Zoonotic potential of viral enteric pathogens in South African domesticated animals
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Date
2020-12
Authors
Segone, Neo
Journal Title
Journal ISSN
Volume Title
Publisher
University of the Free State
Abstract
Diarrhoea is the second leading cause of death in children less than the age of five years of age. Enteric viruses are the major aetiological agents associated with acute diarrhoea. The occurrence of enteric viruses in humans and animals highlights the importance of the One Health approach and interest in investigating the possible potential for zoonosis to occur. Common human enteric viruses include Rotavirus (RV), Sapovirus (SaV), Norovirus (NoV), Adenovirus (AdV) and Astrovirus (AstV). Rotaviruses have been extensively studied as compared to other enteric viruses and there is evidence that rotavirus is a zoonotic virus. In light of the current COVID-19 pandemic, which was caused by a zoonotic transmission, it is vital to investigate and know the zoonotic status of other viruses. In this study, canine (n = 104) and porcine (n = 118) stool samples were screened for human enteric viruses, to identify viral agents with the possible potential for zoonosis. Three water samples from the porcine pen were also evaluated for the presence of enteric viruses. Electropherotyping was used as a primary method for detecting RV. In the canine samples, none (0/104) were positive for RV, whereas for porcine, 13.56% (16/118) were recorded positive for RV. Of the three water samples, none were positive for RV. Real-time RT-PCR (RT-qPCR) was used to expand the study to detect other enteric viruses mentioned above. RT-qPCR was able to identify three more RV positive porcine samples that were not detected by electropherotyping. Therefore, a total of 19/118 (16.10%) porcine samples were positive for RV. Of the 19 RV positive samples, 16 were confirmed to have sufficient RNA by agarose gel electrophoresis and therefore selected for whole genome sequencing. The whole genomes of fifteen group A rotavirus (RVA) strains were determined using the Illumina Miseq platform. One sample displayed a G5P[13] genotype combination, two G5P[6]P[13], three G5P[13]P[23], and nine G5P[23] combinations. One of the fifteen samples also had a co-infection with group C rotavirus (RVC). The average coverage for the RVC strain was too low for phylogenetic analysis but a BLASTn search was used to identify close relatives. Eight of the fifteen samples, were co-infections with picobirnavirus. A group B (RVB) strain was also identified and genotyped. The zoonotic potential of the detected RVAs was determined by phylogenetic analysis. The phylogenetic analysis revealed that study strains are similar to one another and clustered with the South African porcine strains. Exceptions were P[6] and NSP5/6 which were closely related to human strains identified in GenBank. These results suggest possible zoonotic potential for some of the RV strains evaluated. The two P[13]-containing study strains, RVA/Pig-wt/ZAF/UFS BOC009/2018/G5P[6]P[13] and RVA/Pig-wt/ZAF/UFS-BOC035/G5P[6]P[13] were distinct with nucleotide sequence identities of 83% and 83.55% to RVA/Pig-wt/ZAF/UFS-BOC001/2018/G5P[13], respectively, suggesting possible reassortment. The presence of these rotavirus strains on one farm in South Africa, calls for more investigation on the farm and overall surveillance of porcine RV strains in Africa.
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Keywords
Dissertation (M.Sc. (Biochemistry))--University of the Free State, 2020, One Health, Enteric viruses, Zoonosis, Porcine rotavirus, Diarrhoea, Electropherotyping, RT-qPCR, Next generation sequencing, Phylogenetic analysis