Abstract
The zoonotic Plasmodium knowlesi parasite is the most common cause of human malaria in Malaysia. Genetic analysis has shown that the parasites are divided into three subpopulations according to their geographic origin (Peninsular or Borneo) and, in Borneo, their macaque host (Macaca fascicularis or M. nemestrina). Whilst evidence suggests that genetic exchange events have occurred between the two Borneo subpopulations, the picture is unclear in less studied Peninsular strains. One difficulty is that P. knowlesi infected individuals tend to present with low parasitaemia leading to samples with insufficient DNA for whole genome sequencing. Here, using a parasite selective whole genome amplification approach on unprocessed blood samples, we were able to analyse recent genomes sourced from both Peninsular Malaysia and Borneo. The analysis provides evidence that recombination events are present in the Peninsular Malaysia parasite subpopulation, which have acquired fragments of the M. nemestrina associated subpopulation genotype, including the DBPβ and NBPXa erythrocyte invasion genes. The NBPXb invasion gene has also been exchanged within the macaque host-associated subpopulations of Malaysian Borneo. Our work provides strong evidence that exchange events are far more ubiquitous than expected and should be taken into consideration when studying the highly complex P. knowlesi population structure.
Highlights
Www.nature.com/scientificreports can be transmitted through several vector species, including Anopheles latens and A. balbacensis in Malaysian Borneo[5,6,7] and A. hackeri and A. cracens in Peninsular Malaysia[8]
These studies have revealed that the P. knowlesi genome is more polymorphic than P. falciparum, and that three main subpopulations exist based on geographical source (Peninsular-Malaysia vs. Malaysian Borneo) and, within Malaysian Borneo, different hosts (M. nemestrina [Mn-Pk] and M. fascicularis [Mf-Pk] macaques, and humans)[23,24,25]
Evidence of mixed infections was detected in two selective whole genome amplification (SWGA) samples, demonstrating that the method can amplify more than one clone present in an infection, as was observed for P. vivax amplified samples[28]
Summary
Www.nature.com/scientificreports can be transmitted through several vector species, including Anopheles latens and A. balbacensis in Malaysian Borneo[5,6,7] and A. hackeri and A. cracens in Peninsular Malaysia[8]. For P. knowlesi WGS studies, the number of high quality isolates analysed in each study has been small (n < 70)[23,24,25] These studies have revealed that the P. knowlesi genome is more polymorphic than P. falciparum, and that three main subpopulations exist based on geographical source (Peninsular-Malaysia vs Malaysian Borneo) and, within Malaysian Borneo, different hosts (M. nemestrina [Mn-Pk] and M. fascicularis [Mf-Pk] macaques, and humans)[23,24,25]. The resulting genetic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition[12,13] Despite these insights, P. knowlesi isolates from both macaques and humans in Peninsular Malaysia are under-represented in analyses, and the genetic diversity in that geographical region is less clear. We developed a SWGA approach for P. knowlesi, and sequenced 26 isolates across Malaysia, including from Peninsular and Borneo, revealing new insights into the population structure and evolution of this parasite
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