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During 1994 and 1995, the prevalence of hepatitis C virus (HCV) and its genotypes were studied in several rural and urban populations in three West African countries: Guinea, Burkina Faso, and Benin. The following groups were screened for antibodies to HCV (anti-HCV): 459 villagers in the forest region of Guinea; 965 individuals in urban, suburban, and rural populations of the Bobo Dioulasso area, Burkina Faso; and 582 blood donors in Cotonou, Benin. In Benin, 60 patients with sickle cell anemia (30 with and 30 without history of multiple transfusion) and 13 hospital patients with liver disease were also tested. RT-PCR detection of HCV-RNA was carried out on all anti-HCV positive samples, followed by genotyping and sequencing of unrecognized subtypes. The prevalence rates of anti-HCV were 1.1% in the Guinean population group, 1.4% among blood donors in Benin, and 4.9% in residents of Burkina Faso. In patients with sickle cell anemia, five of the 30 polytranfused patients (17%) had anti-HCV, whereas none of the patients without a history of blood transfusion had anti-HCV (P < 0.05). Among the 13 patients with liver disease, five had anti-HCV, of whom four had history of blood transfusion. HCV-RNA was detected in 41 anti-HCV positive sera. All belonged to genotypes 1 or 2, with a high genomic diversity; 18 different subtypes were identified, including 2c, 2d, and 16 new subtypes. Such genetic diversity poses a challenge for vaccine development and also implies that HCV infection is long-established in these West African regions.