High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between  Zambia and the Democratic Republic of the Congo

Julia C. Pringle1* , Amy Wesolowski2, Sophie Berube3, Tamaki Kobayashi2, Mary E. Gebhardt1, Modest Mulenga4, Mike Chaponda4, Thierry Bobanga5, Jonathan J. Juliano6, Steven Meshnick7, William J. Moss2, Giovanna Carpi8 and Douglas E. Norris1*


Background : While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role for parasite genomics in driving these high burden settings towards elimination will enhance future control programme planning.

Methods : Amplicon deep sequencing was used to characterize parasite population genetic diversity at polymorphic Plasmodium falciparum loci, Pfama1 and Pfcsp, at two timepoints in June–July 2016 and January–March 2017 in a high transmission region along the international border between Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC).

Results : High genetic diversity was observed across both seasons and in both countries. No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone. Despite a decline in parasite prevalence at the sampling locations in Haut-Katanga Province, no genetic signatures of a population bottleneck were detected, suggesting that larger declines in transmission may be required to reduce parasite genetic diversity. Analysing rare variants may be a suitable alternative approach for detecting epidemiologically important genetic signatures in highly diverse populations; however, the challenge is distinguishing true signals from potential artifacts introduced by small sample sizes.

Conclusions : Continuing to explore and document the utility of various parasite genotyping approaches for understanding malaria transmission in holoendemic settings will be valuable to future control and elimination programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.

Keywords: Malaria, Genetic, Border, Diversity, Control, Amplicon deep sequencing, csp, ama1

Pringle et al. Malar J (2019) 18:400

Malaria Journal