No evidence of P. falciparum K13 artemisinin conferring mutations over a 24-year analysis in Coastal Kenya, but a near complete reversion to chloroquine wild type parasites.

Kevin Wamae,Lynette Isabella Ochola-Oyier,Abdirahman I Abdi,Victor Osoti,Colin Sutherland,Leonard Ndwiga,Dorcas Okanda,Kelvin M Kimenyi,Philip Bejon

doi:10.1128/aac.01067-19

Abstract

Antimalarial drug resistance is a substantial impediment to malaria control. The spread of resistance has been described using genetic markers which are important epidemiological tools. We carried out a temporal analysis of changes in allele frequencies of 12 drug resistance markers over two decades of changing antimalarial drug policy in Kenya. We did not detect any of the validated kelch 13 (k13) artemisinin resistance markers, nonetheless, a single k13 allele, K189T, was maintained at a stable high frequency (>10%) over time. There was a distinct shift from chloroquine resistant transporter (crt)-76, multi-drug resistant gene 1 (mdr1)-86 and mdr1-1246 chloroquine (CQ) resistance alleles to a 99% prevalence of CQ sensitive alleles in the population, following the withdrawal of CQ from routine use. In contrast, the dihydropteroate synthetase (dhps) double mutant (437G and 540E) associated with sulfadoxine-pyrimethamine (SP) resistance was maintained at a high frequency (>75%), after a change from SP to artemisinin combination therapies (ACTs). The novel cysteine desulfurase (nfs) K65 allele, implicated in resistance to lumefantrine in a West African study, showed a gradual significant decline in allele frequency pre- and post-ACT introduction (from 38% to 20%), suggesting evidence of directional selection in Kenya, potentially not due to lumefantrine. The high frequency of CQ-sensitive parasites circulating in the population suggests that the re-introduction of CQ in combination therapy for the treatment of malaria can be considered in the future. However, the risk of a re-emergence of CQ resistant parasites circulating below detectable levels or being reintroduced from other regions remains.

Highlights

Antimalarial drug resistance is a substantial impediment to malaria control
Other than K189T, the only other polymorphism observed across all time points is the asparagine (Asn) repeat at codon 137
Many of the polymorphic codons occurred in the N-terminal region compared to the C-terminal region, and from 1995/1996 to 2015/2016, the Ka/Ks ratio for the whole k13 gene ranged from 2.25 to 5

Summary

Introduction

Antimalarial drug resistance is a substantial impediment to malaria control. The spread of resistance has been described using genetic markers, which are important epidemiological tools. Resistance to former first-line antimalarials, chloroquine (CQ) and sulfadoxine-pyrimethamine (SP), was imported to Africa via strains from South East (SE) Asia [1,2,3], some drug resistance markers to pyrimethamine emerged independently in Africa [4] and were associated with increased malaria-related mortality in sub-Saharan Africa [5, 6] For this reason, the recent emergence and spread of artemisinin resistance in SE Asia [7,8,9], as December 2019 Volume 63 Issue 12 e01067-19. While these mutations have been identified in parasites from Africa, they occur at very low frequencies (arps-10-V127M, 0%; fd-D193Y, 0.1%; mdr2-T484I, 0.1%; crt-N326S, 0.8%) [16] It is crucial for regions outside SE Asia to monitor the emergence of artemisinin resistance signatures, including the selection of markers associated with changes in antimalarial drug policy, drug trials, and experimental analyses. Its impact has yet to be elucidated, a novel dhps I431V allele has been detected in West Africa, Cameroon, and Nigeria [33, 34]

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Conclusion