Background Elimination of gambiense Human African Trypanosomiasis (gHAT) as public health problem has been achieved in countries like Côte d’Ivoire and Burkina Faso. The World Health Organization (WHO) has set targets for interruption of transmission of gHAT by 2030. In this context, the performance of diagnostic algorithms for early detection of HAT re-emergence remains to be assessed.

Methods Our study represents a further step in the analysis on 8,648 dried blood spots collected during HAT rapid diagnostic tests (RDT) screening in gHAT historical foci in South West Burkina Faso and Centre West Côte d’Ivoire. We assessed the specificity of three molecular tests on 1,000 randomly selected samples from each country. We performed the Trypanozoon subgenus-specific m18S qPCR and RIME LAMP and the Trypanosoma brucei gambiense-specific TgsGP qPCR.

Results No parasites were detected using parasitological investigations. The overall seroprevalence based on positivity to at least one RDT was 1.19% (103/8648, (0.83–1.55%). The specificities of m18S qPCR and TgsGP qPCR were 99% (990/1,000, 98.9–99.8%) and 99.8% (998/1,000, 95.5–100%) respectively. The RIME LAMP test was negative for all 1,000 specimens (specificity 100%).

Conclusion All molecular tests qPCR m18S, qPCR TgsGP and RIME LAMP showed high diagnostic specificity. A previous study demonstrated low analytical sensitivities for qPCR m18S and qPCR TgsGP (respectively 1,000 and 10,000 trypanosomes/mL) while that of the RIME LAMP (100 trypanosomes/mL) was in the range of parasitaemias commonly observed in HAT patients. However, none of the three tests was entirely suitable for high-throughput use. To decide what is the best algorithm for HAT post-elimination monitoring, data on costs for all possible algorithms including serological and parasitological diagnostics need to be considered, according to the epidemiological context.

Funding from the EDCTP2 Programme supported by the European Union (Project DRIA-2014-306-DiTECT-HAT).