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The genus Capripoxvirus of the family Poxviridae consists of the species lumpy skin disease virus, sheeppox virus and goatpox virus that affect cattle, sheep and goats, respectively. Whereas lumpy skin disease virus (LSDV) is transmitted mainly mechanically via blood-feeding insects and possibly hard ticks, the major transmission routes of sheeppox virus (SPPV) and goatpox virus (GTPV) are via direct contact and aerosols. Affected animals develop fever and display clinical signs such as ocular and nasal discharge, lymphadenopathy and characteristic lesions of the skin. Severe clinical course, especially in combination with respiratory signs, can result in the death of the affected animals. In endemic regions, mortality of capripox virus-induced diseases is low (1-10%). However, mortalities of up to 75% have been reported for LSDV and up to 100% for SPPV and GTPV in exotic breeds and high-producing dairy or beef animals. The loss of quality of the leather, reduced weight gain and milk yield as well as complete loss of affected animals have severe impact on national and global economies. Therefore, capripox virus-induced diseases have significant impact on both the affected individual animal as well as on the existence of small-scale farmers and large agricultural enterprises. However, until now, only live attenuated vaccines are commercially available. These attenuated vaccines are not authorized in the European Union and their administration would comprise the disease-free status of the respective country. Thus, reliable diagnostic tools for the detection and characterization of capripox viruses as well as safe and efficient control measures are of high importance.
The objectives of the present thesis were the development, validation and comparison of diagnostic tools, the establishment of challenge infection models and the performance of pathogenesis studies for all three capripox virus species, and the development and testing of different inactivated prototype vaccine candidates against LSDV.
First, new real-time quantitative polymerase chain reaction (qPCR) assays for robust detection and differentiation of LSDV field strains, LSDV vaccine strains, SPPV and GTPV were developed and extensively validated. In the following, two single assays were combined to duplex assays, one for the differentiation between LSDV field strains and LSDV vaccine strains, and the second for discrimination of SPPV and GTPV. Finally, a diagnostic workflow based on these new duplex assays in combination with already published methods was established. This workflow enables time-saving, robust and reliable detection, species-specific identification and genetic and phylogenetic characterization of all three capripox virus species. In addition, already existing serological examination methods (serum neutralization assay and commercial enzyme-linked immunosorbent assay) were compared regarding their sensitivity and specificity. Furthermore, pathogenesis studies with different capripox virus isolates were performed in the respective target species, and the suitability of selected virus isolates as challenge viruses for future vaccine studies was analyzed. Pathogenesis studies with isolates GTPV-“V/103” and LSDV-“Macedonia2016” revealed that both are proper candidates for challenge models. Finally, three different SPPV isolates (SPPV-“V/104”, SPPV-“India/2013/Surankote” and SPPV-“Egypt/2018”) were tested in sheep regarding their virulence to find a suitable challenge model for SPPV, and SPPV-“India/2013/Surankote” was chosen for future vaccine studies.
Once appropriate challenge models were established, different inactivated prototype vaccines against LSDV were developed, and vaccine safety as well as vaccine efficacy were tested in cattle. Eventually, a Polygen-adjuvanted inactivated LSDV-vaccine candidate was selected that is able to fully prevent cattle from any LSDV-related clinical signs after severe challenge infection. Furthermore, molecular and serological data indicate that this inactivated prototype vaccine is even able to induce a kind of “sterile immunity” against LSDV in those cattle. It has to be mentioned that a commercially available vaccine similar to this prototype vaccine would be a great advance for the control of LSDV.
In the future, additional studies addressing diagnostics and optimized control of capripox viruses should be performed. Firstly, probe-based real-time qPCR assays for the differentiation of SPPV and GTPV vaccine strains from their respective virulent field strains should be developed and included into the diagnostic workflow. Secondly, further tests of the inactivated prototype vaccine, e.g. determination of the minimum protective dose and the possibility of cross-protection in sheep and goats against SPPV and GTPV, respectively, should be performed.
African swine fever virus (ASFV) is one of the most threatening animal viruses which has dramatically expanded its distribution range within the last years. ASFV was first described and is endemic in sub-Saharan Africa where it is transmitted in a sylvatic cycle between indigenous suids and Ornithodoros soft ticks. Therefore, ASFV is the only known DNA-arbovirus and, in addition to that, the only member of the genus Asfivirus within the family Asfarviridae. Being highly infectious to domestic pigs and wild boar, the virus was introduced into Georgia in 2007 and has subsequently spread throughout eastern Europe reaching the European Union in 2014. Despite almost 100 years of intensive research and the occurrence of African swine fever (ASF) on four continents including Europe, many aspects of its epidemiology, vector dynamics and virus evolution are unknown. In our study, first evidence is presented on endogenous ASFV-like (EASFL)- elements which are integrated into the genome of ASFV natural vectors, O. moubata soft ticks. Through a series of experiments including next-generation sequencing, infection experiments, phylogenetic and BEAST analyses as well as PCR-screening, evidence is provided that these elements belong to an ancestral ASFV strain that might have existed 50,000 to 30,000 years BCE. Further results suggest that the EASFL-elements are involved in protecting ticks against ASFV infection and might belong to a generalised tick defence mechanism. In order to evaluate factors influencing ASFV epidemiology in eastern Europe, experiments were conducted on possible indigenous vector species and circulating virus isolates. In the absence of the natural tick vector, blow fly larvae were considered as possible mechanical vectors involved in ASFV transmission and persistence. Results are presented that even after feeding on highly infectious wild boar tissue, fly larvae and pupae showed no contamination with infectious virus. On the contrary, the maggots appeared to have inactivated the virus in the organ tissue through their salivary secretions. Further experiments conducted on an ASFV-strain isolated from northeastern Estonia resulted in the first report of an ASFV-strain with attenuated phenotype isolated in Eastern Europe. Results from NGS-analyses provided evidence for a major genome reorganisation in that strain that included a large deletion and a duplication of multiple ASFV genes.
Taken together, this study provides novel insights into the epidemiology of ASF and evolution of ASFV one of the major threats to animal health worldwide and therefore does not only contribute significantly to basic research but possibly also to specific knowledge necessary for future disease management.
The advances in high-throughput sequencing technologies have revolutionized the possibilities for pathogen identification in cases of unknown disease origin. Diagnostic metagenomics allows the unbiased and simultaneous detection of almost all nucleic acids in a clinical sample, with the potential to provide pivotal insights into otherwise undeterminable causes of human or animal disease.
In this thesis, possibilities, pitfalls and the suitability of Ion Torrent and Illumina sequencing platforms for comprehensive use in diagnostic metagenomics were assessed and optimized procedures developed. Clinical field samples, undiagnosable by standard diagnostics, were taken as real-life examples for the investigations. The results show that cross-contamination due to index swapping and run-to-run-carryover constitute a major issue on Illumina platforms, severely compromising the correct interpretation of results for clinical specimens. In contrast, Ion Torrent platforms did not display any form of cross-contamination, however, the commercial library preparation method is less efficient. Combining the advantages of both platforms, customized Y adapters, facilitating highly efficient library preparation, were developed for Ion Torrent sequencing and applied in further experiments. The obstacles of strongly degraded RNA in formalin-fixed paraffin-embedded samples were identified and the workflow adapted to meet the requirements of smaller fragments. Additionally, it was shown that adequate sampling is a very important step, if not the most important step, in the workflow, as well as subsequent validation of the obtained results in terms of causation. The achievements in this study allow other researchers the application of a sensitive and optimized diagnostic metagenomics workflow.
Furthermore, the investigations on the clinical samples resulted in the discovery of a novel respirovirus with putative zoonotic potential, the first description of Borna disease virus 1 in human organ transplant recipients, and the discovery of a very distantly related novel ovine picornavirus. These discoveries build a basis for further research and expand the knowledge regarding new and emerging viruses.