1. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania.
- Author
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Holzschuh, Aurel, Lerch, Anita, Gerlovina, Inna, Fakih, Bakar, Al-Mafazy, Abdul-Wahid, Reaves, Erik, Ali, Abdullah, Abbas, Faiza, Ali, Mohamed, Hetzel, Manuel, Yukich, Joshua, and Koepfli, Cristian
- Subjects
Humans ,Plasmodium falciparum ,Malaria ,Falciparum ,Tanzania ,Drug Resistance ,Polymerase Chain Reaction - Abstract
Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
- Published
- 2023