Genetic diversity of rabies virus in different host species and geographic regions of Zambia and Zimbabwe

One Health Lens on Rabies: Human-Bat Interactions and Genomic Insights of Rabies Virus in Rural Lilongwe, Malawi

Rabies, a fatal zoonotic disease, affects humans, domestic animals, and wildlife predominantly in Africa, Asia, and Latin America. In Malawi, rabies virus (RABV) is primarily transmitted by infected dogs, impacting humans and cattle. Lyssavirus has also been documented in insectivorous bats. A community survey near bat roosts assessed knowledge, attitudes, and practices regarding bat-borne zoonoses. Bat samples were tested for lyssavirus using RT-PCR, and RABV genomes from humans and domestic animals were sequenced and analysed phylogenetically. The survey revealed that 50% of participants consumed bat meat, and 47% reported bats entering their homes. Reduced bat presence indoors significantly lowered contact risk (aOR: 0.075, p = 0.021). All 23 bat samples tested negative for lyssavirus. Malawian RABV genomes, 11,801 nucleotides long, belonged to the Africa 1b lineage, showing >95% similarity with GenBank sequences. Phylogenetic analysis indicated close clustering with strains from Tanzania, Zimbabwe, and South Africa. Human and cattle strains shared 99% and 92% amino acid similarity with dog strains, respectively, with conserved critical sites and unique substitutions across all five RABV genes. Frequent human-bat interactions pose zoonotic risks. While no lyssavirus was detected in bats, ongoing surveillance is crucial. This first comprehensive genome analysis of Malawian RABVs highlights their regional transmission and signifies the need for regional collaboration in rabies control, community education, and further study of genetic adaptations.

Integrating one health strategies for rabies control: Insights from Jackal-mediated human rabies in Northeast India

INTRODUCTION

Rabies is an ancient, lethal zoonotic disease caused by viruses of the genus Lyssavirus, affecting a wide variety of mammals. Though domestic dogs are the main vectors of rabies transmission to humans, other domestic and wildlife species also contribute to the spread of the disease in endemic regions like India. This report presents a case of human rabies following jackal exposure in India, along with the molecular characterization of the rabies virus (RABV) from both the jackal and the affected human patient.

METHODS

RNA was extracted from brain tissue samples of a suspected rabid jackal and a 42-year-old male patient who died following exposure to the jackal. The extracted RNA was subjected to rabies-specific real-time PCR, followed by whole genome sequencing using the Illumina MiSeq platform. Phylogenetic analysis was performed using these sequences, along with other publicly available RABV whole genome sequences, with the IQ-TREE2 software and the General Time Reversible (GTR+F+I+G4) model.

RESULTS

Real-time PCR confirmed the presence of rabies viral RNA in both the jackal and human brain samples. Whole genome sequencing yielded complete sequences of RABV from the jackal brain, and partial sequences from the human brain sample. These sequences belonged to the Arctic AL1a lineage, and were closely related to RABV strains found in dogs and other animals in India.

CONCLUSION

This case underscores the potential for wildlife, such as jackals, to contribute significantly to human rabies cases and highlights the need for comprehensive surveillance and control measures to effectively combat rabies in endemic regions like India.

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.

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.

Current status and molecular epidemiology of rabies virus from different hosts and regions in Malawi

Although rabies is endemic in Malawi, there have been no studies in which rabies virus was systematically investigated and characterized in multiple animal hosts in that country. In order to provide molecular epidemiological data on rabies virus in Malawi, 683 suspected rabies case reports from 2008 to 2021 were examined, and 46 (dog = 40, cow = 5, and cat = 1) viable rabies-positive brain samples archived at the Central Veterinary Laboratory (CVL), Lilongwe, Malawi, were analyzed genetically. The results showed an increase in the submission of brain samples from 2008 to 2010, with the highest number of submissions observed in 2020. Of the 683 case reports analyzed for the period under review, 38.1% (260/683) (CI: 34.44 - 41.84) were confirmed by direct fluorescent antibody test. Among the confirmed cases, 65.4% (170/260) (CI: 59.23 - 71.09) were canine rabies. Further, phylogenetic analysis revealed that sequences from different animal hosts clustered together within the Africa 1b lineage, suggesting that the strains circulating in livestock are similar to those in domestic dogs. This finding supports the hypothesis that canine rabies is spilling over to livestock and emphasizes the need for further studies to provide data for effective control of rabies in Malawi.

Isolation, discrimination, and molecular detection of Listeria species from slaughtered cattle in Namwala District, Zambia

BACKGROUND

The food industry is increasingly becoming more scrutinized, given the frequency and intensity with which zoonotic diseases are being reported. Pathogen tracking has become more applicable with regards food safety. It is in this regard that the present study was formulated to track Listeria species. in freshly slaughtered cattle carcasses by utilizing standard and molecular biological techniques.

METHODS

A cross-sectional study design was conducted from March to December 2020 with 200 samples being equally collected in the rainy and dry seasons. A total of 180 and 20 swabs were aseptically collected from carcasses and the environment respectively. Samples were first subjected to pre-enrichment in half-strength Fraser broth followed by enrichment in full strength Fraser broth and subsequent plating on Listeria agar. Listeria growth characteristics were identified up to species level based on their morphological and biochemical characteristics. Further, molecular detection and phylogenetic analysis was conducted. Quantitative proportionate survey data were analyzed using Stata Version 15 software to estimate crude prevalence taking into account complex design at abattoir level. Factors associated with contamination were characterized using logistic regression. Sequences were analyzed using, Genetyyx version 12 and phylogenetic Mega.

RESULTS

Of the 200 samples, 19 were positive for Listeria species identified as L.innocua 14/19 (73.7%) and L. monocytogenes 5/19 (26.3%). All isolates were from freshly slaughtered carcasses, and none from environment. Siginificant differences in contamination levels were observed based on season: rainy season yielded 14 (73.6%) whilst the dry season 5 (26.3%). The L. monocytogenes strains showed a high degree of homogeneity on phylogenetic analysis and clustered based on abattoir. Seasonality was identified as a major determinant influencing contamination based on the final logistic regression model.

CONCLUSION

This study found evidence of L. monocytogenes contamination on traditionally raised beef carcasses across various abattoirs surveyed. The failure to find Listeria contamination on the abattoir environment may to a greater extent intimate cattle carccases as primary sources of contamination. However, a more comprerehnsive study incorporating different geographical regions is needed to conclusively ascertain these present findings.

Rabies in the Tropics

Purpose of Review

Rabies is an ancient yet still neglected tropical disease (NTD). This review focuses upon highlights of recent research and peer-reviewed communications on the underestimated tropical burden of disease and its management due to the complicated dynamics of virulent viral species, diverse mammalian reservoirs, and tens of millions of exposed humans and animals - and how laboratory-based surveillance at each level informs upon pathogen spread and risks of transmission, for targeted prevention and control.

Recent Findings

While both human and rabies animal cases in enzootic areas over the past 5 years were reported to PAHO/WHO and OIE by member countries, still there is a huge gap between these "official" data and the need for enhanced surveillance efforts to meet global program goals.

Summary

A review of the complex aspects of rabies perpetuation in human, domestic animal, and wildlife communities, coupled with a high fatality rate despite the existence of efficacious biologics (but no therapeutics), warrants the need for a One Health approach toward detection via improved laboratory-based surveillance, with focal management at the viral source. More effective methods to prevent the spread of rabies from enzootic to free zones are needed.

Immunization Coverage and Antibody Retention against Rabies in Domestic Dogs in Lusaka District, Zambia

Rabies remains endemic in Zambia. Despite conducting canine vaccinations in Lusaka district, the vaccination coverage and actual seropositivity in the dog population in Lusaka district are rarely evaluated. This study estimated the seropositivity-based immunization coverage in the owned dog population in Lusaka district using the expanded program on immunization cluster survey method. The time-series trend of neutralizing antibodies against rabies in vaccinated dogs was also evaluated. Of 366 dogs in 200 dog-owning households in Lusaka district, blood samples were collected successfully from 251 dogs. In the sampled dogs, 42.2% (106/251) had an antibody titer ≥0.5 IU/mL. When the 115 dogs whose blood was not collected were assumed to be seronegative, the minimum immunization coverage in Lusaka district's owned dog population was estimated at 29.0% (95% confidence interval: 22.4-35.5). It was also found that a single vaccination with certified vaccines is capable of inducing protective levels of antibodies. In contrast, higher antibody titers were observed in multiple-vaccinated dogs than in single-vaccinated dogs, coupled with the observation of a decline in antibody titer over time. These results suggest the importance of continuous booster immunization to maintain herd immunity and provide useful information to plan mass vaccination against rabies in Zambia.

Domestic dog demographics and estimates of canine vaccination coverage in a rural area of Zambia for the elimination of rabies

Background

An estimated 75% or more of the human rabies cases in Africa occur in rural settings, which underscores the importance of rabies control in these areas. Understanding dog demographics can help design strategies for rabies control and plan and conduct canine mass vaccination campaigns effectively in African countries.

Methodology/Principal findings

A cross-sectional survey was conducted to investigate domestic dog demographics in Kalambabakali, in the rural Mazabuka District of Zambia. The population of ownerless dogs and the total achievable vaccination coverage among the total dog population was estimated using the capture-recapture-based Bayesian model by conducting a canine mass vaccination campaign. This study revealed that 29% of the domestic dog population was under one year old, and 57.7% of those were under three months old and thus were not eligible for the canine rabies vaccination in Zambia. The population growth was estimated at 15% per annum based on the cross-sectional household survey. The population of ownerless dogs was estimated to be small, with an ownerless-to-owned-dog ratio of 0.01–0.06 in the target zones. The achieved overall vaccination coverage from the first mass vaccination was estimated 19.8–51.6%. This low coverage was principally attributed to the owners’ lack of information, unavailability, and dog-handling difficulties. The follow-up mass vaccination campaign achieved an overall coverage of 54.8–76.2%.

Conclusions/Significance

This paper indicates the potential for controlling canine rabies through mass vaccination in rural Zambia. Rabies education and responsible dog ownership are required to achieve high and sustainable vaccination coverage. Our findings also propose including puppies below three months old in the target population for rabies vaccination and emphasize that securing an annual enforcement of canine mass vaccination that reaches 70% coverage in the dog population is necessary to maintain protective herd immunity.

Because dogs are the main transmitter of rabies to humans, controlling rabies in dogs is essential for preventing rabies in humans. Canine vaccination is well-known as the most effective measure for controlling rabies in dogs. Understanding the demographics and dynamics of dog populations is important when designing efficient canine vaccination strategies. Furthermore, protective herd immunity in the total dog population should be attained through the vaccination of owned dogs since ownerless dogs are not usually covered in such campaigns. This study investigated domestic dog demographics and estimated the number of ownerless dogs to finally estimate the vaccination coverage among the overall dog population achievable through a mass vaccination campaign in a rural setting in Mazabuka District, Zambia. The target domestic dog population was young, and population growth was estimated at 15% annually based on the cross-sectional survey. The vaccination coverage attained by providing free canine mass vaccination campaigns was eventually estimated as 54.8–76.2% in the overall dog population, coupled with the estimate that the ownerless dog population was quite small. Our findings emphasize the necessity of conducting annual canine mass vaccinations, including puppies, that target 70% coverage in the dog population to maintain protective herd immunity.

A rabies virus vectored severe fever with thrombocytopenia syndrome (SFTS) bivalent candidate vaccine confers protective immune responses in mice

The Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne hemorrhagic zoonotic disease, which is potentially fatal in human with mortality rates ranging from 16.2%-32%. The rabies virus (RABV) LBNSE vector expressing foreign antigens have shown considerable promise as vaccines against viral diseases, which is effective and safe. In the present study, we generated a recombinant RABV rLBNSE-Gn expressing a SFTSV glycoprotein Gn by reverse genetic technology to control rabies and SFTS in animals. An extra insertion of Gn gene did not impact replication of the recombinant virus rLBNSE-Gn in NA and BHK-21 cells compared to the parent rLBNSE strain. The SFTSV Gn gene together with RABV N and G genes were efficiently expressed in rLBNSE-infected Vero cells by immunostaining and immune blots. A single dose of 10⁷ FFU of the rLBNSE-Gn intramuscularly inoculated in BALB/c mice induced rapid and robust humoral responses against both RABV and SFTSV without any signs of disease or weight loss. Compared to the rLBNSE and DMEM groups, the extra Gn expression contributed to the recruitments and/or activations of the dendritic cells and B cells from inguinal lymph nodes of BALB/c mice vaccinated with rLBNSE-Gn. The protective efficacy of rLBNSE-Gn against SFTSV in C57BL/6 mice was evaluated, and the virus loading in the spleens reduced to 10 TCID₅₀/mg at 7 days post SFTSV infections, which indicated that the rLBNSE-Gn conferred efficacious protective immune responses from SFTSV in C57BL/6 mice. All the mice immunization with rLBNSE-Gn and rLBNSE survived after a lethal RABV challenge, suggesting a 100 % protection from RABV. Therefore, the rLBNSE-Gn would be a promising bivalent candidate vaccine against SFTS and rabies in animals.

Molecular characterization of rabies viruses from two western provinces of the Democratic Republic of the Congo (2008-2017)

Although rabies is enzootic in the Democratic Republic of the Congo, there is very little molecular epidemiological information about the viruses circulating in animals. In this study, a fragment of the rabies virus (RABV) nucleoprotein gene was amplified and sequenced from 21 animal brain samples collected in two western provinces of the country between 2008 and 2017. The samples tested were from cat (n = 1), dog (n = 17), goat (n = 2), and sheep (n = 1). Phylogenetic analysis revealed that the sequences generated were highly similar to each other and belonged to lineage Africa 1b clustering with a single sample identified in a canine in the Republic of Congo in 2014. This is the first molecular epidemiological study of RABV in the DRC and the data generated will assist authorities in the development of effective control strategies for rabies in the country.

Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept

Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.