High genetic diversity of Plasmodium falciparum in the low transmission setting of the Kingdom of Eswatini

Background: To better understand transmission dynamics, we characterized Plasmodium falciparum (Pf) genetic diversity in Eswatini, where transmission is low and sustained by importation. Methods: 26 Pf microsatellites were genotyped in 66% of all confirmed cases from 2014-2016 (n=582). Population and within-host diversity were used to characterize differences between imported and locally-acquired infections, as determined by travel history. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone. Results: The parasite population in Eswatini was highly diverse (HE=0.75) and complex, with 67% polyclonal infections, a mean MOI of 2.2, and mean FWS of 0.84. Imported cases had comparable diversity to local cases, but exhibited higher MOI (2.4 versus 2.0; p=0.004) and lower mean FWS (0.82 vs. 0.85; p=0.03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections. Discussion: In contrast to the commonly held perception that Pf diversity declines with decreasing transmission intensity, isolates from Eswatini exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.