Plasmodium spp. Comparative Genomics
The malaria parasite is one of the most widespread eukaryotic pathogens in the world today. Malaria remains a major global health threat with an estimated 300 ? 500 million cases per year and deaths of over a million children in Africa. Resistance to currently effective drugs?including drugs given in combinations to decrease the spread of resistance?is rapidly expanding. The next five years will see billions of dollars spent implementing interventions, particularly in Africa. Past experience suggests that large scale deployment of control measures will lead to selection for drug resistance in the malaria parasite and insecticide resistance in the mosquito vector. The combined need to have genomic tools to monitor the evolutionary consequences of these large scale interventions and to discover new therapies and diagnostics provides a powerful argument to support the overall goal of this white paper to prepare for malaria disease surveillance and control in the 21st century.
We propose here a comprehensive sequencing program with the sequencing of a total of approximately 16 billion base pairs (equivalent to a 5X coverage of the human genome) including significant additional sequencing of Plasmodium falciparum, the most deadly form of human malaria, additional sequencing of Plasmodium vivax, the second most prevalent of the human malarias, and sequencing of selected non-human primate, other mammalian, avian and reptile malarias and related apicomplexan parasites.
Strains have been selected from four distinct geographic sites. We will survey parasites from sites where both good biologic questions are studied?emerging drug resistance, vaccine trial setting, important clinical phenotypes?and good sample collection has been obtained?material preserved for culture-adaptation, numerous samples collected across time and with good patient information. The sites are broadly distributed, representing America, West Africa, East Africa and Asia and are sites with ongoing drug and vaccine trials. The specific sites selected include Iquitos, Peru; Bandiagara, Mali; Kampala, Uganda; and Thailand.
Samples are in the queue for sequencing, check back for data.
This sequencing project was supported by the National Institute of Allergy and Infectious Disease, National Institutes of Health funded Genome Sequencing Center for Infectious Diseases at the Broad Institute.