Identification and characterisation of paramyxoviruses in species-rich small mammals from South Africa

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dc.contributor.advisorPreiser, Wolfgangen_ZA
dc.contributor.advisorIthete, Ndapewa Laudikaen_ZA
dc.contributor.advisorDrexler, Jan Felixen_ZA
dc.contributor.authorKleinhans, Bronwynen_ZA
dc.contributor.otherStellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology.en_ZA
dc.date.accessioned2022-09-20T07:23:04Zen_ZA
dc.date.accessioned2023-01-23T06:50:02Zen_ZA
dc.date.available2023-03-24T03:00:09Zen_ZA
dc.date.issued2022-12en_ZA
dc.descriptionThesis (PhD)--Stellenbosch University, 2022.en_ZA
dc.description.abstractENGLISH ABSTRACT: Paramyxoviruses are negative-sense RNA viruses and include a substantial collection of ubiquitous viruses, comprising one of the most important viral groups with numerous pathogens historically impacting on public and veterinary health. The Paramyxoviridae family consists of four subfamilies including Avulavirinae (genera: Metaavulavirus, Orthoavulavirus and Paraavulavirus), Metaparamyxovirinae (genus: Synodonvirus), Orthoparamyxovirinae (genera: Aquaparamyxovirus, Ferlavirus, Henipavirus, Jeilongvirus, Morbillivirus, Narmovirus, Respirovirus and Salemvirus) and Rubulavirinae (genera: Orthorubulavirus and Pararubulavirus). Over the past three decades, an increasing number of novel paramyxoviruses of especially the Orthoparamyxovirinae and Rubulavirinae subfamilies have emerged from small mammal reservoir hosts, some of which, especially the deadly henipaviruses, Hendra- and Nipah virus, have demonstrated a propensity to spillover from their natural reservoir hosts into human and domestic animal populations. Although some small mammals have been implicated as potential hosts for novel paramyxoviruses within southern Africa, little to no data exists on such discovery in insectivorous bats, rodents and particularly shrews and sengis in South Africa. This study identified an additional 23 previously unimplicated species representing four different orders (Chiroptera, Eulipotyphla, Macroscelidea and Rodentia), greatly expanding on the known host and geographic range of these putative paramyxoviruses, reiterating this group of virus’ ubiquitous nature and high diversity. The presumptive paramyxoviruses discovered in this study demonstrated phylogenetic relatedness to at least five of the known genera including: Henipavirus, Jeilongvirus, Morbillivirus, Narmovirus and Rubulavirus as well as to previously discovered viral sequences clustering within the Orthoparamyxovirinae subfamily but that could not be assigned to any of the currently known genera. Unique to this study and of particular value in the South African context was the discovery that: Cape horseshoe bats (Rhinolophus capensis) harbour different variants / strains of a paramyxovirus displaying multiple nonsynonymous mutations resulting in amino acid changes, raising concerns over these putative paramyxoviruses’ zoonotic potential; the widely distributed and populous Rhabdomys (R. bechuanae, R. dilectus, R. intermedius and R. pumilio), endemic to southern Africa, harbour diverse and abundant (overall prevalence of 19.41% [106/546]) paramyxoviruses, displaying diversity on the individual, species and population levels; at least four different shrew species commonly found in South Africa were implicated as hosts for putative henipaviruses; the sustained presence of one of these novel viruses in greater red musk shrews (Crocidura flavescens) implicated this particular species as the reservoir host thereof, of which the near full-length genome sequence further revealed a close phylogenetic relationship to the rat-borne henipavirus, Mòjiāng virus. Given the abundance and diversity of novel potential paramyxoviruses discovered herein and the implication of a multitude of previously unimplicated species as potential reservoir hosts, this study reaffirms the importance and need for ongoing surveillance efforts of especially small mammals in South Africa. This study further highlights the importance of not only the identification of novel paramyxoviruses but also their characterisation, especially those demonstrating close relation to pathogenic members within the family. Further investigation into host-pathogen dynamics at the wildlife – domestic animal – human interface is however warranted to establish the potential for these viruses’ ability to spillover into humans and/or their domestic animals.en_ZA
dc.description.abstractAFRIKAANS OPSOMMING: Paramyxovirusse is negatiewe-sin RNA-virusse en sluit 'n aansienlike versameling alomteenwoordige virusse in en is een van die belangrikste virale groepe met talle patogene wat impak op openbare en veeartsenykundige gesondheid. Die Paramyxoviridae familie bestaan uit vier subfamilies, insluitend Avulavirinae (genera: Metaavulavirus, Orthoavulavirus en Paraavulavirus), Metaparamyxovirinae (genus: Synodonvirus), Orthoparamyxovirinae (genera: Aquaparamyxovirus, Ferlavirus, Henipavirus, Jeilongvirus, Morbillivirus, Narmovirus, Respirovirus en Salemvirus ) en Rubulavirinae (Orthorubulavirus en Pararubulavirus). Oor die afgelope drie dekades is daar 'n toenemende aantal nuwe paramyxovirusse van veral die Orthoparamyxovirinae- en Rubulavirinae-subfamilies uit klein soogdier reservoir gashere ontdek, waarvan sommige, veral die dodelike henipavirusse, Hendra- en Nipah-virus, 'n geneigdheid getoon het om uit hul natuurlike reservoir gashere in menslike en huisdier bevolkings oortespoel. Alhoewel sommige klein soogdiere geïmpliseer is as potensiële gashere vir nuwe paramyxovirusse in Suider-Afrika, bestaan daar min tot geen data oor so 'n ontdekking in insekvretende vlermuise, knaagdiere en veral skeerbekmuise en sengis in Suid-Afrika. Hierdie studie het 'n bykomende 23 voorheen ongeïmpliseerde spesies geïdentifiseer wat vier verskillende ordes verteenwoordig (Chiroptera, Eulipotyphla, Macroscelidea en Rodentia), wat grootliks op die bekende gasheer en geografie van hierdie vermeende paramyxovirusse uitbrei, wat hierdie groep virus se alomteenwoordige aard en hoë diversiteit herhaal. Die vermoedelike paramyxovirusse wat in hierdie studie ontdek is, het filogenetiese verwantskap getoon met ten minste vyf van die bekende genera, insluitend: Henipavirus, Jeilongvirus, Morbillivirus, Narmovirus en Rubulavirus sowel as met voorheen ontdekte virale volgordes wat binne die Orthoparamyxovirinae-subfamilie groepeer, maar wat nie aan enigeen van die tans bekende genera toegewys kon word nie. Uniek aan hierdie studie en van besondere waarde in die Suid-Afrikaanse konteks was die ontdekking dat: Kaapse hoefyster vlermuise (Rhinolophus capensis) verskillende variante / stamme van 'n paramyxovirus bevat wat veelvuldige nie-sinonieme mutasies vertoon wat aminosuur veranderinge tot gevolg het, wat kommer wek oor hierdie vermeende paramyxovirusse se soönotiese potensiaal; die wydverspreide en volop Rhabdomys (R. bechuanae, R. dilectus, R. intermedius en R. pumilio), endemies aan Suider-Afrika, huisves diverse en volop (algehele voorkoms van 19.41% [106/546]) paramyxovirusse, wat diversiteit toon op die individu, spesie en bevolkings vlakke; ten minste vier verskillende skeerbekmuis spesies wat algemeen in Suid-Afrika voorkom, is geïmpliseer as gashere vir vermeende henipavirusse; die volgehoue teenwoordigheid van een van hierdie nuwe virusse in Groter Skeerbekmuise (Crocidura flavescens) het hierdie spesifieke spesie geïmpliseer as die reservoir gasheer daarvan, waarvan die byna vollengte genoom volgorde verder 'n noue filogenetiese verwantskap met die rot-gedraagde henipavirus, Mòjiāng-virus, aan die lig gebring het. Gegewe die oorvloed en diversiteit van nuwe potensiële paramyxovirusse wat hierin ontdek is en die implikasie van 'n menigtheid voorheen ongeimpliseerde spesies as potensiële gashere, bevestig hierdie studie die belangrikheid en behoefte aan voortdurende toesig pogings van veral klein soogdiere in Suid-Afrika. Hierdie studie beklemtoon verder die belangrikheid van nie net die identifikasie van nuwe paramyxovirusse nie, maar ook hul karakterisering, veral dié wat noue verwantskap met patogeniese lede binne die familie toon. Verdere ondersoek na gasheer-patogeen-dinamika by die wild-huisdier/vee-mens-koppelvlak is egter geregverdig om die potensiaal vas te stel vir hierdie virusse se vermoë om na mense en/of hul huisdiere/vee oor te spoel.af_ZA
dc.description.versionDoctoralen_ZA
dc.embargo.terms2023-03-22en_ZA
dc.format.extent344 pages : illustrationsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/126277en_ZA
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshMammals -- South Africaen_ZA
dc.subject.lcshParamyxovirusesen_ZA
dc.titleIdentification and characterisation of paramyxoviruses in species-rich small mammals from South Africaen_ZA
dc.typeThesisen_ZA
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