Highly multiplexed ddPCR-amplicon sequencing reveals strong Plasmodium falciparum population structure and isolated populations amenable to local elimination efforts in Zanzibar

Holzschuh, A.; Lerch, A.; Gerlovina, I.; Fakih, B. S.; Al-Mafazy, A.-W.; Reaves, E. J.; Ali, A.; Abbas, F.; Ali, M. H.; Ali, M. A.; Hetzel, M. W.; Yukich, J. O.; Koepfli, C.

doi:10.1101/2023.01.05.522832

bioRxiv · 10.1101/2023.01.05.522832

Highly multiplexed ddPCR-amplicon sequencing reveals strong Plasmodium falciparum population structure and isolated populations amenable to local elimination efforts in Zanzibar

Holzschuh, A.·Lerch, A.·Gerlovina, I.·Fakih, B. S.·Al-Mafazy, A.-W.·Reaves, E. J.·Ali, A.·Abbas, F.·Ali, M. H.·Ali, M. A.·Hetzel, M. W.·Yukich, J. O.·Koepfli, C.

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Abstract

Over the past 15 years, Zanzibar has made great strides towards malaria elimination; yet progress has stalled. Parasite genetic data of Plasmodium falciparum may inform strategies for malaria elimination by helping to identify contributory factors to parasite persistence. Here we elucidate fine-scale parasite population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. We sequenced 518 P. falciparum samples from 5 districts covering both main islands using a novel, highly multiplexed droplet digital PCR (ddPCR)-based amplicon deep sequencing method targeting 35 microhaplotypes and drug-resistance loci. Despite high genetic diversity, we observe strong fine-scale spatial and temporal structure of local parasite populations, including isolated populations on Pemba Island and genetically admixed populations on Unguja Island, providing evidence of ongoing local transmission. We observe a high proportion of highly related parasites in individuals living closer together, including between clinical index cases and the mostly asymptomatic cases surrounding them, consistent with isolation-by-distance. We identify a substantial fraction (2.9%) of related parasite pairs between Zanzibar, and mainland Tanzania and Kenya, consistent with recent importation. We identify haplotypes known to confer resistance to known antimalarials in all districts, including multidrug-resistant parasites, but most parasites remain sensitive to current first-line treatments. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and reveals actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination.

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Holzschuh, A., Lerch, A., Gerlovina, I., Fakih, B. S., Al-Mafazy, A.-W., Reaves, E. J., Ali, A., Abbas, F., Ali, M. H., Ali, M. A., Hetzel, M. W., Yukich, J. O., Koepfli, C.. 2023-01-06. Highly multiplexed ddPCR-amplicon sequencing reveals strong Plasmodium falciparum population structure and isolated populations amenable to local elimination efforts in Zanzibar. https://doi.org/10.1101/2023.01.05.522832

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