Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes

Abstract

Word Count : 246 Main Text Word Count: 3,649ABSTRACT High-throughput Plasmodium genomic data is increasingly useful in assessing prevalence of clinically important mutations and malaria transmission patterns. Understanding parasite diversity is important for identification of specific human or parasite populations that can be targeted by control programs, and to monitor the spread of mutations associated with drug resistance. An up-to-date understanding of regional parasite population dynamics is also critical to monitor the impact of control efforts. However, this data is largely absent from high-burden nations in Africa, and to date, no such analysis has been conducted for malaria parasites in Tanzania country-wide. To this end, over 1,000 P. falciparum clinical isolates were collected in 2017 from 13 sites in seven administrative regions across Tanzania, and parasites were genotyped at 1,800 variable positions genome-wide using molecular inversion probes. Population structure was detectable among Tanzanian P. falciparum parasites, roughly separating parasites from the northern and southern districts and identifying genetically admixed populations in the north. Isolates from geographically close districts were more likely to be genetically related compared to parasites sampled from more distant districts. Known drug resistance mutations were seen at increased frequency in northern districts, and additional variants with undetermined significance for antimalarial resistance also varied by geography. Malaria Indicator Survey (2017) data corresponded with genetic findings, including average region-level complexity-of-infection and malaria prevalence estimates. The parasite populations identified here provide important information on extant spatial patterns of genetic diversity of Tanzanian parasites, to which future surveys of genetic relatedness can be compared. 4 SIGNIFICANCE: Documenting dynamics of malaria parasite genomics in high-transmission settings at scale in sub-Saharan Africa is critical for policy and decision making to support ongoing malaria elimination initiatives.Using molecular inversion probes, we genotyped over 1,000 Tanzanian Plasmodium falciparum samples collected country-wide in 2017 at hundreds of variable polymorphic positions across the genome. Frequencies of known drug resistance mutations were higher in northern districts of the country compared to the south.Results also showed a distinct isolation-by-distance pattern (whereby increasing geographic distance was correlated with decreasing genetic relatedness), as well as signals of higher genetic sharing between several southern districts. These results provide, for the first time, a picture of current within-country diversity of Tanzanian P. falciparum populations.

Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes

“…Extracted DNA underwent capture and sequencing using two MIP panels previously described (Aydemir et al, 2018 (Moser et al, 2020).…”

The protective effect of sickle cell haemoglobin against severe malaria depends on parasite genotype

“…Taking together these new findings with other population genetic evidence from multiple locations across Africa, including observations of frequency differentiation within and across P.falciparum populations 17,21,22 and other metrics at these loci indicative of selection 20,23,24 , it appears likely that the allele frequencies and strong linkage disequilibrium between Pfsa1 , Pfsa2 and Pfsa3 are maintained by natural selection. However, the mechanism for this is unclear.…”

Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study

“…The utility of AmpSeq for molecular surveillance of infectious diseases is evidenced by the growing number of protocols recently published or under development for Plasmodium and other pathogens (Aydemir et al, 2018;Fola et al, 2020;Jacob et al, 2021;Mitchell et al, 2021;Moser et al, 2021;Ruybal-Pesántez et al, 2021;Schwabl et al, 2020;Tessema et al, 2020) . Here, we demonstrate 24 the performance of two new panels for P. falciparum , designed to serve different use cases and exhibiting different per-sample costs and levels of complexity.…”