title: Complex Subtype Diversity of HIV-1 Among Drug Users in Major Kenyan Cities.
abstract: Drug users are increasingly recognized as a key population driving human immunodeficiency virus (HIV) spread in sub-Saharan Africa. To determine HIV-1 subtypes circulating in this population group and explore possible geographic differences, we analyzed HIV-1 sequences among drug users from Nairobi, Mombasa, and Kisumu in Kenya. We sequenced gag and env from 55 drug users. Subtype analysis from 220 gag clonal sequences from 54 of 55 participants (median = 4/participant) showed that 44.4% were A, 16.7% were C, 3.7% were D, and 35.2% were intersubtype recombinants. Of 156 env clonal sequences from 48 of 55 subjects (median = 3/participant), 45.8% were subtype A, 14.6% were C, 6.3% were D, and 33.3% were recombinants. Comparative analysis of both genes showed that 30 (63.8%) participants had concordant subtypes, while 17 (36.2%) were discordant. We identified one genetically linked transmission pair and two cases of dual infection. These data are indicative of extensive HIV-1 intersubtype recombination in Kenya and suggest decline in subtype D prevalence.
authors.affiliation: 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .|2 Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .
authors.forename: Kamini
authors.initials: K
authors.lastname: Gounder
authors.affiliation: 3 Immunology Unit, Department of Human Pathology, University of Nairobi , Nairobi, Kenya .
authors.forename: Micah
authors.initials: M
authors.lastname: Oyaro
authors.affiliation: 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .|2 Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .
authors.forename: Nagavelli
authors.initials: N
authors.lastname: Padayachi
authors.affiliation: 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .|2 Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .
authors.forename: Thando Mbali
authors.initials: TM
authors.lastname: Zulu
authors.affiliation: 4 School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal , Durban, South Africa .|5 Africa Centre for Population Health, University of KwaZulu-Natal , Durban, South Africa .
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
authors.affiliation: 6 Department of Medical Microbiology, University of Manitoba , Winnipeg, Canada .
authors.forename: John
authors.initials: J
authors.lastname: Wylie
authors.affiliation: 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .|2 Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa .|7 Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University , Boston, Massachusetts.|8 Max Planck Institute for Infection Biology , Berlin, Germany .
authors.forename: Thumbi
authors.initials: T
authors.lastname: Ndung'u
mesh_terms: D000293:Adolescent; D000328:Adult; D002947:Cities / Q000453:epidemiology; D060085:Coinfection / Q000821:virology; D003430:Cross-Sectional Studies; D018562:Disease Transmission, Infectious; D055030:Drug Users; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D008297:Male; D017720:Molecular Epidemiology; D017422:Sequence Analysis, DNA; D019966:Substance-Related Disorders / Q000150:complications*; D055815:Young Adult; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus
keywords: HIV-1 subtypes; Kenya; drug users; intersubtype recombinants