Detection of copy number variation and single nucleotide polymorphisms in genes involved in drug resistance and other phenotypic traits in P. falciparum clinical isolates collected from Uganda

There is an increasing interest in mapping the genes of pathogens which underlie important phenotypic traits such as virulence and drug resistance. The Plasmodium falciparum genome exhibits sequence variation that contributes to the pathogenic mechanisms of the parasite. Determining the prevalence of resistance markers could provide a prediction about drug efficacy. Copy number polymorphism (CNP) of genes has been shown to influence important parasite phenotypes. In this work, CNPs within genes involved in drug resistance and other phenotypic traits namely P. falciparum multidrug resistance 1 (pfmdr-1), GTP cyclo hydrolase (gch1), Ring infected erythrocyte surface antigen precursor (resa) and a hypothetical protein coding gene were analyzed by quantitative real time-polymerase reaction (qRT-PCR) among clinical isolates collected from Uganda. The pfmdr-1 codons 86 and 1246 and P. falciparum chloroquine resistance (pfcrt) codon 76 were genotyped for single nucleotide polymorphisms (SNPs) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and the proportion of resistance associated mutations were determined among mild and severe malaria cases using the chi-square test. Forty and 42 P. falciparum isolates collected from children with mild and severe malaria respectively were analyzed for CNPs. Seventy five and 81 P. falciparum isolates from children with mild or severe malaria were analyzed for SNPs. No pfmdr-1, gch1 or novel gene amplifications were identified among the P. falciparum clinical isolates. Although chloroquine was officially withdrawn from policy use since 7 years, all P. falciparum isolates presented the associated pfcrt K76T mutation, whatever the clinical status and no specific mutation in the pfmdr-1 gene was associated with disease type. In conclusion, this study provides baseline measures for continued surveillance for changes in copy number and SNP types among genes implicated in drug resistance and other important phenotypes that may have a potential role in parasite virulence mechanisms or drug treatment outcomes. (c) 2012 Elsevier B.V. All rights reserved.