The amino acid transporter pfaat1 modulates chloroquine resistance and fitness in malaria parasites

The chloroquine (CQ) resistance transporter (pfcrt) is the main focus of CQ-resistance research in Plasmodium falciparum, with little emphasis on the role of other loci. Longitudinal genomic analyses of Gambian parasites revealed temporal signatures of selection on the amino acid transporter (pfaat1)-S258L variant which increased from 0-87% in frequency between 1984 and 2014 in parallel with pfcrt1-K76T. We conducted parasite genetic crosses identifying a chromosome 6 quantitative trait locus (QTL) containing pfaat1 that interacts epistatically with pfcrt to determine CQ-resistance. Gene editing demonstrated that pfaat1-S258L potentiates CQ-resistance but at a cost of reduced fitness, while pfaat1-F313S, a common Southeast Asian polymorphism, reduces CQ-resistance while restoring fitness. Our combined experimental and population genomic analyses reveal hidden complexity in CQ-resistance evolution and a central role for pfaat1. ### Competing Interest Statement The authors have declared no competing interest.