London School of Hygiene & Tropical Medicine Malaria Centre

Blog | Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

27 September 2017
Ernest Diez Benavente & Robert Moon

Malaria infections are caused by single celled parasites that generally can only infect humans and are spread from person to person by mosquitoes.  However, in South East Asia, a monkey malaria parasite, known as Plasmodium knowlesi, has been able to jump the species barrier and is now recognized as a significant cause of infections of humans. Its prevalence appears to be rising in some areas and its infections now account for 70% of the cases of human malaria in Malaysian Borneo.


The parasite naturally infects two different species of monkey native to South East Asia – the long-tailed and the pig-tailed macaque. Understanding how this parasite is able to adapt to grow successfully in at least 3 different primates (including humans) as well as be transmitted by a variety of different mosquitoes in each environment is critical to combating this new threat. Sequencing the genomes of parasites collected from each of the different host can provide invaluable information about how the parasite adapts to each one, as well as how often they switch between hosts. This can provide invaluable information to assist surveillance by malaria control programmes, and to understand the genetics underpinning Plasmodium knowlesi transmission and the switch from monkey hosts into humans.


A report published in PloS Genetics (Benavente ED et al., 2017) presents a comprehensive analysis of the largest assembled set of Plasmodium knowlesi genome sequences from Malaysia. This analysis supported previous work on this subject and found that parasites causing Plasmodium knowlesi infections in Borneo are split into 3 deeply branched lineages of ancient origin, which founded the two divergent populations associated with the two macaque hosts and a third, highly diverse population, on the Peninsular mainland.


It also revealed regions in the genome that have been recently exchanged between the parasite subpopulations associated with the long-tailed and pig-tailed macaques. These regions contain genes associated with adaptation and transmission within specific mosquito host, indicating that the parasite population has recently adapted to a new mosquito host species in the region and has “borrowed” genes from another subpopulation to enable this. It is likely that this rapid adaptive shift has been driven by accelerated deforestation in the region which, combined with encroachment on the wild macaque habitats will also potentiate the risk of infections in humans.


Understanding these processes will provide for a better understanding of the complex parasite evolution events occurring in the species and help determine the likelihood of further host transitions.  Ultimately this could help meet some of the unique challenges of controlling malaria in South East Asian countries like Malaysia.




Benavente ED, de Sessions PF, Moon RW, Holder AA, Blackman MJ, Roper C, Drakeley CJ, Pain A, Sutherland CJ, Hibberd ML, Campino S, Clark TG. Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulationsPloS Genetics. 2017; Sep 18; 13(9):e1007008.