The diversity of coronaviruses in Southern African bat populations

Cronje, Nadine (2017-12)

Thesis (PhD)--Stellenbosch University, 2017.

Thesis

ENGLISH ABSTRACT: Coronaviruses are RNA viruses encompassing four genera. The alpha- and betacoronaviruses have commonly been associated with mild disease in humans. However, outbreaks of severe respiratory disease in 2002 and 2012 led to the identification of novel highly pathogenic human coronaviruses, SARS- and MERS-CoV, respectively. Bats, order Chiroptera, are believed to be the reservoir host from which all mammalian coronaviruses have emerged. To date, few studies have been published on coronaviruses in South African bats. With little known about the diversity and prevalence of bat coronaviruses in this region; this study aimed to describe the existing coronavirus diversity within South African bat populations as well as factors that might influence bat-coronavirus ecology. It detected nine different coronavirus species, eight alphacoronaviruses and one betacoronavirus, from ten different bat species. The study not only demonstrated that diverse coronaviruses can be found in different bat species of Southern Africa but lends additional support to an ongoing circulation of MERS-related betacoronaviruses in South African bats, with divergent variants detected in two different vespertilionid bat species. A species-specific surveillance of Neoromicia capensis (Cape serotine) bats detected three different bat coronavirus species and revealed genetic diversity across different geographic regions. Several instances of coinfection with two different coronaviruses were detected, demonstrating the potential for recombination that could lead to the emergence of a new coronavirus that might have zoonotic potential. This study demonstrated that both host and environmental factors may influence CoV ecology. Female Neoromicia capensis bats trapped at low altitude sites within the Forest biome had the highest likelihood of being coronavirus positive. Discrepancies between detection rates obtained with different screening assays led to the adoption of an improved approach and recommendations for future bat coronavirus surveillance studies were made.

AFRIKAANSE OPSOMMING: Koronavirusse is RNA virusse wat vier genera insluit. Die alfa- en betakoronavirusse word algemeen geassosieer met minder ernstige siektes by mense. Uitbrakings van ernstige respiratoriese siektes in 2002 en 2012 het egter gelei tot die identifisering van nuwe hoogs patogeniese menslike koronavirusse, SARS- en MERS-koronavirus, onderskeidelik. Vlêrmuise, orde Chiroptera, word beskou as die reservoir gasheer, wat tot die oorsprong van alle soogdierkoronavirusse gelei het. Tot dusver is min studies oor koronavirusse in Suid-Afrikaanse vlêrmuise gepubliseer. Met min kennis van die diversiteit en voorkoms van vlêrmuiskoronavirusse in hierdie streek; het hierdie studie ten doel om die bestaande koronavirusdiversiteit binne Suid-Afrikaanse vlêrmuispopulasies asook faktore wat vlêrmuis-koronavirus-ekologie kan beïnvloed, te ondersoek en beskryf. Nege verskillende koronavirus spesies, agt alfakoronavirusse en een betacoronavirus, is in tien verskillende vlêrmuis spesies geïdentifiseer. Die studie het nie net gedemonstreer dat diverse koronavirusse in verskillende vlêrmuise van Suider-Afrika voorkom nie, maar ook addisionele ondersteuning aan 'n deurlopende verspreiding van MERS-verwante betakoronavirusse in Suid- Afrikaanse vlêrmuise verleen, met uiteenlopende variante wat in twee verskillende vespertilioniedvlêrmuise aangetref word. 'n Spesiespesifieke waarneming van Neoromicia capensis (Kaapse serotien) vlêrmuise het drie verskillende koronavirus spesies opgespoor en genetiese diversiteit in verskillende geografiese streke opgemerk.Verskeie gevalle van meervoudige infeksies met twee verskillende koronavirusse is opgemerk, wat die potensiaal vir rekombinasie aantoon, wat kan lei tot „n nuwe koronavirus wat soönotiese potensiaal kan hê. Hierdie studie het getoon dat beide gasheer- en omgewingsfaktore koronavirus ekologie kan beïnvloed. Vroulike Neoromicia capensis vlêrmuise wat voorkom in laagliggende areas in die Woud bioom het die hoogste waarskynlikheid om koronavirus positief te wees. Afwykings tussen opsporingsyfers wat met verskillende siftingsmetodes verkry is, het gelei tot die aanvaarding van 'n verbeterde benadering en aanbevelings vir toekomstige vlêrmuiskoronavirus toesigstudies is gemaak.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/102585
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