Next Generation Sequencing In the Understanding of Neglected Malaria Parasites
Open Access
- Author:
- Brashear, Awtum
- Graduate Program:
- Immunology and Infectious Diseases
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- November 13, 2019
- Committee Members:
- Runze Li, Dissertation Advisor/Co-Advisor
Runze Li, Committee Chair/Co-Chair
Margarita Maria Lopez-Uribe, Committee Member
Maciej F Boni, Committee Member
Santhosh Girirajan, Outside Member
Liwang Cui, Special Member
Margherita Teresa-Anna Cantorna, Program Head/Chair - Keywords:
- Malaria
Genomics
Transcriptomics
RNA Sequencing
Southeast Asia
China
Myanmar
Thailand
Border
Plasmodium vivax
Plasmodium ovale
Antigenic Variation
Drug Resistance
Anti-Malarial Resistance - Abstract:
- In 2018 over 200 million people were estimated to have suffered a malaria infection. Malaria is a disease caused by blood-borne infection with parasites from the genus Plasmodium. There are at least 6 species of Plasmodium parasites which can cause malaria in humans. Here we focus on Plasmodium vivax and Plasmodium ovale, two species for which little research has been done thus far. The same methodology used to study P. falciparum is limited in these species due to the lack of a functioning in vitro culture system, low in vivo parasitemia and frequent mixed infection. Studying these species of malaria is therefore going to require analyses using innovative techniques. This dissertation presents approaches to closing the knowledge gap in neglected malaria parasites using Next Generation Sequencing technologies. Plasmodium ovale is globally important to malaria eradication because of how capable it is of travelling internationally and evading prophylactics due to its particularly long latency period. Chapter 2 of this dissertation provides the first resource for studying RNA-level biology in Plasmodium ovale curtisi. It demonstrates that the expanded antigenic gene families within P. ovale display signs of repression within blood stages. No other species of malaria for which transcriptomic data is available has as many members of the STP1 gene family as P. ovale curtisi, and this suggests that the expansion of this gene family allows for a larger repertoire of the surface protein, which may provide a benefit in terms of long-term immune evasion. Additional results from this chapter, including gene expression analyses and UTR and alternative splicing models, will provide a resource for researchers to study P. ovale in the future. The Greater Mekong Subregion is crucial to global malaria eradication due to its role in drug resistance. Within the GMS, P. vivax makes up a large portion of the malaria present. Additionally, border areas, such as the China-Myanmar border, sometimes allow malaria to transmit from high-density regions to regions which have eliminated or nearly eliminated malaria. In chapter 3, we use whole genome sequencing to establish that parasites on the China-Myanmar border are distinct from other regions within the Greater Mekong Subregion, and seem to have lower rates of multi-clonal infections. Our results suggest that a recent clonal expansion may have occurred during a P. vivax outbreak in 2013. Additionally this chapter attempts to characterize this novel population of P. vivax and how it compares to other nearby populations of P. vivax. One notable example is that samples from the China-Myanmar border displayed a lack of fixation on alleles that have been linked to sulfadoxine-pyrimethamine resistance. Research in this chapter poses the China-Myanmar border as a fascinating population of non-falciparum malaria for which focused studies may accelerate the path to elimination. Finally, using whole genome sequences obtained in chapter 3, chapter 4 introduces 4 new P. vivax draft genomes from the China-Myanmar border. These assemblies are of similar quality to the highest quality existing reference and constitute a new resource for researchers studying P. vivax in the Greater Mekong Subregion. Most variability found within the genomes was found within antigenic gene families, which are explored in further depth. Next Generation Sequencing is a valuable tool increasingly championed in biological studies because it can be used for high-throughput analytics in which multiple questions are addressed at once. It also empowers scientists to find new information a priori which can expedite discovery. Due to the limited amount of material and information regarding neglected malaria species, these traits position Next Generation Sequencing technology to be an essential tool going forward.