Browsing by Author "Juma, John"
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Item Genomic epidemiology of Rift Valley fever in East Africa(University of the Western Cape, 2023) Juma, John; Christoffels, AlanRift Valley fever (RVF) is a climate-driven zoonotic disease of significant importance to public and livestock health given its epidemic potential. The disease was first identified in 1930 in the great rift valley region of Kenya following massive abortion among pregnant ewes in a sheep farm. RVF is caused by the Rift Valley fever virus (RVFV) belonging to the genus Phlebovirus, family Phenuiviridae and order Bunyavirales. RVF primarily affects domestic ruminants, wild animals and humans with varying degrees of fatalities. In this PhD research, tools and methods that will be of immense importance in conducting genomic surveillance of RVFV were developed. Furthermore, we have applied phylodynamic and phylogeographic approaches to understand the transmission dynamics of the virus in East Africa. In the second chapter, we utilized publicly available genetic sequence data of the virus to build a tool that rapidly detects circulating lineages. A general observation made in this work is the paucity of RVFV genetic data globally. Only a handful of sequence data is available from countries that have previously experienced RVF outbreaks such as South Africa, Kenya and Madagascar. The genetic information in the sequence data is crucial in identifying lineage defining single nucleotide polymorphisms (SNPs) or mutations. Using these mutations, we developed a command line tool that rapidly characterizes RVFV isolates using the 15 alphabet (A to O) nomenclature.Item Using multiplex amplicon pcr technology to efficiently and timely generate rift valley fever virus sequence data for genomic surveillance(MDPI, 2023) Juma, John; Christoffels, Alan; Roesel, KristinaRift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.Item Using multiplex amplicon pcr technology to efficiently and timely generate rift valley fever virus sequence data for genomic surveillance(MDPI, 2023) Juma, John; Konongoi, Samson L.; Nsengimana, IsidoreRift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination.