SNPs in the HIV-1 TATA box and the AIDS pandemic

J Bioinform Comput Biol. 2010 Jun;8(3):607-25. doi: 10.1142/s0219720010004677.

Abstract

Evolutionary trends have been examined in 146 HIV-1 forms (2662 copies, 2311 isolates) polymorphic for the TATA box using the "DNA sequence-->affinity for TBP" regression (TBP is the TATA binding protein). As a result, a statistically significant excess of low-affinity TATA box HIV-1 variants corresponding to a low level of both basal and TAT-dependent expression and, consequently, slow replication of HIV-1 have been detected. A detailed analysis revealed that the excess of slowly replicating HIV-1 is associated with the subtype E-associated TATA box core sequence "CATAAAA". Principal Component Analysis performed on 2662 HIV-1 TATA box copies in 70 countries revealed the presence of two principal components, PC1 (75.7% of the variance) and PC2 (23.3% of the variance). They indicate that each of these countries is specifically associated with one of the following trends in HIV-1 evolution: neutral drift around the normal TATA box; neutral drift around the slowly replicating TATA box core sequence (phylogenetic inertia); an adaptive increase in the frequency of the slowly replicating form.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acquired Immunodeficiency Syndrome / epidemiology*
  • Acquired Immunodeficiency Syndrome / virology*
  • DNA Mutational Analysis / methods*
  • Disease Outbreaks / statistics & numerical data*
  • HIV-1 / genetics*
  • Humans
  • Internationality
  • Polymorphism, Single Nucleotide / genetics*
  • Prevalence
  • TATA Box / genetics*