Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections

Abstract

BackgroundGenetic analyses of Plasmodium have potential to inform on transmission dynamics, but few studies have evaluated this on a local spatial scale. We used microsatellite genotyping to characterise the micro-epidemiology of P. vivax and P. falciparum diversity to inform malaria control strategies in Timika, Papua Indonesia.MethodsGenotyping was undertaken on 713 sympatric P. falciparum and P. vivax isolates from a cross-sectional household survey and clinical studies conducted in Timika. Standard population genetic measures were applied, and the data was compared to published data from Kalimantan, Bangka, Sumba and West Timor.ResultsHigher diversity (HE = 0.847 vs 0.625; p = 0.017) and polyclonality (46.2% vs 16.5%, p<0.001) were observed in P. vivax versus P. falciparum. Distinct P. falciparum substructure was observed, with two subpopulations, K1 and K2. K1 was comprised solely of asymptomatic infections and displayed greater relatedness to isolates from Sumba than to K2, possibly reflecting imported infections.ConclusionsThe results demonstrate the greater refractoriness of P. vivax versus P. falciparum to control measures, and risk of distinct parasite subpopulations persisting in the community undetected by passive surveillance. These findings highlight the need for complimentary new surveillance strategies to identify transmission patterns that cannot be detected with traditional malariometric methods.

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

“…Whilst we were conservative in our selection of regions under positive selection, and identified signatures in previously reported regions, the population structure in Sabah presents a challenge in this low-endemic setting. Furthermore, comparison with the Indonesian isolates, where high-grade CQR has been reported previously, may have been confounded by the high rate of local transmission 36 , which may have rapidly reduced haplotype homozygosity surrounding any drug resistance alleles in this population.…”

Mathematical modelling of the impact of expanding levels of malaria control interventions on Plasmodium vivax

“…Chief amongst these is understanding the contribution of low-density blood-stage infections to onwards transmission to mosquitoes 45 , systematic differences in blood-stage infections resulting from mosquito bites or relapses, and the duration of naturally acquired immunity. Furthermore, we do not account for the genetic diversity of P. vivax parasites, which typically exhibits greater diversity than P. falciparum parasites in co-endemic regions, suggesting that in comparison to P. falciparum , transmission of P. vivax is stable with a large effective population size 46 , 47 .…”

Evaluation of the implementation of single screening and treatment for the control of malaria in pregnancy in Eastern Indonesia: a systems effectiveness analysis

“…In the absence of screening, these women would not have been diagnosed for malaria. Sub-microscopic infections and asymptomatic infections have previously been identified in Papua [ 2 , 24 ], yet the associated clinical outcomes of these infection are not well understood. In an observational study of ANC visits in eastern India, blood tests were typically obtained if a patient complained of fever, though enquiries into presence of fever in patients were made in only a minority of patients [ 25 ].…”