Table 1 P. falciparum genes and variants targeted in amplicon assay

From: Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana

Gene name and ID in the 3D7 parasite clone

Key mutations targeted for genotyping

Associated antimalarial resistance or other phenotype

Chloroquine resistance transporter, crt (PF3D7_0709000)

K76T*

Chloroquine resistance marker

Dihydrofolate reductase, dhfr (PF3D7_0417200)

N51I, C59R, S108N*, I164L

Pyrimethamine resistance markers

Dihydropteroate synthase, dhps (PF3D7_0810800)

S436A, A437G*, K540E, A581G, A613S/T

Sulfadoxine resistance markers

Multidrug resistance protein 1, mdr1 (PF3D7_0523000)

N86Y, N86F, Y184F

No direct inferences, but possibly associated with resistance to several antimalarials including lumefantrine

kelch13 (PF3D7_1343700)

Different mutations in the propeller domain, for example, C580Y

Artemisinin partial resistance markers

Circumsporozoite protein, csp (PF3D7_0304600)

SNPs in the C-terminal region; assess full-length consensus sequence

Leading vaccine and monoclonal antibody target antigen

Merozoite surface protein 1, msp1 (PF3D7_0930300)

Assess full-length consensus sequence

Previously explored as a vaccine candidate; potential for use as a marker of complexity of infection

  1. A multiplex PCR targeted the drug resistance marker genes (crt, dhfr, dhps, mdr1 and kelch13) and the vaccine and monoclonal antibody target, csp, in a single assay. The msp1 PCR was performed in a separate reaction. Mutations in bold with asterisk were used as key markers of antimalarial drug susceptibility phenotyping. Details on primer sequences, amplicons and antimalarial drug susceptibility inference rules are provided in Supplementary Notes.
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