Novel pfk13 polymorphisms in Plasmodium falciparum population in Ghana

Abstract

The molecular determinants of Plasmodium falciparum artemisinin resistance are the single nucleotide polymorphisms in the parasite's kelch propeller domain, pfk13. Validated and candidate markers are under surveillance in malaria endemic countries using artemisinin-based combination therapy. However, pfk13 mutations which may confer parasite artemisinin resistance in Africa remains elusive. It has therefore become imperative to report all observed pfk13 gene polymorphisms in malaria therapeutic efficacy studies for functional characterization. We herein report all novel pfk13 mutations observed only in the Ghanaian parasite population. In all, 977 archived samples from children aged 12 years and below with uncomplicated malaria from 2007 to 2017 were used. PCR/Sanger sequencing analysis revealed 78% (763/977) of the samples analyzed were wild type (WT) for pfk13 gene. Of the 214 (22%) mutants, 78 were novel mutations observed only in Ghana. The novel SNPs include R404G, P413H, N458D/H/I, C473W/S, R529I, M579T/Y, C580R/V, D584L, N585H/I, Q661G/L. Some of the mutations were sites and ecological zones specific. There was low nucleotide diversity and purifying selection at the pfk13 locus in Ghanaian parasite population. With increasing drug pressure and its consequent parasite resistance, documenting these mutations as baseline data is crucial for future molecular surveillance of P. falciparum resistance to artemisinin in Ghana.

Figure 1

Sliding window plot of Tajima’s D for the pfk13 gene showing distribution by location/site. The computational analysis of the sequences to reveal the nucleotide diversity of the mutations in the pfk13 gene in Ghanaian isolates by study sites. Nucleotide positions is from 1000 to 2181 bp. Window length is 100 bp and step size is 25 bp.

Figure 2

Sliding window plot of Tajima’s D for the pfk13 gene showing temporal distribution. The computational analysis of the sequences to reveal the nucleotide diversity of the mutations in the pfk13 gene in Ghanaian isolates by year.Nucleotide positions is from 1000 to 2181 bp. Window length is 100 bp and step size is 25 bp.

Figure 3

Sliding window plot of Tajima’s D for the pfk13 gene showing distribution by ecological zones. The computational analysis of the sequences to reveal the nucleotide diversity of the mutations in the pfk13 gene in Ghanaian isolates by ecological zones. Nucleotide positions is from 1000 to 2181 bp. Window length is 100 bp and step size is 25 bp.

Figure 4

A map of Ghana showing the study sites in the ecological zones. These sites are designated for antimalarial drug therapeutic efficacy studies in all regions of Ghana.