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Accurate assessment and monitoring of the Plasmodium falciparum Kelch 13 (pfk13) gene associated with artemisinin resistance is critical to understand the emergence and spread of drug-resistant parasites in malaria-endemic regions. In this study, we evaluated the genomic profile of the pfk13 gene associated with artemisinin resistance in P. falciparum in Nigerian children by targeted sequencing of the pfk13 gene. Genomic DNA was extracted from 332 dried blood (DBS) spot filter paper samples from three Nigerian States. The pfk13 gene was amplified by nested polymerase chain reaction (PCR), and amplicons were sequenced to detect known and novel polymorphisms across the gene. Consensus sequences of samples were mapped to the reference gene sequence obtained from the National Center for Biotechnology Information (NCBI). Out of the 13 single nucleotide polymorphisms (SNPs) detected in the pfk13 gene, five (F451L, N664I, V487E, V692G and Q661H) have not been reported in other endemic countries to the best of our knowledge. Three of these SNPs (V692G, N664I and Q661H) and a non-novel SNP, C469C, were consistent with late parasitological failure (LPF) in two States (Enugu and Plateau States). There was no validated mutation associated with artemisinin resistance in this study. However, a correlation of our study with in vivo and in vitro phenotypes is needed to establish the functional role of detected mutations as markers of artemisinin resistance in Nigeria. This baseline information will be essential in tracking and monitoring P. falciparum resistance to artemisinin in Nigeria. [ABSTRACT FROM AUTHOR]

• Over 50% of parasites considered in this study harboured the mutant C 72 I 74 E 75 T 76 haplotype of the Pfcrt gene. • As it stands, CQ cannot be re-introduced as treatment for malaria in Nigeria if ACT resistance were to emerge. • 21.1% of parasites had the Pfmdr- 1 mutant N 86 F 184 haplotype in Nigeria which suggests an increase in prevalence. • The three ACTs considered in this study, i.e. AA, AL and DHP, are still effective antimalarials with DHP slightly superior. The emergence and spread of Plasmodium falciparum parasites resistant to artemisinin derivatives and their partners in southeastern Asia threatens malaria control and elimination efforts, and heightens the need for an alternative therapy. We have explored the distribution of P. falciparum chloroquine resistance transporter (Pfcrt) and multidrug-resistant gene 1 (Pfmdr- 1) haplotypes 10 years following adoption of artemisinin-based combination therapies in a bid to investigate the possible re-emergence of Chloroquine-sensitive parasites in Nigeria, and investigated the effect of these P. falciparum haplotypes on treatment outcomes of patients treated with artemisinin-based combination therapies. A total of 271 children aged <5 years with uncomplicated falciparum malaria were included in this study. Polymorphisms on codons 72–76 of the Pfcrt gene and codon 86 and 184 of Pfmdr -1 were determined using the high resolution melting assay. Of 240 (88.6%) samples successfully genotyped with HRM for Pfcrt , wildtype C 72 M 74 N 75 K 76 (42.9%) and mutant C 72 I 74 E 75 T 76 (53.8%) were observed. Also, wildtype N 86 Y 184 (62.9%) and mutant N 86 F 184 (21.1%), Y 86 Y 184 (6.4%), and Y 86 F 184 (0.4%) haplotypes of Pfmdr -1 were observed. Measures of responsiveness to ACTs were similar in children infected with P. falciparum crt haplotypes (C 72 I 74 E 75 T 76 and C 72 M 74 N 75 K 76) and major mdr -1 haplotypes (N 86 Y 184 , N 86 F 184 and Y 86 Y 184). Despite a 10 year gap since the malaria treatment policy changed to ACTs, over 50% of the P. falciparum parasites investigated in this study harboured the Chloroquine-resistant C 72 I 74 E 75 T 76 haplotype, however this did not compromise the efficacy of artemisinin-based combination therapies. Should complete artemisinin resistance emerge from or spread to Nigeria, chloroquine might not be a good alternative therapy. [ABSTRACT FROM AUTHOR]