Widespread resistance to chloroquine (CQ) informed the switch to artemisinin combination therapy (ACT) for treatment in the early 2000s. CQ sensitive P. falciparum have re-expanded in Ghana, after withdrawal of CQ. In Ghana, the genomic signatures of clinical isolates suggest differential selection at the drug transporter genes, Pfcrt and Pfmdr1. What is happening to the spread of resistance genes in the large reservoir of asymptomatic infections compared to clinical cases has been poorly studied. Hence we investigated this question in Bongo District, Ghana at the end of the 2012 dry season.
P. falciparum isolates were sequenced at Pfcrt (codons 72-76; N=170) and Pfmdr1 (codons 86,184; N=198). The prevalence of the CQ sensitive haplotype, Pfcrt CVMNK was 88.2% and the resistant haplotype, CVIET, was 3.5%. For Pfmdr1, the prevalences of the wildtype (NY) and mutant (NF) were 17.7% and 69.7%, respectively.
To investigate selection of these haplotypes, isolates with single genomes were further typed at microsatellite loci linked to Pfcrt (N=48) and Pfmdr1 (N=46). The percentage of unique multilocus haplotypes was high for Pfcrt CVMNK (95.8%) and the diversity was also high (He=0.75), suggestive of soft selective sweeps. Our results indicate that the CQ sensitive parasites have re-expanded from a genetically diverse reservoir that predates ACT introduction. For Pfmdr1 NY and NF, all isolates had unique multilocus haplotypes, and there was no significant difference in the He (NY: 0.85, NF: 0.83), suggestive of equal selective advantage. ACTs have a role in diversifying Pfmdr1, which warrants further investigation to decipher the patterns of selection.
We have shown that the asymptomatic reservoir, which has limited exposure to antimalarials at the end of the dry season, harboured highly diverse Pfcrt and Pfmdr1 haplotypes. The treatment policy change has influenced this diversity and as such, it is important to prioritize this reservoir during monitoring programs.