title: Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi.
abstract: BACKGROUND
  Malawi experienced prolonged use of sulfadoxine/pyrimethamine (SP) as the front-line anti-malarial drug, with early replacement of chloroquine and delayed introduction of artemisinin-based combination therapy. Extended use of SP, and its continued application in pregnancy is impacting the genomic variation of the Plasmodium falciparum population.
  
  
  METHODS
  Whole genome sequence data of P. falciparum isolates covering 2 years of transmission within Malawi, alongside global datasets, were used. More than 745,000 SNPs were identified, and differences in allele frequencies between countries assessed, as well as genetic regions under positive selection determined.
  
  
  RESULTS
  Positive selection signals were identified within dhps, dhfr and gch1, all components of the parasite folate pathway associated with SP resistance. Sitting predominantly on a dhfr triple mutation background, a novel copy number increase of ~twofold was identified in the gch1 promoter. This copy number was almost fixed (96.8% frequency) in Malawi samples, but found at less than 45% frequency in other African populations, and distinct from a whole gene duplication previously reported in Southeast Asian parasites.
  
  
  CONCLUSIONS
  SP resistance selection pressures have been retained in the Malawian population, with known resistance dhfr mutations at fixation, complemented by a novel gch1 promoter duplication. The effects of the duplication on the fitness costs of SP variants and resistance need to be elucidated.
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Matt
authors.identifier: http://orcid.org/0000-0002-7818-2348
authors.initials: M
authors.lastname: Ravenhall
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Ernest Diez
authors.initials: ED
authors.lastname: Benavente
authors.affiliation: Department of Physiology, College of Medicine, University of Malawi, Blantyre, Malawi.
authors.forename: Mwapatsa
authors.initials: M
authors.lastname: Mipando
authors.affiliation: Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Anja T R
authors.initials: AT
authors.lastname: Jensen
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Colin J
authors.initials: CJ
authors.lastname: Sutherland
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Cally
authors.initials: C
authors.lastname: Roper
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.|Centre for Statistics and Applications of University of Lisbon, Lisbon, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Sepúlveda
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Dominic P
authors.initials: DP
authors.lastname: Kwiatkowski
authors.affiliation: Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.|Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi.
authors.forename: Jacqui
authors.initials: J
authors.lastname: Montgomery
authors.affiliation: School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi.
authors.forename: Kamija S
authors.initials: KS
authors.lastname: Phiri
authors.affiliation: Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.|Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi.
authors.forename: Anja
authors.initials: A
authors.lastname: Terlouw
authors.affiliation: Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.
authors.forename: Alister
authors.initials: A
authors.lastname: Craig
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. susana.campino@lshtm.ac.uk.
authors.forename: Susana
authors.initials: S
authors.lastname: Campino
authors.affiliation: Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi. harold.ocholla@gmail.com.|School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi. harold.ocholla@gmail.com.
authors.forename: Harold
authors.initials: H
authors.lastname: Ocholla
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. taane.clark@lshtm.ac.uk.|Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK. taane.clark@lshtm.ac.uk.
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
mesh_terms: D000962:Antimalarials / Q000627:therapeutic use*; D002675:Child, Preschool; D004338:Drug Combinations; D004351:Drug Resistance; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D018503:Genome, Protozoan; D005838:Genotype; D006801:Humans; D007223:Infant; D016778:Malaria, Falciparum / Q000188:drug therapy*; D008295:Malawi; D008297:Male; D009154:Mutation; D010963:Plasmodium falciparum / Q000145:classification* / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide; D011739:Pyrimethamine / Q000627:therapeutic use*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013413:Sulfadoxine / Q000627:therapeutic use*
chemical_list: D000962:Antimalarials; D004338:Drug Combinations; C001205:fanasil, pyrimethamine drug combination; D013413:Sulfadoxine; D011739:Pyrimethamine