title: Routine HIV-1 genotyping as a tool to identify dual infections.
abstract: OBJECTIVE
  The incidence of HIV-1 dual infections is generally thought to be low, but as dual infections have been associated with accelerated disease progression, its recognition is clinically important. Methods to identify HIV-1 dual infections are time consuming and are not routinely performed.
  
  
  METHODS
  Genotyping of the HIV-1 protease and reverse transcriptase (prot/RT) genes is commonly performed in the western world to detect drug-resistance mutations in clinical isolates. In our hospital, prot/RT baseline sequencing is part of the patient care for all newly infected patients in the Amsterdam region since 2003. We reasoned that degenerate base codes in this sequence could indicate either extensive viral evolution or infection with multiple HIV-1 strains.
  
  
  METHODS
  We amplified, cloned and sequenced multiple HIV-1 envelope (env)-V3 and gag sequences from patients with 34 or more (range 34-99) degenerate base codes in the ViroSeq genotyping RT sequence (37 out of 1661 available records) to estimate the number of HIV-1 dual infections in this group.
  
  
  RESULTS
  Of the 37 patients included in this study, 16 (43.2%, equal to 1% of the 1661 total records) had an HIV-1 dual infection based on phylogenetic analysis of env-V3/gag sequences. If only sequences with 45 or more degenerate base codes were taken into account, 73.3% of patients showed evidence of a dual infection.
  
  
  CONCLUSIONS
  We describe an additional use of routinely performed HIV-1 genotyping. In patients with a high number of degenerate bases (> or = 34) in RT it is important to consider the possibility of a dual HIV-1 infection.
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Centre of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands.
authors.forename: Marion
authors.initials: M
authors.lastname: Cornelissen
authors.forename: Suzanne
authors.initials: S
authors.lastname: Jurriaans
authors.forename: Karolina
authors.initials: K
authors.lastname: Kozaczynska
authors.forename: Jan M
authors.initials: JM
authors.lastname: Prins
authors.forename: Raditijo A
authors.initials: RA
authors.lastname: Hamidjaja
authors.forename: Fokla
authors.initials: F
authors.lastname: Zorgdrager
authors.forename: Margreet
authors.initials: M
authors.lastname: Bakker
authors.forename: Nicole
authors.initials: N
authors.lastname: Back
authors.forename: Antoinette C
authors.initials: AC
authors.lastname: van der Kuyl
mesh_terms: D000328:Adult; D018791:CD4 Lymphocyte Count; D005260:Female; D015686:Gene Products, env / Q000235:genetics; D015750:Genes, gag; D005838:Genotype; D015658:HIV Infections / Q000276:immunology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D019562:Viral Load
chemical_list: D015686:Gene Products, env