Lagos bat virus, an under-reported rabies-related lyssavirus

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.This research is supported in part by the South African Research Chair Initiative (held by Wanda Markotter) of the Department of Science and Innovation and administered by the National Research Foundation of South Africa (UID: 98339). The National Research Foundation funded the equipment based at the DNA Sanger sequencing facility in the Faculty of Natural and Agricultural Sciences, University of Pretoria (UID: 78566).https://www.mdpi.com/journal/virusesdm2022Medical Virolog

Overview of bat and wildlife coronavirus surveillance in Africa : a framework for global investigations

The ongoing coronavirus disease 2019 (COVID-19) pandemic has had devastating health and socio-economic impacts. Human activities, especially at the wildlife interphase, are at the core of forces driving the emergence of new viral agents. Global surveillance activities have identified bats as the natural hosts of diverse coronaviruses, with other domestic and wildlife animal species possibly acting as intermediate or spillover hosts. The African continent is confronted by several factors that challenge prevention and response to novel disease emergences, such as high species diversity, inadequate health systems, and drastic social and ecosystem changes. We reviewed published animal coronavirus surveillance studies conducted in Africa, specifically summarizing surveillance approaches, species numbers tested, and findings. Far more surveillance has been initiated among bat populations than other wildlife and domestic animals, with nearly 26,000 bat individuals tested. Though coronaviruses have been identified from approximately 7% of the total bats tested, surveillance among other animals identified coronaviruses in less than 1%. In addition to a large undescribed diversity, sequences related to four of the seven human coronaviruses have been reported from African bats. The review highlights research gaps and the disparity in surveillance efforts between different animal groups (particularly potential spillover hosts) and concludes with proposed strategies for improved future biosurveillance.The National Research Foundation (NRF) of South Africa: the DSI-NRF South African Research Chair fellowship funding; the Department of the Defense, Defense Threat Reduction Agency and the University of Pretoria’s postdoctoral funding program.http://www.mdpi.com/journal/virusespm2021Medical Virolog

Seasonal shedding patterns of diverse henipavirus-related paramyxoviruses in Egyptian rousette bats

Bat-borne viruses in the Henipavirus genus have been associated with zoonotic diseases of high morbidity and mortality in Asia and Australia. In Africa, the Egyptian rousette bat species (Rousettus aegyptiacus) is an important viral host in which Henipavirus-related viral sequences have previously been identified. We expanded these fndings by assessing the viral dynamics in a southern African bat population. A longitudinal study of henipavirus diversity and excretion dynamics identified 18 putative viral species circulating in a local population, three with difering seasonal dynamics, and the winter and spring periods posing a higher risk of virus spill over and transmission. The annual peaks in virus excretion are most likely driven by subadults and may be linked to the waning of maternal immunity and recolonization of the roost in early spring. These results provide insightful information into the bat-host relationship that can be extrapolated to other populations across Africa and be communicated to at-risk communities as a part of evidence-based public health education and prevention measures against pathogen spill over threats.The National Research Foundation (NRF) of South Africa; the Poliomyelitis Research Foundation; the Department of the Defense, Defense Treat Reduction Agency, the South African Medical Research Council and the University of Pretoria’s postdoctoral funding program.http://www.nature.com/srep/index.htmlMedical Virolog

Advances in understanding bat infection dynamics across biological scales

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes

Detection and characterization of coronaviruses from African bat species

The severe acute respiratory disease syndrome or SARS epidemic emerged in Hong Kong, China, in 2002 with a mortality rate of 15%. The etiological agent for SARS was identified to be a previously unrecognized coronavirus (SARS-CoV) which was found to be zoonotic in origin. A possible reservoir for the SARS-CoV was proposed to be the Chinese horseshoe bat species (Rhinolophus spp.) due to the detection of SARS-related bat coronaviruses (BtCoV) within these bat species. Since the SARS-CoV epidemic, new interest regarding the origin and pathogenicity of coronaviruses has been generated. As such, surveillance studies of BtCoV in numerous bat species have been performed in Asia, Europe, North and South America as well as 3 African countries. Recent BtCoV investigations in Kenya, Ghana and Nigeria identified BtCoV from both the Alpha- and Betacoronavirus genera and provided the first evidence for the presence of coronaviruses in African bats. Previously, the presence of antibodies against SARS-related CoV has been reported in two bat species native to South Africa. This study investigated the possible presence of BtCoV in a panel of bat specimens collected from sites in South Africa and Rwanda, and how they are related to previously detected BtCoVs from other parts of the world. Here we report the development of two PCR assays, the PanBtCoV/9 primer nested RT-PCR and PanBat/AB/6 primer hemi-nested RT-PCR assay, which were used in coronavirus detection from alimentary specimens collected from 15 bat genera. The combined assays amplified coronavirus RNA from 5 samples of the 201 analysed samples collected in South Africa (n=113) and Rwanda (n=88). Three alphacoronaviruses were detected in 3 different South African bat species, Miniopterus spp. (Miniopterus-Bat coronavirus/Irene/South Africa/2009), Neoromicia capensis (Neoromicia-Bat coronavirus/167/South Africa/2007), and Mops midas (Mops-Bat coronavirus/1364/South Africa/2011). From Rwanda, a single betacoronavirus, a SARSrCoV was detected within 2 Rhinolophus spp. individuals (Rh-BtCoV/441/Rwanda/08 and Rh- BtCoV/445/Rwanda/08). Phylogenetic analysis of these sequences was performed and showed that the South African Miniopterus alphacoronavirus and the Rwandan betacoronavirus cluster together with previously detected African BtCoV from the same host genera. The South African alphacoronavirus from Mops midas was closely related to an alphacoronavirus identified within another member of the Molossidae family, Chaerephon spp. from Kenya. Being the first BtCoV identified from the Neoromicia genus, no African BtCoV sequences were available for comparison and as such the virus clustered together with European BtCoV from the Nyctalus spp., another member of the Vespertilioninae subfamily. This study has detected the first BtCoV viral RNA from the native bat species of South Africa and Rwanda, providing confirmation to the presence of bat coronaviruses circulating in these countries. From these preliminary results further investigations into the prevalence and infection cycles of bat coronaviruses in specific bat populations can be performed in the future. The possibility of either these alpha- or betacoronaviruses spilling over and eventually adapting to and infecting other species, though unlikely, cannot be excluded since such rare events are hypothetically responsible for the establishment coronaviruses in humans, livestock, poultry and pets. Caution may still be merited when interacting with bats in roosts and caves.Dissertation (MSc)--University of Pretoria, 2012.National Research foundation (NRF)Poliomyelitis Research Foundation (PRF)Microbiology and Plant PathologyMScUnrestricte

Detection and Characterization of an H9N2 Influenza A Virus in the Egyptian Rousette Bat in Limpopo, South Africa

In recent years, bats have been shown to host various novel bat-specific influenza viruses, including H17N10 and H18N11 in the Americas and the H9N2 subtype from Africa. Rousettus aegyptiacus (Egyptian Rousette bat) is recognized as a host species for diverse viral agents. This study focused on the molecular surveillance of a maternal colony in Limpopo, South Africa, between 2017–2018. A pan-influenza hemi-nested RT-PCR assay targeting the PB1 gene was established, and influenza A virus RNA was identified from one fecal sample out of 860 samples. Genome segments were recovered using segment-specific amplification combined with standard Sanger sequencing and Illumina unbiased sequencing. The identified influenza A virus was closely related to the H9N2 bat-influenza virus, confirming the circulation of this subtype among Egyptian fruit bat populations in Southern Africa. This bat H9N2 subtype contained amino acid residues associated with transmission and virulence in either mammalian or avian hosts, though it will likely require additional adaptations before spillover

Host-Associated Distribution of Two Novel Mammarenaviruses in Rodents from Southern Africa

Mammarenaviruses are hosted by several rodent species, a small number of which have been known to be zoonotic. Host surveillance among small mammals has identified a large diversity of previously undescribed mammarenaviruses. Intensified biosurveillance is warranted to better understand the diversity of these agents. Longitudinal host surveillance involving non-volant small mammals at a site in the Limpopo province, South Africa, was conducted. The study reports on the screening results of 563 samples for the presence of mammarenavirus RNA. PCR-positive samples were subjected to sequencing using Miseq amplicon sequencing. Sequences with close similarity to Mariental and Lunk viruses were identified from two rodent species, Micaelamys namaquensis and Mus minutoides. This represents the first description of these viruses from South Africa. The genomic sequences reported here partially satisfied the requirements put forward by the International Committee on the Taxonomy of Viruses’ criteria for species delineation, suggesting that these may be new strains of existing species. The known distribution of these mammarenaviruses is thus expanded further south in Africa

Coronaviruses in south africanbats

Recent studies in several African countries have provided the first evidence for the presence of coronaviruses in African bats. Here we describe, for the first time, the detection of RNA of 3 unique coronavirus species in the tissues of South African bats

Seasonal shedding patterns of diverse henipavirus-related paramyxoviruses in Egyptian rousette bats

International audienc

Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony: considerations for spillover

Abstract Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission