Doctoral Degrees (Medical Virology)

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Browsing Doctoral Degrees (Medical Virology) by Author "Barnard, Karlien"

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    Diversity and Ecology of Astroviruses in South African Bats
    (Stellenbosch : Stellenbosch University, 2020-03) Barnard, Karlien; Preiser, Wolfgang; Schultz-Cherry, Stacey; Ithete, Ndapewa Laudika; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Medical Virology.
    ENGLISH ABSTRACT: Emerging infectious diseases are mostly zoonotic in origin and defined as “infections that have newly emerged in a population or have existed but are rapidly increasing in incidence or geographic range". Zoonotic viruses are directly (e.g. bite from a rabid bat) or indirectly (via an intermediate host or vector) transmitted from animals to humans. Bats have received increasing attention as potential hostsfor zoonotic diseases. Bats belong to the order Chiroptera, which consists of two suborders: Yinpterochiroptera and Yangochiroptera. More than 1 300 species have been described globally, occurring on almost all continents excluding Antarctica. Specific physiological and ecological characteristics make bats extraordinary evolutionary vessels to carry numerous infectious agents including pathogens. Astroviruses (AstVs) are amongst the vast array of viruses that have been detected in bats. AstVs are single stranded, positive sense, RNA viruses that are transmitted via the faecal-oral route. Infection with AstVs causes acute diarrhoea, however, more serious clinical presentations such as neurological deficits, stunted growth and encephalitis have also been documented. Bats on the other hand, seem to be asymptomatically infected with AstVs. Little attention has been given to the evolution, phylogenetic relationship, ecology and diversity of AstVs in South African bats. In 2013 the first study in South Africa screening for a variety of viruses in small mammals, including SAn bats, found that bats were frequently co-infected with AstVs and coronaviruses. The overall aims of the current study were to describe the prevalence, diversity and ecology of AstVs in South African bats, to determine the potential threat to environmental and animal health at wastewater treatment works (WWTW) through testing water and bat samples for the presence of AstVs, to monitor AstV and CoV co-infection in a Neoromicia capensis colony over time and to isolate and propagate a bat AstV in vitro. The results will be used to determine the potential One Health implications of AstVs in a South African setting. Sample collection was done via non-invasive capture and release methods by collaborating zoologists. Morphological and ecological data of each bat were recorded. Bat faecal samples (n=500) were screened for AstVs using the hemi-nested screening assay that targets the RNA-dependent RNA polymerase (RdRP) gene of the virus. Plasmid positive controls were generated to ensure an optimal AstV screening PCR assay. The One Health concept emphasizes the interlinkage between human, animal and environmental health. To determine the impact that potential exposure to human AstVs at WWTW might have on animal and environmental health, water samples upstream and downstream of two WWTW were also collected and screened for AstVs. The overall detection rate of AstVs across bat species was 13%, but it differed significantly between species (Miniopterus natalensis, 55%; Rhinolophus capensis, 39%; and R. clivosus, 17%). Positive samples were further analysed to try and amplify the capsid protein gene (ORF2), which is highly variable and only one ORF2 gene fragment was obtained. Twenty-five novel AstV RdRp sequences and one ORF2 sequence were identified, bringing the total RdRp sequences available for South African bat AstVs to forty-four. Maximum likelihood analyses of the RdRp gene fragments suggest that South African bat AstVs are not restricted by host species identity or geographical location. Interestingly, the maximum likelihood analyses of the ORF2 sequence suggest that the South African bat AstVs might be more similar to human AstVs from Japan compared to any bat AstVs. The water samples collected from the WWTW tested negative for the presence of AstVs and only one bat sample collected at the WWTW tested positive for AstV. Two real-time PCR assays were designed to monitor AstVs and coronaviruses in a N. capensis colony over time, as these two viruses regularly co-infect bats. The results indicated that both these viruses had a single amplification peak that was associated with colony formation after migration. Interestingly the peak in viral loads did not correlate with the pupping season of the bats, as was found by another study conducted on these two viruses in Germany. Statistical analyses of ecological and individual bat factors suggest that being a sexually active adult male bat, species identity and occurrence in the Succulent Karoo biome could contribute to AstV positivity. The current study was the first ever to successfully isolate and propagate a Miniopterus bat derived AstV in vitro. During the isolation attempts three different cell lines were used, human adenocarcinoma, Neoromicia capensis kidney and baby hamster kidney cells. Isolation and propagation was only successful in the baby hamster kidney cells. The refined protocol for isolation and propagation of bat AstVs in cell culture will enable future studies to successfully isolate bat AstVs as well as enable genomic and functional studies. The results also gave insight into the potential zoonotic risk of bat AstVs. The findings of the current study indicated that bat AstVs are diverse and relatively prevalent in South African bats. Phylogenetic analyses of the 24 novel RdRp and one ORF2 genes from this study indicated that the virus was not limited by species identity or host geographical range. Furthermore, the phylogenetic analyses of the bat AstV ORF2 gene would suggest that the bat AstV is more similar to human AstVs, which could imply that South African bat AstVs have zoonotic potential. The results of current study gave some potential insights into the One Health implications of AstVs in the SA setting.