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In order to study the hepatitis C virus (HCV) epidemiology in Flanders, Belgium, the HCV genotype of 2,301 patients diagnosed with HCV between 2001 and 2009 was determined. HCV genotyping was conducted using the Versant LiPA 1.0 or Versant LiPA 2.0 assay. To explore the transmission history of a remarkable cluster of the rarely found HCV genotype 5a, face-to-face interviews based on detailed questionnaires and maximum likelihood phylogenetic analysis were performed. HCV genotype 1 was the most prevalent genotype in all provinces, followed by HCV genotype 3 in East Flanders, Antwerp, Flemish Brabant and Limburg. In Brussels, HCV genotype 4 was the second most prevalent genotype. This observation is due to the immigration of patients from the Middle East and Africa. Remarkably, a cluster of HCV genotype 5a was found in West Flanders, where it represents the second most prevalent genotype, accounting for 26.2% of HCV infections. We could not identify one major transmission source explaining the whole HCV genotype 5a epidemic. Instead, several smaller possible transmission chains were identified and confirmed phylogenetically. Overall, the HCV genotype 5a epidemic in West Flanders seems to be mainly associated with blood transfusion and unsafe medical practices. [ABSTRACT FROM AUTHOR]