title: Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster.
abstract: In this study, we characterize HIV-1 subtype C (HIV-1C) strains at the near full-length genome (NFLG) level and perform genotypic drug resistance testing (GRT) and genotypic tropism testing (GTT) from Ethiopia (HIV-1CET). Plasma samples (n = 150) were obtained from therapy-naive individuals residing in Addis Ababa, Ethiopia in 2008. HIV-NFLG was performed in a subset of patients (n = 30). GRT (pol) and GTT (V3 env) were performed using in-house methods. GTT was analyzed by PhenoSeq-C. The phylogenetic analysis of the NLFG identified two separate clusters of HIV-1CET, although all strains formed one large overarching cluster together. At NFLG, greater diversity was found among HIV-1CET strains compared to HIV-1C strains from other geographical locations. The geographic clustering was weak in the small subgenomic (pol and env) regions. The primary drug-resistant mutations were identified at a low level (<5%). GTT identified that 12% (12/102) of the patients were predicted to be harboring X4-tropic or both R5/X4-tropic viruses.
authors.affiliation: 1 Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .|2 Department of Medicine, Faculty of Medicine, Addis Ababa University , Addis Ababa, Ethiopia .
authors.forename: Wondwossen
authors.initials: W
authors.lastname: Amogne
authors.affiliation: 1 Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .
authors.forename: Irene
authors.initials: I
authors.lastname: Bontell
authors.affiliation: 3 Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .
authors.forename: Sebastian
authors.initials: S
authors.lastname: Grossmann
authors.affiliation: 2 Department of Medicine, Faculty of Medicine, Addis Ababa University , Addis Ababa, Ethiopia .
authors.forename: Getachew
authors.initials: G
authors.lastname: Aderaye
authors.affiliation: 1 Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .
authors.forename: Lars
authors.initials: L
authors.lastname: Lindquist
authors.affiliation: 1 Department of Medicine, Unit of Infectious Diseases, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .|3 Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .
authors.forename: Anders
authors.initials: A
authors.lastname: Sönnerborg
authors.affiliation: 3 Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital , Karolinska Institutet, Stockholm, Sweden .
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
mesh_terms: D000328:Adult; D001483:Base Sequence; D024882:Drug Resistance, Viral / Q000235:genetics*; D005002:Ethiopia; D005260:Female; D016679:Genome, Viral / Q000235:genetics*; D005843:Geography; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics; D012367:RNA, Viral / Q000097:blood; D017423:Sequence Analysis, RNA; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D012367:RNA, Viral; D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus; D054302:pol Gene Products, Human Immunodeficiency Virus