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Molecular Surveyor pfcrt & pfmdr1 Methodology

Methodology

PubMed Search terms: malaria AND (pfcrt OR pfmdr1) (2001-2014)

Inclusion criteria:

  • At least one pfcrt or pfmdr1 genotype from clinical isolate/infection
  • Original data
  • Baseline/pre-treatment infections
  • Genotype must be linked to study site/country

Exclusion criteria:

  • Publication not accessible
  • Publication in another language than English, French, Spanish or Italian
  • Cultured strains (e.g. 3D7)
  • Genotype data that have been previously published (data from original publication is included)
  • Post-treatment infections
  • Biased selection of baseline samples (e.g. only treatment failures, half resistant and half sensitive samples)
  • Regional pooled genotype data (i.e. from West Africa) where the origin of the infection cannot be deduced on country level
  • Genotype prevalences (%) presented in article,  without sample size

Decisions on data extraction

  • If the prevalence of only one allele (e.g. pfcrt 76T) is presented in the publication, the prevalence of the other allele (pfcrt K76) is calculated (as long as the mixed infections [pfcrt 76K/T] are clearly accounted for)
  • If only haplotype prevalence (e.g. pfcrt 72-76 or pfmdr1 86 184 1246) is presented in the publication, the genotypes of the single loci (pfcrt 76 or pfmdr1 86) are calculated from the haplotype frequencies (as long as there is nothing in the publication indicating that the prevalence of the haplotype is not representative for the prevalence of the single loci)
  • If there was no information about mixed infections in the publication and the total prevalence of the wild-type+the mutant allele was > 100%, it was assumed that mixed infections were included in the prevalence of both the wild-type and the mutant allele
  • Data in the publication are extracted “as is”, referred publications are not explored to find missing information; study year, study site etc
  • If there are multiple study sites and the genotype prevalence cannot be separated by site, the combined prevalence for all study sites is displayed with a pin pointing at the capital of the country

If you have any questions about the Molecular Surveyor or our Molecular Scientific Group, please email: molecular [at] wwarn [dot] org