Fast analysis of genomic homologies: Primate immunodeficiency virus

Abstract

We have recently published a new probabilistic algorithm which performs genomic comparisons on a huge scale. In the present paper it was applied to immunodeficiency viral sequences extracted from international gene databanks. During global sequence analysis of human (HIV1 and HIV2) and simian viruses by means of dot-matrix representation, series of homology were obtained which permitted the definition of families of viruses overlapping the species divisions. Sequences of interest were characterized to the lexical base sentence through successive zoomings. Strain-to-strain comparison confirmed subfamily classifications and led, for example, to the identification of divergent LTR sequences. By way of example, we described the application of the algorithm to the ANT70C and MVP5180 HIV1-O viruses, for which the observed differences were shown to correspond to a deletion in the U3 region, situated between the LEF and NF-kappaB sites. It was of interest to consider these data in a tentative phylogenetic interpretation.

Identification of conserved lentiviral sequences as landmarks of genomic flexibility

“…For example, CPZ viruses exhibited a striking analogy with HIV-1s, while AGM, macaque and sooty mangabey genomes showed a CLS organization rather similar to that found in HIV-2s, confirming molecular data. CPZ viruses also presented such a similarity with HIV-1s at the molecular level, yet they belonged to the simian viruses concerning the immunological characterization (e.g., [1,8,43]). Besides, the Sykes' monkey virus appeared to be particular since it presented only six CLSs, four of them being at the hinge of the pol/vif genes.…”

“…Using a previously published program [8,37], a general analysis was carried out to identify the highly conserved sequences common to all or a maximum of lentiviral genomes. We first established the length of sub-sequences with the following trial/error method selecting parts of genomes.…”

“…Studies of the HIV genetic variability required computerized methods to investigate genomic divergences [8][9][10][11]. A Recombinant Identification Program was applied to the HIV-1 gag and env coding regions and allowed to determine putative large recombination segments -thus delimiting 'recombination cassettes' -and to create phylogenetic trees [12].…”

“…Comparison of whole genomes of related 'species' (with the meaning of taxons) is currently considered to identify the genomic organization and functionality without prior biological characterization [8,18]. In our global approach concerning complete genomes in all situations, we carried out the detection of Conserved Lentiviral Sequences (CLSs), their precise location being harmonized thanks to the use of a single MMy 1 ® sequence starting reference (see Section 2).…”