Fig. 5

Global diversity of clinical isolates and PfSPZ strains. Principal coordinate analyses (PCoA) of clinical isolates (n = 654) from malaria-endemic regions and PfSPZ strains were conducted using biallelic non-synonymous SNPs across the entire genome (left, n = 31,761) and in a panel of 42 pre-erythrocytic genes of interest (right, n = 1060). For the genome-wide dataset, coordinate 1 separated South American and African isolates from Southeast Asian and Papua New Guinean isolates (27.6% of variation explained), coordinate two separated African isolates from South American isolates (10.7%), and coordinate three separated Southeast Asian isolates from Papua New Guinea (PNG) isolates (3.0%). Similar trends were found for the first two coordinates seen for the pre-erythrocytic gene data set (27.1 and 12.6%, respectively), but coordinate three separated isolates from all three regions (3.8%). In both datasets, NF54 (black cross) and NF166.C8 (orange cross) cluster with West African isolates (isolates labeled in red and dark orange colors), 7G8 (bright green cross) cluster with isolates from South America (greens and browns), and NF135.C10 (pink cross) clusters with isolates from Southeast Asia (purples and blues)