Maritz-Olivier, Christine2024-12-042024-12-042025-042024-08-06*http://hdl.handle.net/2263/99745DOI:https://doi.org/10.25403/UPresearchdata.27942267.v1Dissertation (MSc (Genetics))--University of Pretoria, 2024.The cattle tick Rhipicephalus microplus, is an invasive hematophagous ecto-parasite in South Africa and is associated with high economic loss in the cattle industry. This tick species transmits pathogens such as Anaplasma marginale, Babesia bigemina and the virulent B. bovis, resulting in high morbidity and mortality in cattle populations. Recently, an RNA virus potentially associated with human disease has been detected in this tick species highlighting the need for proactive pathogen surveillance. The aim of this study was to use Next-generation sequencing to actively detect known and novel pathogens circulating in R. microplus and cattle populations in two South African provinces, Mpumalanga and KwaZulu Natal. RNA-sequencing analyses revealed that R. microplus has a highly diverse virome. Two viruses were detected in the majority of R. microplus samples, Wuhan tick virus 2 (WTV2) and Jingmen tick virus (JMTV), the latter is potentially associated with human disease. To monitor the presence of JMTV and the ubiquitous WTV2, PCR-RFLPs were developed as rapid diagnostic tests. Furthermore, 16S sequencing and microbiome analysis revealed the presence of several genera containing pathogenic bacteria that are a concern for human and animal health such as Coxiella, Anaplasma and Ehrlichia. Using R. microplus ticks reared on pathogen free cattle enabled the prediction of a core microbiome. The analyses suggested the presence of the Coxiella endosymbiont. NGS is an essential tool detecting and monitoring known, emerging and novel pathogens enabling the implementation of prophylactic measures to limit the spread of disease.en© 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria.UCTDSustainable Development Goals (SDGs)Rhipicephalus microplusTargeted metagenomicsRNA-sequencingJingmen tick virusPathogen surveillanceDissertationu1805710210.25403/UPresearchdata.27900216