Which Pf lab isolates carry Pfsa+ alleles?

As part of our recent work on human-malaria genetic interactions I tried to figure out what the Pfsa genotypes of available Pf isolates are. It turns out that, even though these alleles are common in many African populations, not very many of the available lab isolates carry them. This table lists those that I know of. The genotypes are presented based on inspecting three locations in available sequence data:

  • Pfsa1: Pf3D7_02_v3:631,190 T > A

  • Pfsa2: Pf3D7_02_v3:814,288 C > T

  • Pfsa3: Pf3D7_11_v3:1,058,035 T > A

These alleles are presented below as - for the reference allele and + for the alternate / second allele at the three loci.

IsolatePfsa genotypeReferences / links
3D7- - -reference sequence
P.falciparum Uganda Palo Alto (FUP/H)+ + +Sequence read archive,
NF166+ - +Moser et al 2020
CD01 (Congo)+ + +Otto et al 2018
GA01 (Gabon)+ - +Otto et al 2018
SN01 (Senegal)+ - +Otto et al 2018
ML01 (Mali) (mixed)- - +Otto et al 2018