Structural defects and variations in the HIV-1 nef gene from rapid, slow and non-progressor children

Nicoletta Casartelli, Gigliola Di Matteo, Claudio Argentini, Caterina Cancrini, Stefania Bernardi, Guido Castelli, Gabriella Scarlatti, Anna Plebani, Paolo Rossi, Margherita Doria

Research output: Contribution to journalArticlepeer-review


Objectives: Evaluation of sequence evolution as well as structural defects and mutations of the human immunodeficiency virus-type 1 (HIV-1) nef gene in relation to disease progression in infected children. Design: We examined a large number of nef alleles sequentially derived from perinatally HIV-1-infected children with different rates of disease progression: six non-progressors (NPs), four rapid progressors (RPs), and three slow progressors (SPs). Methods: Nef alleles (182 total) were isolated from patients' peripheral blood mononuclear cells (PBMCs), sequenced and analysed for their evolutionary pattern, frequency of mutations and occurrence of amino acid variations associated with different stages of disease. Results: The evolution rate of the nef gene apparently correlated with CD4+ decline in all progression groups. Evidence for rapid viral turnover and positive selection for changes were found only in two SPs and two RPs respectively. In NPs, a higher proportion of disrupted sequences and mutations at various functional motifs were observed. Furthermore, NP-derived Nef proteins were often changed at residues localized in the folded core domain at cytotoxic T lymphocytes (CTL) epitopes (E105, K106, E110, Y132, K164, and R200), while other residues outside the core domain are more often changed in RPs (A43) and SPs (N173 and Y214). Conclusions: Our results suggest a link between nef gene functions and the progression rate in HIV-1-infected children. Moreover, non-progressor-associated variations in the core domain of Nef, together with the genetic analysis, suggest that nef gene evolution is shaped by an effective immune system in these patients.

Original languageEnglish
Pages (from-to)1291-1301
Number of pages11
JournalAIDS (London, England)
Issue number9
Publication statusPublished - Jun 13 2003


  • Disease progression
  • HIV
  • Nef
  • Pediatrics
  • Sequence variability

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

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