title: Molecular Epidemiology and Transmission Dynamics of Recent and Long-Term HIV-1 Infections in Rural Western Kenya.
abstract: OBJECTIVE
  To identify unique characteristics of recent versus established HIV infections and describe sexual transmission networks, we characterized circulating HIV-1 strains from two randomly selected populations of ART-naïve participants in rural western Kenya.
  
  
  METHODS
  Recent HIV infections were identified by the HIV-1 subtype B, E and D, immunoglobulin G capture immunoassay (IgG BED-CEIA) and BioRad avidity assays. Genotypic and phylogenetic analyses were performed on the pol gene to identify transmitted drug resistance (TDR) mutations, characterize HIV subtypes and potential transmission clusters. Factors associated with recent infection and clustering were assessed by logistic regression.
  
  
  RESULTS
  Of the 320 specimens, 40 (12.5%) were concordantly identified by the two assays as recent infections. Factors independently associated with being recently infected were age ≤19 years (P = 0.001) and history of sexually transmitted infections (STIs) in the past six months (P = 0.004). HIV subtype distribution differed in recently versus chronically infected participants, with subtype A observed among 53% recent vs. 68% chronic infections (p = 0.04) and subtype D among 26% recent vs. 12% chronic infections (p = 0.012). Overall, the prevalence of primary drug resistance was 1.16%. Of the 258 sequences, 11.2% were in monophyletic clusters of between 2-4 individuals. In multivariate analysis factors associated with clustering included having recent HIV infection P = 0.043 and being from Gem region P = 0.002.
  
  
  CONCLUSIONS
  Recent HIV-1 infection was more frequent among 13-19 year olds compared with older age groups, underscoring the ongoing risk and susceptibility of younger persons for acquiring HIV infection. Our findings also provide evidence of sexual networks. The association of recent infections with clustering suggests that early infections may be contributing significant proportions of onward transmission highlighting the need for early diagnosis and treatment as prevention for ongoing prevention. Larger studies are needed to better understand the structure of these networks and subsequently implement and evaluate targeted interventions.
authors.affiliation: US Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention (CDC), Kisumu, Kenya.
authors.forename: Clement
authors.initials: C
authors.lastname: Zeh
authors.affiliation: Kenya Medical Research Institute (KEMRI)/CDC Research and Public Health Collaboration, Kisumu Field Research Station, Kisumu, Kenya.|Amsterdam Institute of Global Health and Development (AIGHD), Department of Global Health of the Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: Seth C
authors.initials: SC
authors.lastname: Inzaule
authors.affiliation: Amsterdam Institute of Global Health and Development (AIGHD), Department of Global Health of the Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: Pascale
authors.initials: P
authors.lastname: Ondoa
authors.affiliation: Kenya Medical Research Institute (KEMRI)/CDC Research and Public Health Collaboration, Kisumu Field Research Station, Kisumu, Kenya.
authors.forename: Lillian G
authors.initials: LG
authors.lastname: Nafisa
authors.affiliation: Kenya Medical Research Institute (KEMRI)/CDC Research and Public Health Collaboration, Kisumu Field Research Station, Kisumu, Kenya.
authors.forename: Alex
authors.initials: A
authors.lastname: Kasembeli
authors.affiliation: Kenya Medical Research Institute (KEMRI)/CDC Research and Public Health Collaboration, Kisumu Field Research Station, Kisumu, Kenya.
authors.forename: Fredrick
authors.initials: F
authors.lastname: Otieno
authors.affiliation: Institute of Tropical Medicine (ITM), Antwerp, Belgium.
authors.forename: Hilde
authors.initials: H
authors.lastname: Vandenhoudt
authors.affiliation: US Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention (CDC), Kisumu, Kenya.
authors.forename: Pauli N
authors.initials: PN
authors.lastname: Amornkul
authors.affiliation: US Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention (CDC), Kisumu, Kenya.|Kenya Medical Research Institute (KEMRI)/CDC Research and Public Health Collaboration, Kisumu Field Research Station, Kisumu, Kenya.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Mills
authors.affiliation: Division of Global HIV and Tuberculosis, Center for Global Health, CDC Atlanta, Georgia, United States of America.
authors.forename: John N
authors.initials: JN
authors.lastname: Nkengasong
mesh_terms: D000293:Adolescent; D000328:Adult; D000914:Antibodies, Viral / Q000097:blood*; D005260:Female; D015751:Genes, pol; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000523:psychology / Q000635:transmission* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D007074:Immunoglobulin G / Q000097:blood; D007630:Kenya / Q000453:epidemiology; D016015:Logistic Models; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D005810:Multigene Family; D010802:Phylogeny; D015995:Prevalence; D012309:Risk-Taking; D012424:Rural Population; D012747:Sexual Partners / Q000523:psychology
chemical_list: D000914:Antibodies, Viral; D007074:Immunoglobulin G