Background: Hepatitis C virus (HCV) causes about 900 deaths per year in Burkina Faso. In the absence of a vaccine, HCV infection remains a major public health problem. In addition to prevention efforts, an important strategy in the fight against HCV is therapy. Knowledge of the different genotypes circulating can allow for better treatment tailoring. This study aimed to 1) determine the HCV genotypes among blood donors and among patients, and 2) to assess the performance of the rapid diagnostic tests used extensively in sub-Saharan Africa by comparing their results to those of molecular methods. Methods: A total of 85 anti-HCV-positive samples were tested for viral RNA and sequenced. The analysis was performed in three centers: The Molecular Biology and Genetic Laboratory/PIETRO Annigoni Biomolecular Research Centre (CERBA/LABIOGENE), the University of Ouagadougou, the National Blood Transfusion Centre (CNTS), Burkina Faso, and the National Blood Transfusion Institute (INTS), Paris, France. Data were analyzed using the software CLC and Mega. Results: Nineteen (19) samples from 85 (22.35%) were confirmed positives by Monolisa; 9 from patients and 10 blood donors, but only 47.36% (9/19) of these were RNA positive. The median viral load was 204,807 IU/ml. The nine RNA-positive samples were found through sequencing to be 88.88% of genotype 2 and 11.11% of genotype 1. The identified Subtypes of genotype 2 are subtypes 2f and 2d; subtype 1d for genotype 1. Conclusion: There is an important number of false positive results from serology. The HCV genotype 2 is the most frequent in Burkina Faso.
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