SNPs in the HIV-1 TATA box and the AIDS pandemic.
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.
Suslov
Valentin V
VV
Sector of Evolutionary Bioinformatics, Institute of Cytology and Genetics, 10 Lavrentyev Ave, Novosibirsk 630090, Russia. valya@bionet.nsc.ru
Ponomarenko
Petr M
PM
Efimov
Vadim M
VM
Savinkova
Ludmila K
LK
Ponomarenko
Mikhail P
MP
Kolchanov
Nikolay A
NA
D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology* / Q000821:virology*; D004252:DNA Mutational Analysis / Q000379:methods*; D004196:Disease Outbreaks / Q000706:statistics & numerical data*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D038622:Internationality; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015995:Prevalence; D016385:TATA Box / Q000235:genetics*