Increasing prevalence of non-clade B HIV-1 strains in heterosexual men and women, as monitored by analysis of reverse transcriptase and protease sequences

Claudia Balotta, Guido Facchi, Michela Violin, Sonia Van Dooren, Alessandro Cozzi-Lepri, Federica Forbici, Ada Bertoli, Chiara Riva, Daniela Senese, Pietro Caramello, Giuseppe Carnevale, Giuliano Rizzardini, Laura Cremonini, Laura Monno, Giovanni Rezza, Carlo Federico Perno, Giuseppe Ippolito, Antonella D'Arminio-Monforte, Anne Mieke Vandamme, Mauro Moroni

Research output: Contribution to journalArticlepeer-review


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. Conclusion: 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 nonclade 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.

Original languageEnglish
Pages (from-to)499-505
Number of pages7
JournalJournal of Acquired Immune Deficiency Syndromes
Issue number5
Publication statusPublished - Aug 15 2001


  • Circulating HIV-1 recombinant forms
  • HIV-1 pol sequences
  • HIV-1 subtypes
  • Italian Cohort Naive for Antiretrovirals

ASJC Scopus subject areas

  • Virology
  • Immunology


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