Genotyping data from P. falciparum isolates taken from primary and secondary symptomatic malaria episodes in four UK patients

PatientSex and age (yrs)TravelEpisode 1Episode 2 (elapsed time since previous episode)Mutation(s) or haplotypeWGSf clonality
1Male over 65AngolaAugust 2015 Lys189ThrCVIETTyr184PhedSer160AsnWT
43 daysLys189ThrCVIETTyr184PheSer160AsnWT
2Female under 21UgandaJanuary 2016 WTCVIETWTWTGlu1525Gln
28 days (cultured)aWTCVIETWTWTGlu1525Gln
3Male over 21LiberiaFebruary 2016 WT Gly112GluCVIET CVMNKTyr184Pheins_Lys233,e ins_Asn233WT≥2 clones
17 daysGly112GluCVMNKTyr184Pheins_Lys233WT1 clone
4Female under 21UgandaJanuary 2016 Lys189ThrCVIETWTins_Asn226, ins_Asn326Thr1500Ile
34 daysLys189ThrCVIETWTins_Asn226, ins_Asn326Thr1500Ile
  • a Parasites from the second malaria episode of patient 2 were successfully established in in vitro culture for estimation of drug susceptibility.

  • b The nomenclature used shows the wild-type (WT) (reference) amino acid encoded at the codon of interest, followed by the amino acid encoded by the observed variant. Mutations in the pfk13 locus previously associated with reduced susceptibility to artemisinin in vitro and in vivo in the Mekong region occur between codon 440 and the 3′ end of the coding region.

  • c The nomenclature used shows the single-letter amino acid code for codons 72 to 76, strongly associated with chloroquine resistance. The CVMNK haplotype has been associated with AL treatment failures in Kenya (5).

  • d The single mutation Tyr to Phe at codon 184 identifies the NFD genotype at codons 86, 184, and 1246 in the pfmdr1 locus, previously associated with AL failure in Tanzania and Kenya (5, 8).

  • e ins, insertion of one amino acid, relative to the reference sequence, after the codon shown.

  • f Whole-genome sequencing results for both parasite isolates from patient 3. In the primary episode, heterozygosity (variant allele frequencies of between 5% and 95% of total reads) was seen in over 4,000 loci. About 50% of reads at informative positions comprised variants also present in the monoclonal recrudescent episode (17 days later).