Population genetic structure and genomic divergence in Plasmodium knowlesi

Divis, P; (2017) Population genetic structure and genomic divergence in Plasmodium knowlesi. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04398418

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Plasmodium knowlesi infections in humans have been increasingly seen in many countries across Southeast Asia, with cases mainly concentrated in Malaysia, since a major focus of infections was first described in Malaysian Borneo over 10 years ago. Clinical presentations show a wide spectrum of illness from mild to fatal, with the possible occurrence of asymptomatic infections. Two monkey species have been identified as the chief reservoir hosts; long-­‐tailed macaque (Macaca fascicularis) and pig-­‐tailed macaque (M. nemestrina). In order to explore the transmission of P. knowlesi infections, it is important to study the population genetic structure of this parasite. To address this, a microsatellite genotyping toolkit consisting of 10 loci specific for P. knowlesi was developed and validated. Using these highly polymorphic markers, analysis of more than 500 P. knowlesi infections from human and wild macaque hosts across Malaysian Borneo and humans of peninsular Malaysia showed remarkable population genetic structure. Human clinical isolates were shown to comprise highly divergent subpopulations, respectively associated with forest-­‐dwelling long-­‐tailed macaque (Cluster 1) and pig-­‐tailed macaque (Cluster 2) reservoir hosts. After analysis of initial whole genome sequence data, re-­‐assessment of population genetic structure was undertaken by microsatellite analysis of more samples from wild macaques and humans from peninsular Malaysia, showing profound geographical divergence between Borneo (sympatric Cluster 1 and Cluster 2) and mainland peninsular Malaysia (Cluster 3). The overall three major subpopulations demonstrated by microsatellite 4 analyses matched the analysis inferred by the genome-­‐wide sequence analysis of clinical isolates. To allow further investigation of variation in genome-­‐wide divergence between the sympatric subpopulations in Borneo, a simple laboratory kit consisting of allele-­‐specific PCR assays was developed to distinguish the two subpopulations. This eased in identifying to which subpopulations P. knowlesi infections belonged, and subsequently generating more genome-­‐wide sequences for comparative study. Further analyses revealed remarkable heterogeneity in the level of divergence between the sympatric subpopulation across the genome. Genomic architectures showed 20 high-­‐divergence regions scattered in different chromosomes. These findings suggest independent adaption of parasites in different macaque hosts that persist sympatrically.

Item Type: Thesis
Thesis Type: Doctoral
Thesis Name: PhD
Contributors: Conway, DJ (Thesis advisor);
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Funders: Funded by Ministry of Higher Education, Malaysia
Copyright Holders: Paul Cliff Simon Divis
URI: http://researchonline.lshtm.ac.uk/id/eprint/4398418


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