title: HIV-1 tropism: a comparison between RNA and proviral DNA in routine clinical samples from Chilean patients.
abstract: BACKGROUND
  HIV in Chile has a notification rate of 0.01%. Coreceptor antagonists are a family of antiretroviral drugs that are used with the prior knowledge of patients HIV-1 tropism. Viral RNA-based tropism detection requires a plasma viral load ≥1000 copies/mL, while proviral DNA-based detection can be performed regardless of plasma viral load. This test is useful in patients with low or undetectable viral loads and would benefit with a proper therapy. The aim of this study was to determine the correlation between HIV RNA and proviral genotypic DNA tropism tests.
  
  
  RESULTS
  Forty three Chilean patients were examined using population-based V3 sequencing, and a geno2pheno false-positive rate (FPR) cutoff values of 5, 5.75, 10 and 20%. With cutoff 5.75% a concordance of 88.4% in tropism prediction was found after a simultaneous comparison between HIV tropism assessment by RNA and DNA. In total, five discrepancies (11.6%) were found, 3 patients were RNA-R5/DNA-X4 and two were RNA-X4/DNA-R5. Proviral DNA enabled the prediction of tropism in patients with a low or undetectable viral load. For cutoff 5 and 5.75% genotypic testing using proviral DNA showed a similar sensitivity for X4 as RNA. We found that the highest sensitivity for detecting the X4 strain occurred with proviral DNA and cutoff of 10 and 20%. Viral loads were higher among X4 strain carriers than among R5 strain carriers (p < 0.05).
  
  
  CONCLUSIONS
  A high degree of concordance was found between tropism testing with RNA and testing with proviral DNA. Our results suggest that proviral DNA-based genotypic tropism testing is a useful option for patients with low or undetectable viral load who require a different therapy.
authors.affiliation: Laboratorio de Medicina Molecular, Hospital Clínico Universidad de Chile, Santiago, Chile. pferrer40@gmail.com.
authors.forename: Pablo
authors.initials: P
authors.lastname: Ferrer
authors.forename: Luisa
authors.initials: L
authors.lastname: Montecinos
authors.forename: Mario
authors.initials: M
authors.lastname: Tello
authors.forename: Rocio
authors.initials: R
authors.lastname: Tordecilla
authors.forename: Consuelo
authors.initials: C
authors.lastname: Rodríguez
authors.forename: Marcela
authors.initials: M
authors.lastname: Ferrés
authors.forename: Carlos M
authors.initials: CM
authors.lastname: Pérez
authors.forename: Carlos
authors.initials: C
authors.lastname: Beltrán
authors.forename: Maria A
authors.initials: MA
authors.lastname: Guzmán
authors.forename: Alejandro
authors.initials: A
authors.lastname: Afani
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002677:Chile; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D012367:RNA, Viral / Q000235:genetics*; D056189:Viral Tropism; D014773:Virology / Q000379:methods*; D055815:Young Adult
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral