Molecular Characterization of Antimalarial Drug Resistance

The DNA sequences were analysed using the sequence analysis software 5 and then blasted on to the NCBI sequence database to confirm the k13 propeller gene sequence identity by using the Basic Local Alignment Search Tool (BLAST) at http://blast.ncbi.nlm.nih.gov/Blast.cgi. The sequences were exported to bio edit sequence alignment editor 7.2.5 for manual editing and then in to MEGA 5 software version 5.10 for detection of polymorphism using the PF3D7_1343700 and K13-propeller gene sequences present in the NCBI database were used as the reference sequence. Additional single-nucleotide polymorphism (SNPs) analysis within the K13 propeller gene was performed using the DnaSP software version 5.10.01. To assess the selection pressure in P. falciparum parasite population in Kisii County, Tajima’ D statistic and Fu & Li’s D test in DnaSP software 5.10.01 were used. In this analysis, the study evaluated whether the P. falciparum k13 propeller domain sequence data show evidence of deviation from the neutrality theory of molecular evolution. The analysis was done using commands in the DnaSP software. In the DnaSP software, the probability of Tajima’s D and Fu & Li’s D are estimated by simulation. The test uses information on the frequency of mutations (allelic variation) [23 (link)]. Tajima’s D and Fu & Li’s D test is based on the fact that under the neutral model, estimates of the number of polymorphic sites and the average number of nucleotide differences are correlated. The critical values (Tajima’s D and Fu & Li’s D) obtained were used in interpreting the findings under the neutrality assumption [24 (link)].