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This study was designed to investigate the presence of Pfcrt drug- resistance alleles (CQ resistant biomarker) and attempted to analyse the outcome in some states of northern Nigeria. A total of four hundred and thirteen (413) Plasmodium falciparum positive blood samples were collected from Kaduna, Jigawa, Katsina and Kebbi states during the period of April-August 2013. The samples were genotyped at codon 76 using specific primers for Pfcrt gene. The data was analysed using Chi-square to determine significance association. Four hundred and thirteen (413) P. falciparum positive samples were genotyped at codon 76 of pfcrt gene. Sixty eight 68(16.5%) samples contained single K76 (Chloroquine sensitive) alleles, 49(11.9%) contained 76T, while 16(3.9%) contained mixed K76T alleles. K76 alleles were highest in Kaduna state 17(32.1%) and lowest in Kebbi state 10(7.4%), 76T was highest in Jigawa state 11 (25.6%) and lowest in Kebbi state 7(5.2%) while K76T was highest in Jigawa state 5(11.5%) and lowest in Kebbi state 2(1.5%) with significant difference between the states P<0.05. K76 was higher among females 43(17.6%), 76T was also higher females 30(12.2%) while K76T was higher among males 7 (4.2%). K76 was higher among age group of 16-25 years 17(22.4%) and least among 26-40years age group 13 (13.5%). 76T was also higher among 26-40 years age group 17(17.7%) and least among age group >40 years 1(2.0%) and K76T was higher among age group 16-25 years 6(7.9%) and least in >40 years of age 1(2.0%) with high significant difference P<0.05 between the age groups. The results of this study genetically confirms the use of CQ for malaria treatment in the area and attributed the varied distribution across the states, to high irrigation activities, self medication leading to dosage non compliance and improper diagnosis due to use of low sensitive RDT in most government hospitals. The need for enlightenment of the populace cannot over emphasize.