Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa

dc.contributor.authorGwarinda, Hazel B.
dc.contributor.authorTessema, Sofonias K.
dc.contributor.authorRaman, Jaishree
dc.contributor.authorGreenhouse, Bryan
dc.contributor.authorBirkholtz, Lyn-Marie
dc.contributor.emaillbirkholtz@up.ac.zaen_ZA
dc.date.accessioned2021-07-14T09:31:58Z
dc.date.available2021-07-14T09:31:58Z
dc.date.issued2021-02
dc.description.abstractBACKGROUND : South Africa aims to eliminate malaria transmission by 2023. However, despite sustained vector control efforts and case management interventions, the Vhembe District remains a malaria transmission hotspot. To better understand Plasmodium falciparum transmission dynamics in the area, this study characterized 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. Using 26 neutral microsatellite markers, differences in genetic diversity were described using a multiparameter scale of multiplicity of infection (MOI), inbreeding metric (Fws), number of unique alleles (A), expected heterozygosity (He), multilocus linkage disequilibrium (LD) and genetic differentiation, and were associated with temporal and geospatial variances. RESULTS : A total of 747 (65%) samples were successfully genotyped. Moderate to high genetic diversity (mean 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. CONCLUSIONS : Consistent with the Vhembe District’s classification as a ‘high’ transmission setting within South Africa, P. falciparum diversity in the area was moderate to high and complex. This study showed that genetic diversity within the parasite population reflects the continued residual transmission observed in the Vhembe District. This data can be used as a reference point for the assessment of the effectiveness of on-going interventions over time, the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.departmentGeneticsen_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.departmentUP Centre for Sustainable Malaria Control (UP CSMC)en_ZA
dc.description.librarianhj2021en_ZA
dc.description.sponsorshipThe South African National Research Foundation (NRF) South African Research Chair (SARChI) programme and the South African Medical Research Council.en_ZA
dc.description.urihttps://malariajournal.biomedcentral.comen_ZA
dc.identifier.citationGwarinda, H.B., Tessema, S.K., Raman, J. et al. Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa. Malaria Journal 20, 96 (2021). https://doi.org/10.1186/s12936-021-03635-z.en_ZA
dc.identifier.issn1475-2875
dc.identifier.other10.1186/s12936-021-03635-z
dc.identifier.urihttp://hdl.handle.net/2263/80827
dc.language.isoenen_ZA
dc.publisherBMCen_ZA
dc.rights© The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License.en_ZA
dc.subjectPlasmodium falciparumen_ZA
dc.subjectGenetic diversityen_ZA
dc.subjectMicrosatellitesen_ZA
dc.subjectResidual transmissionen_ZA
dc.subjectSouth Africa (SA)en_ZA
dc.subjectVhembe Districten_ZA
dc.subjectLimpopo Province, South Africaen_ZA
dc.subjectRapid diagnostic tests (RDTs)en_ZA
dc.subjectMultiplicity of infection (MOI)en_ZA
dc.titleParasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africaen_ZA
dc.typeArticleen_ZA

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