Novel Plasmodium falciparum K13 Gene Polymorphisms from Kisii County, Kenya during an era of Artemisinin-Based Combination Therapies (ACTs) deployment

Abstract Background Currently, Chemotherapy stands out as the major malaria intervention strategy, however, antimalarial resistance may hamper global elimination programs. Artemisinin Combined Therapies (ACTs) stands as the drug of choice for treatment of Plasmodium falciparum malaria. P. falciparum Kelch13 gene mutations are associated with artemisinin resistance. Thus, this study was aimed at evaluating the circulation of P. falciparum K13 Gene Polymorphisms from Kisii County, Kenya during an era of ACTs deployment. Methods Participants suspected to have malaria were recruited. P. falciparum was confirmed using microscopy method. Malaria-positive patients were treated with Artemether-Lumefantrine (AL). Blood was withdrawn from participants who tested positive for parasites after day 3 and kept in blood filter papers (ET31CHR; Whatman Limited, Kent, UK). DNA was extracted using chelex-suspension method. A nested polymerase chain reaction (PCR) was conducted and the second-round products were sequenced using Sanger’s method. Sequenced products were analyzed using DNAsp 5.10.01 software and then blasted on to the NCBI for K13 propeller gene sequence identity using the Basic Local Alignment Search Tool (BLAST). To assess the selection pressure in P. falciparum parasite population, Tajima’ D statistic and Fu & Li’s D test in DnaSP software 5.10.01 was used. Results Out of 275 enrolled participants, 231 completed the follow-up schedule. 13 (5.6%) had parasites on day 28 hence characterized for recrudescence. Out of the 13 samples suspected for recrudescence, 5 (38%) samples were positively amplified as P. falciparum, with polymorphisms in the K13-propeller gene detected. Polymorphisms at codon 539, 458, 561, 431 and 671 were detected. The sequences have been deposited in NCBI with bio-project number PRJNA885380 and accession numbers SAMN31087430, SAMN31087431, SAMN31087432, SAMN31087433, and SAMN31087434 for Marani, Nyamache, and Bonchari samples, respectively. Conclusions Validated WHO resistant Polymorphisms in the K13-propeller gene previously reported to be associated with artemisinin resistance were not detected in the P. falciparum isolates from Kisii County, Kenya. However, some previously reported un-validated K13 resistant Single Nucleotide Polymorphisms were reported in this study but with limited occurrences. The study has also reported new SNPs. More studies need to be carried out in the entire country to understand the association of reported mutations if any, with ACTs resistance.