Using genomic signatures for HIV-1 sub-typing

Background: Human Immunodeficiency Virus type 1 (HIV-1), the causative agent of Acquired Immune Deficiency Syndrome (AIDS), exhibits very high genetic diversity with different variants or subtypes prevalent in different parts of the world. Proper classification of the HIV-1 subtypes, displaying differential infectivity, plays a major role in monitoring the epidemic and is also a critical component for effective treatment strategy. The existing methods to classify HIV-1 sequence subtypes, based on phylogenetic analysis focusing only on specific genes/regions, have shown inconsistencies as they lack the capability to analyse whole genome variations. Several isolates are left unclassified due to unresolved sub-typing. It is apparent that classification of subtypes based on complete genome sequences, rather than sub-genomic regions, is a more robust and comprehensive approach to address genome-wide heterogeneity. However, no simple methodology exists that directly computes HIV-1 subtype from the complete genome sequence. Results: We use Chaos Game Representation (CGR) as an approach to identify the distinctive genomic signature associated with the DNA sequence organisation in different HIV-1 subtypes. We first analysed the effect of nucleotide word lengths (k = 2 to 8) on whole genomes of the HIV-1 M group sequences, and found the optimum word length of k = 6, that could classify HIV-1 subtypes based on a Test sequence set. Using the optimised word length, we then showed accurate classification of the HIV-1 subtypes from both the Reference Set sequences and from all available sequences in the database. Finally, we applied the approach to cluster the five unclassified HIV-1 sequences from Africa and Europe, and predict their possible subtypes. Conclusion: We propose a genomic signature-based approach, using CGR with suitable word length optimisation, which can be applied to classify intra-species variations, and apply it to the complex problem of HIV-1 subtype classification. We demonstrate that CGR is a simple and computationally less intensive method that not only accurately segregates the HIV-1 subtype and sub-subtypes, but also aid in the classification of the unclassified sequences. We hope that it will be useful in subtype annotation of the newly sequenced HIV-1 genomes.