Molecular methods for tracking residual Plasmodium falciparum transmission in a close-to-elimination setting in Zanzibar

• Published in: Malaria Journal
• Main Authors: Benjamin Grossenbacher, Aurel Holzschuh, Natalie E. Hofmann, Kali Abdullah Omar, Logan Stuck, Bakar Shariff Fakih, Abdullah Ali, Joshua Yukich, Manuel W. Hetzel, Ingrid Felger
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2020
• Subjects: qPCR; Pooling; Community-wide molecular diagnostics; Plasmodium falciparum surveillance; Malaria elimination program; Arctic medicine. Tropical medicine; RC955-962; Infectious and parasitic diseases; RC109-216; Arctic
• Online Access: https://doi.org/10.1186/s12936-020-3127-x; https://doaj.org/article/be468b5f0a4d45829a278bbc8f3fd25c

Abstract Background Molecular detection of low-density Plasmodium falciparum infections is essential for surveillance studies conducted to inform malaria control strategies in close-to-elimination settings. Molecular monitoring of residual malaria infections usually requires a large study size, therefore sampling and diagnostic processes need to be economical and optimized for high-throughput. A method comparison was undertaken to identify the most efficient diagnostic procedure for processing large collections of community samples with optimal test sensitivity, simplicity, and minimal costs. Methods In a reactive case detection study conducted on Zanzibar, parasitaemia of 4590 individuals of all ages was investigated by a highly sensitive quantitative (q) PCR that targets multiple var gene copies per parasite genome. To reduce cost, a first round of positivity screening was performed on pools of dried blood spots from five individuals. Ten cycles of a pre-PCR were performed directly on the filter paper punches, followed by qPCR. In a second round, samples of positive pools were individually analysed by pre-PCR and qPCR. Results Prevalence in household members and neighbors of index cases was 1.7% (78/4590) with a geometric mean parasite density of 58 parasites/µl blood. Using qPCR as gold standard, diagnostic sensitivity of rapid diagnostic tests (RDTs) was 37% (29/78). Infections positive by qPCR but negative by RDT had mean densities of 15 parasites/µl blood. Conclusion The approach of pre-screening reactive case detection samples in pools of five was ideal for a low prevalence setting such as in Zanzibar. Performing direct PCR on filter paper punches saves substantial time and justifies the higher cost for a polymerase suitable for amplifying DNA directly from whole blood. Molecular monitoring in community samples provided a more accurate picture of infection prevalence, as it identified a potential reservoir of infection that was largely missed by RDT. The developed qPCR-based methodology for screening ...