In Africa, bat‐borne zoonoses emerged in the past few decades resulting in large outbreaks or just sporadic spillovers. In addition, hundreds of more viruses are described without any information on zoonotic potential. We discuss important characteristics of bats including bat biology, evolution, distribution and ecology that not only make them unique among most mammals but also contribute to their potential as viral reservoirs. The detection of a virus in bats does not imply that spillover will occur and several biological, ecological and anthropogenic factors play a role in such an event. We summarize and critically analyse the current knowledge on African bats as reservoirs for corona‐, filo‐, paramyxo‐ and lyssaviruses. We highlight that important information on epidemiology, bat biology and ecology is often not available to make informed decisions on zoonotic spillover potential. Even if knowledge gaps exist, it is still important to recognize the role of bats in zoonotic disease outbreaks and implement mitigation strategies to prevent exposure to infectious agents including working safely with bats. Equally important is the crucial role of bats in various ecosystem services. This necessitates a multidisciplinary One Health approach to close knowledge gaps and ensure the development of responsible mitigation strategies to not only minimize risk of infection but also ensure conservation of the species.

Eleven different lyssavirus species, four of which occur on the African continent, are presently recognized. These viruses cause rabies, the burden of which is highest in the developing world, where routine laboratory diagnosis is often not available. From an epidemiological and control perspective, it is necessary that diagnostic methods detect the diversity of lyssaviruses present in different regions of the world. A published and widely used heminested reverse transcription-PCR (hnRT-PCR) was evaluated for its ability to detect a panel of diverse African lyssaviruses. Due to the limitations experienced for this assay, an alternative hnRT-PCR was developed. The new assay was found to be accurate and sensitive in the detection of African lyssavirus RNA in a variety of clinical specimens. The assay was further adapted to a real-time PCR platform to allow rapid, one-step, quantitative, and single-probe detection, and an internal control for the verification of sample preparation was included. The limit of detection of the real-time PCR assay was 10 RNA copies per reaction, with inter- and intra-assay variability below 4%. Subsequently, in demonstrating utility, both assays were successfully applied to antemortem rabies diagnosis in humans. We believe that the quantitative real-time PCR assay could find application as a routine confirmatory test for rabies diagnosis in the future and that it will serve as a valuable research tool in the biology of African lyssaviruses. Alternatively, the hnRT-PCR assay can be used in laboratories that do not have access to expensive real-time PCR equipment for sensitive diagnosis of lyssaviruses.

We detected 3 lyssaviruses in insectivorous bats sampled in South Africa during 2003–2018. We used phylogenetic analysis to identify Duvenhage lyssavirus and a potentially new lyssavirus, provisionally named Matlo bat lyssavirus, that is related to West Caucasian bat virus. These new detections highlight that much about lyssaviruses remains unknown.

Mokola virus (MOKV) appears to be exclusive to Africa. Although the first isolates were from Nigeria and other Congo basin countries, all reports over the past 20 years have been from southern Africa. Previous phylogenetic studies analyzed few isolates or used partial gene sequence for analysis since limited sequence information is available for MOKV and the isolates were distributed among various laboratories. The complete nucleoprotein, phosphoprotein, matrix and glycoprotein genes of 18 MOKV isolates in various laboratories were sequenced either using partial or full genome sequencing using pyrosequencing and a phylogenetic analysis was undertaken. The results indicated that MOKV isolates from the Republic of South Africa, Zimbabwe, Central African Republic and Nigeria clustered according to geographic origin irrespective of the genes used for phylogenetic analysis, similar to that observed with Lagos bat virus. A Bayesian Markov-Chain-Monte-Carlo- (MCMC) analysis revealed the age of the most recent common ancestor (MRCA) of MOKV to be between 279 and 2034 years depending on the genes used. Generally, all MOKV isolates showed a similar pattern at the amino acid sites considered influential for viral properties. According to the World Health Organization, rabies is considered both a neglected zoonotic and tropical disease. Among all the lyssavirus species known to exist today, Mokola virus is unique and appears to be exclusive to Africa. In contrast to all other known virus species in the genus Lyssavirus of the family Rhabdoviridae, its reservoir host has not been identified yet. As only limited sequence information is available, this study significantly contributes to the understanding of the genetic diversity and relatedness of Mokola viruses. In a collective approach, the complete nucleoprotein, phosphoprotein, matrix, and glycoprotein genes of all Mokola viruses isolated to date were sequenced in various rabies laboratories across the world. A phylogenetic analysis was undertaken and the most recent common ancestor was determined. Subsequently, results were linked to epidemiological background data. We also conducted a comparative study of distinct antigenic sites considered influential for viral properties within those genes.

Bats (order Chiroptera) are the principal reservoir host for 14 of the 16 officially recognised lyssavirus species. Rabies virus is the only lyssavirus that is well established in terrestrial carnivores (worldwide), as well as bats (but only in the Americas). The other bat lyssaviruses occur only outside the Americas. They have a distinct geographical distribution and association with specific bat species, with limited cross-species transmission to other animals and humans, resulting in deadend infections. The nucleoprotein gene is well conserved between all lyssavirus species. Therefore, gold-standard diagnostic techniques detect all lyssaviruses but do not discriminate between viral species. Lyssaviruses are divided into at least three phylogroups, based on their immunogenic and phylogenic properties. Owing to the diversity of glycoproteins among phylogroups, rabies vaccines and immunoglobulins only provide protection against phylogroup I, excluding several of the bat lyssaviruses. Africa hosts a high diversity of lyssaviruses, leading to the hypothesis that this region was the site of emergence; however, this has been challenged by more recent phylogenetic analysis, suggesting a Palearctic origin. Serological evidence indicates a more widespread and even higher diversity of lyssaviruses in bats, suggesting that the incidence of known lyssaviruses is underestimated and several new lyssavirus species are yet to be discovered. Most bats are, however, not able to transmit the virus and therefore pose a low risk to human and animal populations. Los murciélagos (orden de los quirópteros) son el principal reservorio de 14 de las 16 especies de Lyssavirus oficialmente descritas. El virus de la rabia es el único lisavirus que está bien implantado a la vez en carnívoros terrestres (en todo el mundo) y en murciélagos (solamente en las Américas). Ninguno de los demás lisavirus de los murciélagos está presente en las Américas. Cada uno presenta características muy definidas en cuanto a su distribución geográfica y su asociación con una u otra especie de murciélago, con escasa transmisión a otras especies animales o al ser humano, lo que se traduce en infecciones cerradas (dead-end). El gen de la nucleoproteína está bien conservado en todas las especies de lisavirus. De ahí que las técnicas de diagnóstico de referencia permitan detectar todos los lisavirus, pero no discriminar entre una u otra especie vírica. En función de sus propiedades inmunógenas y filogenéticas, los lisavirus se dividen en al menos tres filogrupos. Dada la gran variabilidad que presentan las gluproteínas entre esos distintos filogrupos, las vacunas e inmunoglobulinas antirrábicas solo confieren protección contra el filogrupo I, con exclusión de varios lisavirus del murciélago. África alberga muchos y diversos lisavirus, lo que permitió conjeturar que esta región es su lugar de origen, hipótesis que sin embargo parecen desmentir análisis filogenéticos más recientes, que apuntan a un origen paleártico. Los datos serológicos indican una mayor extensión e incluso mayor diversidad de los lisavirus en los murciélagos, lo que lleva a pensar que la incidencia de los lisavirus conocidos está subestimada y que aún quedan por descubrir varias nuevas especies. La mayoría de los murciélagos, sin embargo, son incapaces de transmitir el virus, por lo que entrañan poco riesgo para las poblaciones humanas y animales. Les chauves-souris (ordre des Chiroptères) sont les principaux hôtes réservoirs pour 14 des 16 espèces de lyssavirus officiellement inventoriées. Parmi les lyssavirus, seul le virus de la rage affecte aussi bien les carnivores terrestres (distribution mondiale) que les chauves-souris (uniquement dans les Amériques). Les autres lyssavirus des chauves-souris circulent dans d’autres régions mais pas sur le continent américain. Leur distribution géographique est liée à celle des espèces hôtes de chiroptères, avec des cas limités de transmission interespèces à d’autres animaux ou à l’homme, non suivis d’une adaptation à ces hôtes et aboutissant donc à une impasse écologique. Le gène de la nucléoprotéine est présent dans chacune des espèces de lyssavirus. Par conséquent, les techniques de référence détectent tous les lyssavirus sans les différencier par espèces. Le genre des lyssavirus comporte trois groupes phylogénétiques qui se distinguent par leurs propriétés immunogènes et phylogéniques. En raison de la diversité des glycoprotéines au sein de ces groupes, la protection conférée par les vaccins et les immunoglobulines couvre uniquement le groupe phylogénétique I, ce qui exclut plusieurs virus des chiroptères. L’Afrique héberge un grand nombre de lyssavirus différents, d’où l’idée que cette région du monde était peut-être la source d’émergence des virus, hypothèse toutefois réfutée par de récentes analyses phylogénétiques qui ont mis en avant une probable origine paléarctique. Certains résultats sérologiques font état d’une distribution plus étendue et d’une diversité encore plus élevée des lyssavirus chez les chauves-souris, ce qui laisse supposer que l’incidence des lyssavirus connus est sous-estimée et que nombre d’espèces nouvelles du genre lyssavirus restent à découvrir. Néanmoins, la plupart des chauves-souris ne transmettent pas le virus et par conséquent ne...

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.