Parasite Genetic Diversity Reflects Continued Residual Malaria Transmission in Vhembe District, A Hotspot in the Limpopo Province of South Africa

Abstract

Background: South Africa aims to eliminate malaria transmission by 2023. However, despite sustained vector control efforts and case management interventions, the Vhembe District in the Limpopo Province remains a malaria transmission hotspot. To better understand Plasmodium falciparum transmission dynamics in the area, this study characterised the genetic diversity of parasites circulating within the Vhembe District.Methods: A total of 1153 falciparum-positive rapid diagnostic tests (RDTs) were randomly collected from seven clinics within the district, over three consecutive years (2016, 2017 and 2018) during the wet and dry malaria transmission seasons. Parasite genomic material was isolated from the RDTs and parasite genetic diversity was characterised using 26 neutral microsatellite markers. Differences in genetic diversity were described using a multiparameter scale of multiplicity of infection (MOI), within-host diversity metric (Fws), number of unique alleles (A), expected heterozygosity (He), multilocus linkage disequilibrium (LD) and genetic differentiation (Wright's F-statistic, FST), and were associated with temporal and geospatial variances. Results: A total of 747 (65%) samples were successfully genotyped. High genetic diversity (mean heterozygosity, He = 0.74 ± 0.03) was observed in the parasite population. This was ascribed to high allelic richness (mean A = 12.2 ± 1.2). The majority of samples (99%) had unique multi-locus genotypes, indicating high genetic diversity in the sample set. Complex infections were observed in 66% of samples (mean MOI = 2.13 ± 0.04), with 33% of infections showing high within-host diversity as described by the Fws metric. Low, but significant LD (standardised index of association, ISA = 0.08, P < 0.001) was observed that indicates recombination of distinct clones. Limited impact of temporal (FST range -0.00005 to 0.0003) and spatial (FST = –0.028 to 0.023) variation on genetic diversity existed during the sampling timeframe and study sites respectively. Conclusion: Consistent with the Vhembe District’s classification as a 'high' transmission setting within South Africa, P. falciparum diversity in the area was high and complex. This study showed that genetic diversity within the parasite population reflects the continued residual transmission observed in the Vhembe District. This finding, together with continued surveillance of P. falciparum genetic diversity in South Africa, may influence future intervention strategies by targeting the parasite to decrease transmission intensity for the country to achieve its elimination goals.

Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of connectivity in a low-transmission district in Southern Province, Zambia

“…Genomic studies of local transmission and importation in low and medium endemicity countries are becoming more common in the literature and starting to shed light on the dynamics of parasite movement (Chenet et al, 2012;Daniels et al, 2015;Gwarinda et al, 2021;Kattenberg et al, 2020; Morgan AP, Brazeau NF, Ngasala B, Mhamilawa LE, Denton M, Msellem M, Morris U, Filer DL, Aydemir O, Bailey JA, Parr JB, Mårtensson A, Bjorkman A, Juliano JJ, n.d.; Noviyanti et al, 2015;Roh et al, 2019;Tessema et al, 2019). However, relatively few studies have used genomic approaches to study malaria transmission dynamics and importation on small geographic scales, such as a single district (Searle et al, 2020).…”

“…These low transmission settings offer a unique opportunity to observe long-term dynamics of parasites across seasons, as the smaller number of parasites may be easier to track from a lack of recombination with genetically distinct parasites within the mosquito. A small number of studies have attempted to observe temporal population changes in these regions, and even fewer have been able to combine temporal and geospatial data to identify hotspots over space and time (Chenet et al, 2012;Daniels et al, 2015;Gwarinda et al, 2021;Kattenberg et al, 2020;Noviyanti et al, 2015;Roh et al, 2019;Tessema et al, 2019). Most of these studies evaluated parasite population changes over relatively large geographic distances.…”