title: A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes.
abstract: The epidemiology of HIV-1 in China has unique features that may have led to unique viral strains. We therefore tested the hypothesis that it is possible to find distinctive patterns in HIV-1 genomes sampled in China. Using a rule inference algorithm we could indeed extract from sequences of the third variable loop (V3) of HIV-1 gp120 a set of 14 signature patterns that with 89% accuracy distinguished Chinese from non-Chinese sequences. These patterns were found to be specific to HIV-1 subtype, i.e. sequences complying with pattern 1 were of subtype B, pattern 2 almost exclusively covered sequences of subtype 01_AE, etc. We then analyzed the first of these signature patterns in depth, namely that L and W at two V3 positions are specifically occurring in Chinese sequences of subtype B/B' (3% false positives). This pattern was found to be in agreement with the phylogeny of HIV-1 of subtype B inside and outside of China. We could neither reject nor convincingly confirm that the pattern is stabilized by immune escape. For further interpretation of the signature pattern we used the recently developed measure of Direct Information, and in this way discovered evidence for physical interactions between V2 and V3. We conclude by a discussion of limitations of signature patterns, and the applicability of the approach to other genomic regions and other countries.
authors.affiliation: Research Group Bioinformatics, Center for Medical Biology, University of Duisburg-Essen, Essen, Germany.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Reda
authors.initials: R
authors.lastname: Rawi
authors.forename: Christoph
authors.initials: C
authors.lastname: Wilms
authors.forename: Dominik
authors.initials: D
authors.lastname: Heider
authors.forename: Rongge
authors.initials: R
authors.lastname: Yang
authors.forename: Daniel
authors.initials: D
authors.lastname: Hoffmann
mesh_terms: D000596:Amino Acids; D001482:Base Composition; D002681:China; D019295:Computational Biology; D019143:Evolution, Molecular; D016679:Genome, Viral; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000276:immunology; D006801:Humans; D010446:Peptide Fragments / Q000737:chemistry; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices
chemical_list: D000596:Amino Acids; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments