Molecular epidemiology of Plasmodium falciparum drug resistance and vaccine targets in high-transmission settings in Africa.

The spread of antimalarial drug resistance and the potential emergence of vaccine-escape variants in Plasmodium falciparum threaten progress toward malaria elimination in sub-Saharan Africa. Here, we applied a scalable, Oxford Nanopore-based amplicon sequencing platform to profile five resistance genes (crt, dhfr, dhps, mdr1, k13) and the vaccine target csp in clinical isolates from northern Nigeria. We identified high frequencies of dhfr-IRNI (90%) and dhps-SGKAA (45%) haplotypes, consistent with molecular markers of sulfadoxine-pyrimethamine (SP) resistance. However, no dhfr/dhps quintuple or sextuple mutation combinations associated with SP-IPTp failure were detected, supporting its continued preventive use in pregnancy. The chloroquine-resistant Pfcrt-76T allele persisted at ~ 25% frequency, suggesting both sustained resistant lineages and a potential re-expansion of chloroquine-susceptible parasites. No WHO-validated Pfk13 mutations linked to artemisinin partial resistance were observed, although novel nonsynonymous variants were detected. In parallel, polymorphisms within immunogenic domains of csp, the target of recently approved R21/Matrix-M vaccines were predicted to affect protein stability, though their functional consequences require experimental validation. Geographic analyses revealed localized clustering of resistance haplotypes, particularly in Kano and Yobe, reflecting heterogeneous selection pressures across transmission settings. Together, these findings establish a genomic surveillance framework for real-time monitoring of antimalarial resistance and vaccine-target polymorphisms in high-burden regions, with direct implications for evidence-based treatment policy and vaccine rollout strategies in Africa.