Poxviruses are double stranded (ds) DNA viruses with large brick-shaped virions (~200x300nm) that can be seen by light microscopy. The Chordopoxvirus (ChPV) subfamily demonstrates a vast genetic diversity in poxvirus virulence and evolution, and infects a wide range of vertebrate hosts including human/primates, rodents, birds, squirrels, and many economically important ruminants. There are at least 14 distinct ChPV genera, whose members have genomes that range between 127-360 kbp, and can be either GC-rich (33-38% A+T base composition) or AT-rich (up to 76% A+T). My work in the assembly and annotation of novel poxviruses serves to enrich the poxvirus sequence repository and further virulence characterization, comparative analysis, and phylogenetic studies. Using a variety of programs, as well as tools developed by the Virus Bioinformatics Research Centre, a protocol is created, refined, and applied to the assembly and annotation of novel poxviruses: Pteropox virus (PTPV) from a south Australian megabat Pteropus scapulatus, Eptesipox virus (EPTV) from a north American microbat Eptesicus fuscus, sea otter poxvirus (SOPV) from the north American Enhydra lutris, and two Kangaroopox viruses western and eastern Kangaroopox viruses (WKPV, EKPV) from the Australian Macropus fuliginosus and Macropus giganteus. This is the first time poxviruses from these vertebrate hosts are assembled in full, and the result supports the establishment of 4 new ChPV genera. The two bat-isolated poxviruses, PTPV and EPTV, likely did not co-speciate with their hosts despite infection of related host species. Instead, EPTV forms a sister clade with the Clade II virus, and together forms a sister group with the orthopoxviruses. On the other hand, PTPV and SOPV are each other’s closest extant relatives despite the distant geographical location from which they were isolated; together they share a novel homolog of TRAIL (Tumor necrosis factor-Related Apoptosis-Inducing Ligand) never before seen in poxviruses. SOPV additionally encodes distinct interleukin (IL)-18 binding protein and tumor necrosis factor (TNF) receptor-like protein that could have novel immune-evasion roles. The KPVs present the first case of a putative viral cullin-like protein, which might be involved in regulating the host ubiquitination pathway. Altogether, these novel proteins can potentially serve as new virokines and viroceptors in the form of viromimicry pathogenesis; they demonstrate the capacity and diversity with which poxviruses modulate host immune responses in their favour, and should be studied further. / Graduate / 2019-04-11

Lagos bat virus (LBV) belongs to genotype (gt) 2 of the lyssavirus genus in the family Rhabdoviridae, order Mononegavirales. This virus causes fatal rabies encephalitis in vertebrate animals and has only been reported from the African continent except for an imported case from African origin identified in France. The prototype lyssavirus is in fact rabies virus (gt 1) for which a variety of different vaccines are commercially available. These vaccines, however, do not provide protection against the gt 2 viruses. Genotype 2 viruses have not been well studied to date and the true risk for humans and animals is uncertain. The aim of this study was to investigate the epidemiology and pathogenicity of this uniquely African virus. In this project, our surveillance in South Africa reported six new LBV cases after this virus was not reported for the previous 12 years prior to this study. These results indicated that the incidence of this virus is greatly underestimated due to lack or absence of surveillance or ineffective diagnostic abilities of laboratories in Africa. Molecular epidemiological analysis of previously identified and new gt 2 isolates from this study indicated a high intragenotypic nucleotide and amino acid sequence diversity with respect to the Nucleo-, Phospho-, Matrix- and Glycoprotein genes. Based on these analyses, it has been proposed that two virus isolates that were previously reported as gt 2 LBV, may in fact constitute a new lyssavirus genotype. These findings emphasize the need to investigate different criteria for lyssavirus classification. As more lyssaviruses are discovered and with rapid progress in full genome sequencing, diversity becomes accentuated and challenges the criteria upon which lyssavirus taxonomy is based. As a compliment to these genetic findings, our study of viral pathogenicity in a murine model, identified that the pathogenicity of phylogroup II viruses has previously been underestimated. LBV poses a potential risk to humans and animals and future vaccine strategies should ideally include protection against phylogroup II viruses. / Thesis (PhD)--University of Pretoria, 2011. / Microbiology and Plant Pathology / unrestricted