thus indicating the absence of cross-transmission between the regions. The study emphasizes the importance of phylogenetic analysis in the regions using uniform genotyping and naming systems for rabies surveillance, to coordinate actions of member countries to eliminate dog-mediated human rabies by 2030.

Sequencing and Partial Molecular Characterization of BAB-TMP, the Babeș Strain of the Fixed Rabies Virus Adapted for Multiplication in Cell Lines

The rabies virus is a major zoonosis that causes severe nervous disease in humans, leading to paralysis and death. The world's second anti-rabies center was established in 1888 by Victor Babeș, in Bucharest, where an eponymous strain of rabies was isolated and used to develop a method for immunization. The Babeș strain of the rabies virus was used for over 100 years in Romania to produce a rabies vaccine for human use, based on animal nerve tissue, thus having a proven history of prophylactic use. The present study aimed to sequence the whole genome of the Babeș strain and to explore its genetic relationships with other vaccine strains as well as to characterize its relevant molecular traits. After being adapted for multiplication in cell lines and designated BAB-TMP, 99% of the viral genome was sequenced. The overall organization of the genome is similar to that of other rabies vaccine strains. Phylogenetic analysis indicated that the BAB-TMP strain is closely related to the Russian RV-97 vaccine strain, and both seem to have a common ancestor. The nucleoprotein gene of the investigated genome was the most conserved, and the glycoprotein showed several unique amino acid substitutions within the major antigenic sites and linear epitopes.

Genomic Surveillance of Rabies Virus in Georgian Canines

Rabies is a fatal zoonosis that is considered a re-emerging infectious disease. Although rabies remains endemic in canines throughout much of the world, vaccination programs have essentially eliminated dog rabies in the Americas and much of Europe. However, despite the goal of eliminating dog rabies in the European Union by 2020, sporadic cases of dog rabies still occur in Eastern Europe, including Georgia. To assess the genetic diversity of the strains recently circulating in Georgia, we sequenced seventy-eight RABV-positive samples from the brain tissues of rabid dogs and jackals using Illumina short-read sequencing of total RNA shotgun libraries. Seventy-seven RABV genomes were successfully assembled and annotated, with seventy-four of them reaching the coding-complete status. Phylogenetic analyses of the nucleoprotein (N) and attachment glycoprotein (G) genes placed all the assembled genomes into the Cosmopolitan clade, consistent with the Georgian origin of the samples. An amino acid alignment of the G glycoprotein ectodomain identified twelve different sequences for this domain among the samples. Only one of the ectodomain groups contained a residue change in an antigenic site, an R264H change in the G5 antigenic site. Three isolates were cultured, and these were found to be efficiently neutralized by the human monoclonal antibody A6. Overall, our data show that recently circulating RABV isolates from Georgian canines are predominantly closely related phylogroup I viruses of the Cosmopolitan clade. Current human rabies vaccines should offer protection against infection by Georgian canine RABVs. The genomes have been deposited in GenBank (accessions: OQ603609-OQ603685).

Biodiversity indices and Random Forests reveal the potential for striped skunk (Mephitis mephitis) fecal microbial communities to function as a biomarker for oral rabies vaccination

Wildlife disease surveillance and monitoring poses unique challenges when assessing rates of population vaccination, immunity, or infection prevalence. Non-invasively detected biomarkers can help reduce risk to both animal and field personnel during wildlife disease management activities. In this study, we investigated the utility of fecal microbiome data collected from captive striped skunks (Mephitis mephitis) in predicting rabies virus vaccination and infection status. We sequenced the hypervariable region 4 (V4) of the bacterial 16S gene and estimated alpha and beta diversity across timepoints in three groups of skunks: vaccination then rabies virus infection, sham vaccination then rabies virus infection, and rabies virus infected without vaccination. Alpha diversity did not differ among treatment groups but beta diversity between treatments was statistically significant. The phyla Firmicutes and Proteobacteria were dominant among all samples. Using Random Forests, we identified operational taxonomic units (OTUs) that greatly influenced classification of fecal samples into treatment groups. Each of these OTUs was correlated with fecal volatile organic compounds detected from the samples for companion treatment groups in another study. This research is the first to highlight striped skunk microbiome biodiversity as a vaccination biomarker which pushes the frontier on alternative methods for surveillance and monitoring of vaccination and disease in wildlife populations.

Integrating full and partial genome sequences to decipher the global spread of canine rabies virus

Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to investigate historical pathogen spread between countries. Its application to rabies virus (RABV) yields precise dating and confident estimates of its geographic dispersal. By using full genomes and partial sequences, we reduce both geographic and genetic biases that often hinder studies that focus on specific genes. Our pipeline reveals an emergence of the present canine-mediated RABV between years 1301 and 1403 and reveals regional introductions over a 700-year period. This geographic reconstruction enables us to locate episodes of human-mediated introductions of RABV and examine the role that European colonization played in its spread. Our approach enables phylogeographic analysis of large and genetically diverse data sets for many viral pathogens.

Whole genome sequencing and phylogenetic characterisation of rabies virus strains from Moldova and north-eastern Romania

BACKGROUND

Rabies is the oldest fatal zoonotic disease recognised as a neglected tropical disease and is caused by an RNA virus belonging to the genus Lyssavirus, family Rhabdoviridae.

METHODOLOGY/PRINCIPAL FINDINGS

A deep molecular analysis was conducted on full-length nucleoprotein (N) gene and whole genome sequences of rabies virus from 37 animal brain samples collected between 2012 and 2017 to study the circulation of rabies virus (RABV) variants. The overall aim was to better understand their distribution in Moldova and north-eastern Romania. Both Sanger and high throughput sequencing on Ion Torrent and Illumina platforms were performed. Phylogenetic analysis of the RABV sequences from both Moldova and Romania revealed that all the samples (irrespective of the year of isolation and the species) belonged to a single phylogenetic group: north-eastern Europe (NEE), clustering into three assigned lineages: RO#5, RO#6 and RO#7.

CONCLUSIONS/SIGNIFICANCE

High throughput sequencing of RABV samples from domestic and wild animals was performed for the first time for both countries, providing new insights into virus evolution and epidemiology in this less studied region, expanding our understanding of the disease.

Update on laboratory data of animal rabies at the Centre Pasteur of Cameroon from 2014 to 2021

Rabies is a worldwide zoonotic disease mainly transmitted to humans by an infected dog bite. Despite the endemicity of rabies in dogs and few documented cases in Cameroon, there is still not enough data on frequency of rabies cases in animals. The present study aims to update data on the circulation of rabies in animals screened at the Centre Pasteur of Cameroon (CPC) between 2014 and 2021. The detection of rabies in animals was based on passive surveillance. Animal rabies cases were confirmed on brain biopsies using fluorescent antibody test and SYBR green based real-time RT-PCR for negative results confirmation. The total nucleoprotein (N) gene of animal-derived RABV isolated were amplified by hemi nested RT-PCR and subjected to phylogenetic analyses. From 2014 to 2021, a total of 92 animals including 86 dogs (93.5%), 3 cats, 2 pigs and 1 chiropteran were screened for rabies at the CPC. From the 86 dog sampled, 62.3% (54/86) were tested positive for rabies and 1 out of 3 cat samples was also tested positive. The PEP demand was very high (59,371) during the study period. Phylogenetic analyses assigned all 15 studied isolates successfully sequenced to the Africa-1a lineage belonging to the Cosmopolitan clade. The study highlights the frequent circulation of rabies in Cameroon and the role of dogs and cat as main reservoir and vector of rabies.

Diverse DNA virus genomes identified in fecal samples of Mexican free-tailed bats (Tadarida brasiliensis) captured in Chiricahua Mountains of southeast Arizona (USA)

Bats (order Chiroptera) are some of the most abundant mammals on earth and their species ecology strongly influences zoonotic potential. While substantial research has been conducted on bat-associated viruses, particularly on those that can cause disease in humans and/or livestock, globally, limited research has focused on endemic bats in the USA. The southwest region of the US is of particular interest because of its high diversity of bat species. We identified 39 single-stranded DNA virus genomes in the feces of Mexican free-tailed bats (Tadarida brasiliensis) sampled in the Rucker Canyon (Chiricahua Mountains) of southeast Arizona (USA). Twenty-eight of these belong to the virus families Circoviridae (n = 6), Genomoviridae (n = 17), and Microviridae (n = 5). Eleven viruses cluster with other unclassified cressdnaviruses. Most of the viruses identified represent new species. Further research on identification of novel bat-associated cressdnaviruses and microviruses is needed to provide greater insights regarding their co-evolution and ecology relative to bats.

Pseudotyped Viruses for Lyssavirus

Lyssaviruses, which belong to the family Rhabdoviridae, are enveloped and bullet-shaped ssRNA viruses with genetic diversity. All members of Lyssavirus genus are known to infect warm-blooded animals and cause the fatal disease rabies. The rabies virus (RABV) in lyssavirus is the major pathogen to cause fatal rabies. The pseudotyped RABV is constructed to study the biological functions of G protein and evaluation of anti-RABV products including vaccine-induced antisera, rabies immunoglobulins (RIG), neutralizing mAbs, and other antiviral inhibitors. In this chapter, we focus on RABV as a representative and describe the construction of RABV G protein bearing pseudotyped virus and its applications. Other non-RABV lyssaviruses are also included.

Rabies Virus Populations in Humans and Mice Show Minor Inter-Host Variability within Various Central Nervous System Regions and Peripheral Tissues

Rabies virus (RABV) has a broad host range and infects multiple cell types throughout the infection cycle. Next-generation sequencing (NGS) and minor variant analysis are powerful tools for studying virus populations within specific hosts and tissues, leading to novel insights into the mechanisms of host-switching and key factors for infecting specific cell types. In this study we investigated RABV populations and minor variants in both original (non-passaged) samples and in vitro-passaged isolates of various CNS regions (hippocampus, medulla oblongata and spinal cord) of a fatal human rabies case, and of multiple CNS and non-CNS tissues of experimentally infected mice. No differences in virus populations were detected between the human CNS regions, and only one non-synonymous single nucleotide polymorphism (SNP) was detected in the fifth in vitro passage of virus isolated from the spinal cord. However, the appearance of this SNP shows the importance of sequencing newly passaged virus stocks before further use. Similarly, we did not detect apparent differences in virus populations isolated from different CNS and non-CNS tissues of experimentally infected mice. Sequencing of viruses obtained from pharyngeal swab and salivary gland proved difficult, and we propose methods for improving sampling.

Quantifying intra- and inter-species contact rates at supplemental feeding sites in Ethiopia to inform rabies maintenance potential of multiple host species

Rabies, a multi-host pathogen responsible for the loss of roughly 59,000 human lives each year worldwide, continues to impose a significant burden of disease despite control efforts, especially in Ethiopia. However, how species other than dogs contribute to rabies transmission throughout Ethiopia remains largely unknown. In this study, we quantified interactions among wildlife species in Ethiopia with the greatest potential for contributing to rabies maintenance. We observed wildlife at supplemental scavenging sites across multiple landscape types and quantified transmission potential. More specifically, we used camera trap data to quantify species abundance, species distribution, and intra- and inter-species contacts per trapping night over time and by location. We derived a mathematical expression for the basic reproductive number (R₀ ) based on within- and between-species contract rates by applying the next generation method to the susceptible, exposed, infectious, removed model. We calculated R₀ for transmission within each species and between each pair of species using camera trap data in order to identify pairwise interactions that contributed the most to transmission in an ecological community. We estimated which species, or species pairs, could maintain transmission ( R 0 > 1 ${R_0} &gt; 1$ ) and which species, or species pairs, had contact rates too low for maintenance ( R 0 < 1 ${R_0} &lt; 1$ ). Our results identified multiple urban carnivores as candidate species for rabies maintenance throughout Ethiopia, with hyenas exhibiting the greatest risk for rabies maintenance through intra-species transmission. Hyenas and cats had the greatest risk for rabies maintenance through inter-species transmission. Urban and peri-urban sites posed the greatest risk for rabies transmission. The night-time hours presented the greatest risk for a contact event that could result in rabies transmission. Overall, both intra- and inter-species contacts posed risk for rabies maintenance. Our results can be used to target future studies and inform population management decisions.

Genetic Diversity, Evolutionary Dynamics, and Pathogenicity of Ferret Badger Rabies Virus Variants in Mainland China, 2008–2018

In contrast to dog-associated human rabies cases decline year by year due to the rabies vaccination coverage rates increase in China, ferret badger (FB, Melogale moschata)-associated human rabies cases emerged in the 1990s, and are now an increasingly recognized problem in southeast China. To investigate epidemiology, temporal evolution dynamics, transmission characterization, and pathogenicity of FB-associated rabies viruses (RABVs), from 2008 to 2018, we collected 3,622 FB brain samples in Jiangxi and Zhejiang Province, and detected 112 RABV isolates. Four FB-related lineages were identified by phylogenetic analysis (lineages A–D), the estimated Times to Most Recent Common Ancestor were 1941, 1990, 1937, and 1997 for lineages A–D, respectively. Furthermore, although no FB-associated human rabies case has been reported there apart from Wuyuan area, FB-RABV isolates are mainly distributed in Jiangxi Province. Pathogenicity of FB-RABVs was assessed using peripheral inoculation in mice and in beagles with masseter muscles, mortality-rates ranging from 20 to 100% in mice and 0 to 20% in beagles in the groups infected with the various isolates. Screening of sera from humans with FB bites and no post-exposure prophylaxis to rabies revealed that five of nine were positive for neutralizing antibodies of RABV. All the results above indicated that FB-RABV variants caused a lesser pathogenicity in mice, beagles, and even humans. Vaccination in mice suggests that inactivated vaccine or recombinant subunit vaccine products can be used to control FB-associated rabies, however, oral vaccines for stray dogs and wildlife need to be developed and licensed in China urgently.

Divergent Rabies Virus Variant of Probable Bat Origin in 2 Gray Foxes, New Mexico, USA

In the Western Hemisphere, bat-associated rabies viruses (RABVs) have established independent transmission cycles in multiple mammal hosts, forming genetically distinct lineages. In New Mexico, USA, skunks, bats, and gray foxes are rabies reservoir hosts and represent a public health risk because of encounters with humans. During 2015 and 2019, two previously undescribed RABVs were detected in 2 gray foxes (Urocyon cinereoargenteus) in Lincoln County, New Mexico. Phylogenetic analysis of the nucleoprotein gene indicated that the isolates are a novel RABV variant. These 2 cases probably represent repeated spillover events from an unknown bat reservoir to gray foxes. Molecular analysis of rabies cases across New Mexico identified that other cross-species transmission events were the result of viral variants previously known to be enzootic to New Mexico. Despite a robust rabies public health surveillance system in the United States, advances in testing and surveillance techniques continue to identify previously unrecognized zoonotic pathogens.

Elimination of human rabies in Goa, India through an integrated One Health approach

Dog-mediated rabies kills tens of thousands of people each year in India, representing one third of the estimated global rabies burden. Whilst the World Health Organization (WHO), World Organization for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) have set a target for global dog-mediated human rabies elimination by 2030, examples of large-scale dog vaccination programs demonstrating elimination remain limited in Africa and Asia. We describe the development of a data-driven rabies elimination program from 2013 to 2019 in Goa State, India, culminating in human rabies elimination and a 92% reduction in monthly canine rabies cases. Smartphone technology enabled systematic spatial direction of remote teams to vaccinate over 95,000 dogs at 70% vaccination coverage, and rabies education teams to reach 150,000 children annually. An estimated 2249 disability-adjusted life years (DALYs) were averted over the program period at 526 USD per DALY, making the intervention 'very cost-effective' by WHO definitions. This One Health program demonstrates that human rabies elimination is achievable at the state level in India.

Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses.

The Comparison of Full G and N Gene Sequences From Turkish Rabies Virus Field Strains

The rabies infection is a zoonotic viral disease in humans and is spread by both wild and domestic carnivores. This study aimed to molecularly characterize the field strains of the rabies virus circulating in Turkey between 2013 and 2020. Brain samples obtained from 16 infected animals (8 cattle, one donkey, three foxes, three dogs, and one marten) were tested. Full nucleoprotein (N) and glycoprotein (G) gene sequences were used to determine the genetic and antigenic characteristics of the rabies virus field strains. The phylogenetic analyses revealed that the 16 field strains identified in Turkey belonged to the Cosmopolitan lineage.

The Importance of Accurate Host Species Identification in the Framework of Rabies Surveillance, Control and Elimination

Accurate host identification is paramount to understand disease epidemiology and to apply appropriate control measures. This is especially important for multi-host pathogens such as the rabies virus, a major and almost invariably fatal zoonosis that has mobilized unanimous engagement at an international level towards the final goal of zero human deaths due to canine rabies. Currently, diagnostic laboratories implement a standardized identification using taxonomic keys. However, this method is challenged by high and undiscovered biodiversity, decomposition of carcasses and subjective misevaluation, as has been attested to by findings from a cohort of 242 archived specimens collected across Sub-Saharan Africa and submitted for rabies diagnosis. We applied two simple and cheap methods targeting the Cytochrome b and Cytochrome c oxidase subunit I to confirm the initial classification. We therefore suggest prioritizing a standardized protocol that includes, as a first step, the implementation of taxonomic keys at a family or subfamily level, followed by the molecular characterization of the host species.

Monoclonal antibodies against rabies: current uses in prophylaxis and in therapy

Rabies is a severe viral infection that causes an acute encephalomyelitis, which presents a case fatality of nearly 100% after the manifestation of neurological clinical signs. Rabies can be efficiently prevented with post-exposure prophylaxis (PEP), composed of vaccines and anti-rabies immunoglobulins (RIGs); however, no treatment exists for symptomatic rabies. The PEP protocol faces access and implementation obstacles in resource-limited settings, which could be partially overcome by substituting RIGs for monoclonal antibodies (mAbs). mAbs offer lower production costs, consistent supply availability, long-term storage/stability, and an improved safety profile. Here we summarize the key features of the different available mAbs against rabies, focusing on their application in PEP and highlighting their potential in a novel therapeutic approach.