Fig. 1.

Emergence of novel PfCRT mutations in SE Asia that associate with elevated PSA_0–3 h survival. a Sequence analysis of 869 P. falciparum genomes from multiple Asian countries, generated by the MalariaGEN consortium Pf3K database³⁷, identified three major PfCRT haplotypes (Dd2, Cam734, GB4) and the emergence of multiple variants at low prevalence. Haplotypes and their distribution by country are listed in Supplementary Tables 1, 2. Most isolates were collected in 2011–12, with additional Cambodian samples from 2009 to 2010 and 2013 (Supplementary Fig. 2). b Genome analysis of a separate set of 93 western Cambodian isolates, collected over the period 2010–16 by the Pasteur Institute in Phnom Penh, Cambodia (Supplementary Table 3), provided evidence of a rapid increase in the prevalence of novel PfCRT variants on the Dd2 allelic background. A subset of 51 of these Pasteur Cambodian isolates from the period 2010–13 were also typed for PSA_0–3 h survival rates and pfpm2 and pfmdr1 copy numbers, as shown in c–e. c Isolates harboring mutations H97Y, M343L, or G353V were associated with elevated PSA_0–3 h survival rates, an indicator of PPQ resistance (F145I had not been detected at that time). PPQ-resistant isolates were also observed that lacked these specific mutations. The dashed line of 10% survival represents a previously designated resistance threshold associated with a 32-fold increased risk of clinical failure¹¹. d All PPQ-resistant parasites in this sample set had multiple copies of pfpm2, although some parasites with multiple copies were also in the PPQ-sensitive survival range. All parasites harboring one of the three PfCRT mutations in c and d (designated in magenta) were multicopy pfpm2. e All PPQ-resistant parasites observed were single-copy pfmdr1. Magenta samples harbored novel PfCRT mutations represented in b