We describe a statistical framework for reconstructing the sequence of transmission events between observed cases of an endemic infectious disease using genetic, temporal and spatial information. Previous approaches to reconstructing transmission trees have assumed all infections in the study area originated from a single introduction and that a large fraction of cases were observed. There are as yet no approaches appropriate for endemic situations in which a disease is already well established in a host population and in which there may be multiple origins of infection, or that can enumerate unobserved infections missing from the sample. Our proposed framework addresses these shortcomings, enabling reconstruction of partially observed transmission trees and estimating the number of cases missing from the sample. Analyses of simulated datasets show the method to be accurate in identifying direct transmissions, while introductions and transmissions via one or more unsampled intermediate cases could be identified at high to moderate levels of case detection. When applied to partial genome sequences of rabies virus sampled from an endemic region of South Africa, our method reveals several distinct transmission cycles with little contact between them, and direct transmission over long distances suggesting significant anthropogenic influence in the movement of infected dogs.

BackgroundMokola virus (MOKV) is a rabies-related lyssavirus and appears to be exclusive to the African continent. Only 24 cases of MOKV, which includes two human cases, have been reported since its identification in 1968. MOKV has an unknown reservoir host and current commercial vaccines do not confer protection against MOKV.ResultsWe describe three new isolations of MOKV from domestic cats in South Africa. Two cases were retrospectively identified from 2012 and an additional one in 2014.ConclusionsThese cases emphasize the generally poor surveillance for rabies-related lyssaviruses and our inadequate comprehension of the epidemiology and ecology of Mokola lyssavirus per se.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-017-0948-0) contains supplementary material, which is available to authorized users.

<span style="font-family: arial,helvetica;">Rapid immunodiagnostic test kit was evaluated against a selection of isolates of lyssavirus genotypes occurring in Africa. The test was carried out in parallel comparison with the fluorescent antibody test (FAT) and isolates representing previously established phylogenetic groups from each genotype were included. The specificity of the rapid immunodiagnostic test compared favourably with the FAT and was found to detect all representatives of genotypes 1, 2, 3 and 4 in brain samples of either field cases or suckling mouse brain inoculates.</span>

Strong quantum correlations in matter are responsible for some of the most extraordinary properties of materials, from magnetism to high-temperature superconductivity, but their integration in quantum devices requires a strong, coherent coupling with photons, which still represents a formidable technical challenge in solid state systems. In cavity quantum electrodynamics, quantum gases such as Bose-Einstein condensates or lattice gases have been strongly coupled with light. However, neither Fermionic quantum matter, comparable to electrons in solids, nor atomic systems with controlled interactions, have thus far been strongly coupled with photons. Here we report on the strong coupling of a quantumdegenerate unitary Fermi gas with light in a high finesse cavity. We map out the spectrum of the coupled system and observe well resolved dressed states, resulting from the strong coupling of cavity photons with each spin component of the gas. We investigate spinbalanced and spin-polarized gases and find quantitative agreement with ab initio calculation describing light-matter interaction. Our system offers complete and simultaneous control of atom-atom and atom-photon interactions in the quantum degenerate regime, opening a wide range of perspectives for quantum simulation.

Canine rabies has been enzootic in the dog population of the KwaZulu-Natal province of South Africa since the mid-1970s and has been associated with high rates of human exposures and frequent transmissions to other domestic animal species. Several decades of control efforts, consisting primarily of mass vaccination programs, failed to sufficiently curb rabies in this province. For meaningful progression toward better control and elimination, the factors contributing to the persistence of this disease need to be elucidated and addressed. This paper reports evaluated observations from survey records captured through a cross-sectional observational study regarding owned canine populations in this South African province. We used logistic regression modeling to predict variables associated with risk of nonvaccination of rabies in owned dogs. The study indicated that husbandry practices, rabies knowledge, geographical area/location, and the ages of dogs were important factors associated with the risk of nonvaccination. High population turnover, together with large free roaming dog populations, compromised the levels of vaccination achieved and contributed to the persistence of dog rabies in the province. Dog owners in this study also reported that they were more likely to present their dogs for vaccination when the vaccines were free of charge (52%) and less than a kilometer from their homes (91%). It has been suggested that effective dog rabies control requires 70% or more of the dog population to be vaccinated. Our data showed that this figure was not reached in the surveyed dog population.

BackgroundCanine rabies has been enzootic in the dog population of the KwaZulu-Natal province of South Africa since the mid-1970s and has been associated with high rates of human exposures and frequent transmissions to other domestic animal species. Several decades of control efforts, consisting primarily of mass vaccination programs, have previously failed to sufficiently curb rabies in the province. Despite this history of canine rabies, the target canine population has never been extensively studied or quantified. For efficient and effective vaccination campaign planning, the target population must be evaluated and understood. This study reports evaluated observations from survey records captured through a cross sectional observational study regarding canine populations and dog owners in rabies enzootic KwaZulu-Natal province, South Africa. The objective of this study was to aid government veterinary services in their current and ongoing efforts to eliminate canine rabies in the province by gaining information about the size and distribution of the owned dog population.ResultsThirty-eight percent of the households owned one or more dogs, with rural areas surveyed containing a significantly higher number of owned dogs than urban areas. The mean dog/person ratio for this study was 1:7.7 (range 1:5.4–1:31). The provincial sex ratio was 1.5:1 male to female, with the percentages for male dogs across the communities ranging from 53 to 61.5%. The age structure of this dog population indicates a high turnover rate. Dogs were kept mostly for guarding homes or livestock. Eighty-four percent of dogs had received a rabies vaccine at some point in their lifetime, almost all during a rabies campaign.ConclusionsThe study indicates the majority of owned dogs can be handled by at least one member of the household, thus can be made readily accessible for rabies vaccination during a campaign. Characteristics of owned dogs in the province were similar to those studied in other African countries; however, there were remarkable differences in age, sex and husbandry practices compared to dogs in eastern or northern Africa. These geographical differences lend credence to the theory that canine populations are heterogeneous; therefore, target populations should be evaluated prior to intervention planning.

Lagos bat virus (LBV), one of the 17 accepted viral species of the Lyssavirus genus, was the first rabies-related virus described in 1956. This virus is endemic to the African continent and is rarely encountered. There are currently four lineages, although the observed genetic diversity exceeds existing lyssavirus species demarcation criteria. Several exposures to rabid bats infected with LBV have been reported; however, no known human cases have been reported to date. This review provides the history of LBV and summarizes previous knowledge as well as new detections. Genetic diversity, pathogenesis and prevention are re-evaluated and discussed.

In the resource-poor settings where dog rabies remains endemic, the demonstration of a need to divert scarce funds towards exhaustive surveillance activities is no easy task. Here, we investigate a recent case of human rabies in South Africa, which generated much public interest and wide media coverage. One of the factors contributing to the hype was an uncertainty about the geographical origin of the infection. This provided an opportunity to highlight the importance of increased regional surveillance and basic phylogeographical analyses in rabies control and elimination strategies. Our aim was to elucidate the origins of the virus responsible for this case, as the patient was from a well-vaccinated area that had been free from dog rabies cases for many years. The phylogeographical techniques that we applied would also be most useful in any end-stage infectious disease control programme, specifically in verifying the source of novel cases in order to rapidly respond towards maintaining the integrity of disease-free areas. The most likely origin of our case was shown to be from outside the disease-free area and indeed from outside the country of South Africa. We conclude that phylogeographical techniques can provide rapid and statistically rigorous answers to epidemiologically pertinent questions that impact on disease control strategies and resource allocation, but this will require coordinated regional surveillance practices.