title: Increasing prevalence of non-clade B HIV-1 strains in heterosexual men and women, as monitored by analysis of reverse transcriptase and protease sequences.
abstract: OBJECTIVE
  We evaluated the prevalence of HIV-1 non-clade B over time in a formerly clade B-restricted area. Protease and reverse transcriptase regions of the pol gene were used for phylogenetic and recombination analysis and for clade assignment to HIV-1 A-D, F-H, J, and K strains of the M group.
  
  
  METHODS
  The pol gene of 349 HIV-1 patients belonging to the Italian Cohort Naive for Antiretrovirals (ICONA) were genotypically analyzed to study the prevalence of antiretroviral-associated resistance mutations. All HIV-1 pol sequences and 32 HIV reference strains were analyzed, including the reference strains for the major HIV-1 subtypes. The non-clade B sequences according to the HIV-1 Subtyping Tool program were further studied by a bootscan analysis (SimPlot) to investigate the likelihood of recombination between subtypes.
  
  
  RESULTS
  Phylogenetic analysis detected 19 of 349 (5.4%) non-clade B subtypes. The proportions of patients carrying non-clade B virus before and after 1997 were 1.9% and 8.4%, respectively (p =.008). Among whites, heterosexual infection and female gender were significantly associated with the presence of non-clade B subtypes (p =.001 and.005, respectively). Non-clade B HIV-1 was harbored by 14.5% of the heterosexuals who were found to be HIV-1 positive after 1997, 60% of whom were women. Bootscan analysis identified four strains as F, two as A, one as C, one as G, and 11 (57.9 %) as non-clade B recombinant subtypes.
  
  
  CONCLUSIONS
  Detection of HIV-1 subtypes and intersubtype recombinants in a previously clade B-homogeneous area indicates that the HIV-1 epidemic is evolving in Italy and that heterosexuals and women are at increased risk of infection with non-clade B HIV-1 subtypes. Sequences inferred from the pol gene yield to establish the subtype of circulating HIV-1 strains. As a consequence, genotyping of pol gene for testing resistance to antiretrovirals warrants concomitant surveillance of non-clade B subtypes.
authors.affiliation: Institute of Infectious and Tropical Diseases, L. Sacco Hospital, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy. claudia.balotta@unimi.it
authors.forename: C
authors.initials: C
authors.lastname: Balotta
authors.forename: G
authors.initials: G
authors.lastname: Facchi
authors.forename: M
authors.initials: M
authors.lastname: Violin
authors.forename: S
authors.initials: S
authors.lastname: Van Dooren
authors.forename: A
authors.initials: A
authors.lastname: Cozzi-Lepri
authors.forename: F
authors.initials: F
authors.lastname: Forbici
authors.forename: A
authors.initials: A
authors.lastname: Bertoli
authors.forename: C
authors.initials: C
authors.lastname: Riva
authors.forename: D
authors.initials: D
authors.lastname: Senese
authors.forename: P
authors.initials: P
authors.lastname: Caramello
authors.forename: G
authors.initials: G
authors.lastname: Carnevale
authors.forename: G
authors.initials: G
authors.lastname: Rizzardini
authors.forename: L
authors.initials: L
authors.lastname: Cremonini
authors.forename: L
authors.initials: L
authors.lastname: Monno
authors.forename: G
authors.initials: G
authors.lastname: Rezza
authors.forename: C F
authors.initials: CF
authors.lastname: Perno
authors.forename: G
authors.initials: G
authors.lastname: Ippolito
authors.forename: A
authors.initials: A
authors.lastname: d'Arminio-Monforte
authors.forename: A M
authors.initials: AM
authors.lastname: Vandamme
authors.forename: M
authors.initials: M
authors.lastname: Moroni
mesh_terms: D000328:Adult; D005260:Female; D015751:Genes, pol / Q000235:genetics*; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D020010:Heterosexuality; D006801:Humans; D007558:Italy / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D012367:RNA, Viral / Q000097:blood; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral; D054303:HIV Reverse Transcriptase; D016333:HIV Protease