title: Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa.
abstract: HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650-1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2.
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
authors.forename: James C
authors.initials: JC
authors.lastname: Iles
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
authors.forename: Jayna
authors.initials: J
authors.lastname: Raghwani
authors.affiliation: Department of Infection & Immunity, Walter & Eliza Hall Institute, Victoria 3052, Australia.
authors.forename: G L Abby
authors.initials: GLA
authors.lastname: Harrison
authors.affiliation: Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada.
authors.forename: Jacques
authors.initials: J
authors.lastname: Pepin
authors.affiliation: Global Viral, Yaoundé, Cameroon.
authors.forename: Cyrille F
authors.initials: CF
authors.lastname: Djoko
authors.affiliation: Metabiota, San Francisco, USA.
authors.forename: Ubald
authors.initials: U
authors.lastname: Tamoufe
authors.affiliation: Metabiota, San Francisco, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: LeBreton
authors.affiliation: Metabiota, San Francisco, USA.
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Schneider
authors.affiliation: Metabiota, San Francisco, USA.
authors.forename: Joseph N
authors.initials: JN
authors.lastname: Fair
authors.affiliation: Department of Military Health, Ministry of Defense, Kinshasa, Democratic Republic of the Congo.
authors.forename: Felix M
authors.initials: FM
authors.lastname: Tshala
authors.affiliation: Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo.
authors.forename: Patrick K
authors.initials: PK
authors.lastname: Kayembe
authors.affiliation: National Institute of Biomedical Research, Kinshasa, Democratic Republic of the Congo.
authors.forename: Jean Jacques
authors.initials: JJ
authors.lastname: Muyembe
authors.affiliation: National AIDS Control Program, Reference Laboratory, Kinshasa, Democratic Republic of the Congo.
authors.forename: Samuel
authors.initials: S
authors.lastname: Edidi-Basepeo
authors.affiliation: Metabiota, San Francisco, USA; Stanford University Program in Human Biology, Stanford, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Wolfe
authors.affiliation: Roslin Institute, University of Edinburgh, Edinburgh, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Simmonds
authors.affiliation: Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Klenerman
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. Electronic address: oliver.pybus@zoo.ox.ac.uk.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
mesh_terms: D000328:Adult; D000349:Africa / Q000453:epidemiology; D000368:Aged; D019143:Evolution, Molecular; D005260:Female; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D055815:Young Adult
keywords: Africa; DRC; Egypt; Hepatitis C; Molecular clock; Molecular epidemiology; Phylogeny; Prevalence; Skyline plot
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