title: Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States.
abstract: BACKGROUND
  Human immunodeficiency virus type 1 (HIV-1) dual infection (DI) has been associated with decreased CD4 T-cell counts and increased viral loads; however, the frequency of intrasubtype DI is poorly understood. We used ultradeep sequencing (UDS) to estimate the frequency of DI in a primary infection cohort of predominantly men who have sex with men (MSM).
  
  
  METHODS
  HIV-1 genomes from longitudinal blood samples of recently infected, therapy-naive participants were interrogated with UDS. DI was confirmed when maximum sequence divergence was excessive and supported by phylogenetic analysis. Coinfection was defined as DI at baseline; superinfection was monoinfection at baseline and DI at a later time point.
  
  
  RESULTS
  Of 118 participants, 7 were coinfected and 10 acquired superinfection. Superinfection incidence rate was 4.96 per 100 person-years (95% confidence interval [CI], 2.67-9.22); 6 occurred in the first year and 4 in the second. Overall cumulative prevalence of intrasubtype B DI was 14.4% (95% CI, 8.6%-22.1%). Primary HIV-1 incidence was 4.37 per 100 person-years (95% CI, 3.56-5.36).
  
  
  CONCLUSIONS
  Intrasubtype DI was frequent and comparable to primary infection rates among MSM in San Diego; however, superinfection rates declined over time. DI is likely an important component of the HIV epidemic dynamics, and development of stronger immune responses to the initial infection may protect from superinfection.
authors.affiliation: University of California San Diego, La Jolla, California.
authors.forename: Gabriel A
authors.initials: GA
authors.lastname: Wagner
authors.forename: Mary E
authors.initials: ME
authors.lastname: Pacold
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: Gemma
authors.initials: G
authors.lastname: Caballero
authors.forename: Antoine
authors.initials: A
authors.lastname: Chaillon
authors.forename: Abby E
authors.initials: AE
authors.lastname: Rudolph
authors.forename: Sheldon R
authors.initials: SR
authors.lastname: Morris
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Little
authors.forename: Douglas D
authors.initials: DD
authors.lastname: Richman
authors.forename: Davey M
authors.initials: DM
authors.lastname: Smith
mesh_terms: D000328:Adult; D060085:Coinfection / Q000453:epidemiology* / Q000821:virology*; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing; D018451:Homosexuality, Male; D006801:Humans; D015994:Incidence; D008297:Male; D010802:Phylogeny; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics; D014481:United States / Q000453:epidemiology
chemical_list: D012367:RNA, Viral
keywords: HIV-1 coinfection; HIV-1 superinfection; acute and early infection; intrasubtype HIV-1 dual infection; ultradeep sequencing