Detection and characterization of genetically diverse paramyxoviruses from African bats

In past years, the potential of bats as reservoir for paramyxoviruses was clearly underestimated. Research of the 21st century now provides evidence that bats play an important role as reservoir and host to these viruses. The aim of this study was to detect the presence of any novel paramyxoviruses that may be circulating in bats across Africa. The specific objectives included the screening of specimen panels of insectivorous as well as frugivorous bat species collected from a number of African countries. Two broadly-reactive universal primer sets targeting the Paramyxovirinae subfamily and the Respiro-, Morbilli- and Henipavirus genera were used in two semi-nested PCR reactions. Bat kidney was selected as target organ and bats were sampled from several countries across Africa (Cameroon, Democratic Republic of the Congo, Kenya, Nigeria, South Africa and Swaziland). Based on amino acid analysis it was determined that approximately 31 putative viral species were detected. Viruses detected, clustered phylogenetically with known genera namely Henipavirus, Morbillivirus and the newly proposed Jeilongvirus. Several viral sequences clustered outside the known genera and might belong to yet unclassified genera in the Paramyxovirinae subfamily. Viral exchange between different bat species was also observed in several occasions where sampling from geographically distant locations was done. The ability of some bat species, e.g. Eidolon helvum, to migrate over large distances, likely contributes to the spread of specific virus lineages over significant geographical space. The propensity for many bat species to roost communally is another likely contributor to enhanced virus transmission events. Due to the vast genetic variability among paramyxoviruses in nature, insight into these viruses will be vital in understanding their pathogenic nature and the possible threat they may pose to public and veterinary health sectors. Propagation and isolation in cell-cultures as well as full-genome sequence analysis will be a foremost requirement in future research of these viruses. Clearly, there are geographical limitations in this study which emphasizes the need for a One Health approach from all African countries that will greatly contribute to future research on paramyxoviruses.Thesis (PhD)--University of Pretoria, 2013.Poliomyelitis Research Foundation (PRF)South Africa National Research Foundation (NRF)South Africa University of PretoriaMicrobiology and Plant PathologyMScUnrestricte

Development of a Pan-Filoviridae SYBR green qPCR assay for biosurveillance studies in bats

DATA AVAILABILITY: The data are contained within the article or supplementary materials.SUPPLEMENTARY MATERIALS : TABLE S1: Publically available sequences used for primer design; SUPPLEMENTARY FILE S1: Synthetic constructs sequences, TABLE S2: SYBR Green qPCR results for field samples.Recent studies have indicated that bats are hosts to diverse filoviruses. Currently, no panfilovirus molecular assays are available that have been evaluated for the detection of all mammalian filoviruses. In this study, a two-step pan-filovirus SYBR Green real-time PCR assay targeting the nucleoprotein gene was developed for filovirus surveillance in bats. Synthetic constructs were designed as representatives of nine filovirus species and used to evaluate the assay. This assay detected all synthetic constructs included with an analytical sensitivity of 3–31.7 copies/reaction and was evaluated against the field collected samples. The assay’s performance was similar to a previously published probe based assay for detecting Ebola- and Marburgvirus. The developed pan-filovirus SYBR Green assay will allow for more affordable and sensitive detection of mammalian filoviruses in bat samples.National Research Foundation (NRF) of South Africa.https://www.mdpi.com/journal/virusesMedical 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

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

DATA AVAILABILITY : All data generated during this study are included in this published article (and its Supplementary Information files). All model code as well as diagnostic reports are available in the GitHub project code repository (https://github.com/ecohealthalliance/sabrenet-rousettus-dynamics/, with a version on Zenodo https://zenodo. org/record/7709716).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.The National Research Foundation (NRF) of South Africa, the Poliomyelitis Research Foundation, the Department of the Defense, Defense Threat Reduction Agency and the University of Pretoria’s postdoctoral funding program.https://www.nature.com/srepam2024Medical VirologyNon

Advances in understanding bat infection dynamics across biological scales

DATA ACCESSIBILITY : Data to support authorship network mapping of the bat research community (described in the electronic supplementary material) are available at Zenodo: https://doi.org/10.5281/zenodo.8003910 [154].SUPPLEMENTARY MATERIAL from “Advances in understanding bat infection dynamics across biological scales”. Figshare. (doi:10.6084/m9.figshare.c.7075588)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.The National Institute of Allergy and Infectious Diseases; the Defense Threat Reduction Agency; the South African Research Chair Initiative of the Department of Science and Innovation and administered by the National Research Foundation (NRF) of South Africa ; the Defense Advanced Research Projects Agency; the Bill and Melinda Gates Foundation; the Medical Research Council; and the National Science Foundation.hj2024Medical VirologySDG-03:Good heatlh and well-bein

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

Co-Circulation and Excretion Dynamics of Diverse Rubula- and Related Viruses in Egyptian Rousette Bats from South Africa

International audienceThe Egyptian rousette bat (Rousettus aegyptiacus) has previously been implicated as the natural host of a zoonotic rubulavirus; however, its association with rubulaviruses has been studied to a limited extent. Urine, spleen, and other organs collected from the R. aegyptiacus population within South Africa were tested with a hemi-nested RT-PCR assay targeting a partial polymerase gene region of viruses from the Avulaand Rubulavirus genera. Urine was collected over a 14-month period to study the temporal dynamics of viral excretion. Diverse rubulaviruses, including viruses related to human mumps and parainfluenza virus 2, were detected. Active excretion was identified during two peak periods coinciding with the host reproductive cycle. Analysis of additional organs indicated co-infection of individual bats with a number of different putative rubulaviruses, highlighting the limitations of using a single sample type when determining viral presence and diversity. Our findings suggest that R. aegyptiacus can harbor a range of Rubulaand related viruses, some of which are related to known human pathogens. The observed peaks in viral excretion represents potential periods of a higher risk of virus transmission and zoonotic disease spill-over

Development of a Pan-<i>Filoviridae</i> SYBR Green qPCR Assay for Biosurveillance Studies in Bats

Recent studies have indicated that bats are hosts to diverse filoviruses. Currently, no pan-filovirus molecular assays are available that have been evaluated for the detection of all mammalian filoviruses. In this study, a two-step pan-filovirus SYBR Green real-time PCR assay targeting the nucleoprotein gene was developed for filovirus surveillance in bats. Synthetic constructs were designed as representatives of nine filovirus species and used to evaluate the assay. This assay detected all synthetic constructs included with an analytical sensitivity of 3–31.7 copies/reaction and was evaluated against the field collected samples. The assay’s performance was similar to a previously published probe based assay for detecting Ebola- and Marburgvirus. The developed pan-filovirus SYBR Green assay will allow for more affordable and sensitive detection of mammalian filoviruses in bat samples

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

International audienc