Samples from coastal Tanzania (178) and Zanzibar (213) were previously sequenced through multiple studies (Table 1, Supplemental Figure 1). These samples include 213 dried blood spots (DBS) collected in Zanzibar between February 2016 and September 2017, coming from cross-sectional surveys of asymptomatic individuals (n = 70) and an in vivo efficacy study of artesunate-amodiaquine (ASAQ) with single low dose primaquine (SLDP) in pediatric uncomplicated malaria patients in the western and central districts of Unguja island and Micheweni District on Pemba island (n = 143) (Msellem et al., 2020 (link)). These samples were geolocalized to shehias, the lowest geographic governmental designation of land in Zanzibar, across its two main islands, Unguja and the northern region of Pemba (Supplemental Figure 1). Mainland Tanzania samples were collected in rural Bagamoyo District, where malaria transmission persists, and residents frequently travel to Dar es Salaam, the major port from where travelers depart for Zanzibar. Of the mainland Bagamoyo samples, 138 were whole blood collected from 2015–2017 as part of an in vivo efficacy study of artemether-lumefantrine (AL) in pediatric uncomplicated malaria patients (Topazian et al., 2022 (link)), and the remaining 40 samples were leukodepleted blood collected in 2018 from asymptomatic but RDT-positive children who participated in a study investigating the transmission of P. falciparum to colony reared mosquitos. This project leveraged molecular inversion probe (MIP) data from SRA including PRJNA926345, PRJNA454490, PRJNA545345, and PRJNA545347.
In order to place coastal Tanzanian and Zanzibari samples in the context of African P. falciparum population structure across multiple regions, MIP data from 147 whole blood samples collected in Ahero District, Kenya from the same parasite clearance study were used (Topazian et al., 2022 (link)) in conjunction with a subset of data from 2,537 samples genotyped for a study of the 2013 Demographic Health Survey of the Democratic Republic of the Congo which included samples from DRC, Ghana, Tanzania, Uganda and Zambia (Verity et al., 2020 ) (see Supplemental Figure 2).