Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects

Filippo Canducci, Maria Chiara Marinozzi, Michela Sampaolo, Stefano Berrè, Patrizia Bagnarelli, Massimo Degano, Giulia Gallotta, Benedetta Mazzi, Philippe Lemey, Roberto Burioni, Massimo Clementi

Research output: Contribution to journalArticle

Abstract

The characteristics of intra-host human immunodeficiency virus type 1 (HIV-1) env evolution were evaluated in untreated HIV-1-infected subjects with different patterns of disease progression, including 2 normal progressor [NP], and 5 Long term non-progressor [LTNP] patients. High-resolution phylogenetic analysis of the C2-C5 env gene sequences of the replicating HIV-1 was performed in sequential samples collected over a 3-5 year period; overall, 301 HIV-1 genomic RNA sequences were amplified from plasma samples, cloned, sequenced and analyzed. Firstly, the evolutionary rate was calculated separately in the 3 codon positions. In all LTNPs, the 3rd codon mutation rate was equal or even lower than that observed at the 1st and 2nd positions (p = 0.016), thus suggesting strong ongoing positive selection. A Bayesian approach and a maximum-likelihood (ML) method were used to estimate the rate of virus evolution within each subject and to detect positively selected sites respectively. A great number of N-linked glycosylation sites under positive selection were identified in both NP and LTNP subjects. Viral sequences from 4 of the 5 LTNPs showed extensive positive selective pressure on the CD4-binding site (CD4bs). In addition, localized pressure in the area of the IgG-b12 epitope, a broad neutralizing human monoclonal antibody targeting the CD4bs, was documented in one LTNP subject, using a graphic colour grade 3-dimensional visualization. Overall, the data shown here documenting high selective pressure on the HIV-1 CD4bs of a group of LTNP subjects offers important insights for planning novel strategies for the immune control of HIV-1 infection.

Original languageEnglish
Article number4
JournalRetrovirology
Volume6
DOIs
Publication statusPublished - Jan 15 2009

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HIV-1
Binding Sites
Codon
env Genes
Bayes Theorem
Virus Diseases
Mutation Rate
Glycosylation
Disease Progression
Epitopes
Color
Immunoglobulin G
Monoclonal Antibodies
Viruses
Pressure

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

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Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects. / Canducci, Filippo; Marinozzi, Maria Chiara; Sampaolo, Michela; Berrè, Stefano; Bagnarelli, Patrizia; Degano, Massimo; Gallotta, Giulia; Mazzi, Benedetta; Lemey, Philippe; Burioni, Roberto; Clementi, Massimo.

In: Retrovirology, Vol. 6, 4, 15.01.2009.

Research output: Contribution to journalArticle

Canducci, Filippo ; Marinozzi, Maria Chiara ; Sampaolo, Michela ; Berrè, Stefano ; Bagnarelli, Patrizia ; Degano, Massimo ; Gallotta, Giulia ; Mazzi, Benedetta ; Lemey, Philippe ; Burioni, Roberto ; Clementi, Massimo. / Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects. In: Retrovirology. 2009 ; Vol. 6.
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