Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (F) = 0.21, with 9,293 SNPs having fixed differences of F = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean F values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.
KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank all patients, nurses, doctors, and laboratory technicians at Kapit and Betong Hospitals and core staff in our research institutes for their assistance; Hifzur Rahman Ansari (King Abdullah University of Science and Technology) for submission of the sequences to European Nucleotide Archive; the Malaria Research and Reference Reagent Resource Center for providing the P. knowlesi strains contributed by William E. Collins; and the Director General of Health in Malaysia for permission to publish this paper. This study was supported by Universiti Malaysia Sarawak Grants E14054/F05/54PK1/09/2012(01) and 01(TD03)/1003/2013(01); UK Medical Research Council Grants MRC G1100123, MR/K000551/1, and MR/M01360X/1; European Research Council Advanced Award AdG-2011-294428; NIH Grant 5R01AI091787; Bill and Melinda Gates Foundation Grant OPP1023594; a postgraduate scholarship from the Ministry of Education in Malaysia; and faculty baseline funding from King Abdullah University of Science and Technology.