Understanding the diversification of HIV-1 groups M and O

Archer, J. and Robertson, D. L. (2007) Understanding the diversification of HIV-1 groups M and O. AIDS, 21(13), pp. 1693-1700. (doi: 10.1097/QAD.0b013e32825eabd0) (PMID:17690566)

Abstract

Objective: To quantify the similarity (or lack of) between the phylogenetic substructure of HIV-1 groups O and M. Methods: Two phylogenetic tree statistics – the subtype diversity ratio (SDR) and the subtype diversity variance (SDV) – were used in conjunction with bootstrap replicates on gag, pol and env sequence alignments of group O and M strains. Randomly generated phylogenetic trees were used as a control. Results: We show that, as expected, the established global-group M subtypes have a high degree of phylogenetic symmetry in relation to each other in terms of inter- and intra-subtype diversification. They are significantly different from the substructure present amongst the random trees. To the contrary, the group O diversification does not display this highly symmetrical substructure and is not significantly different from the substructure present on randomly generated trees. Phylogenies comprised of group M strains from the epicentre of the HIV/AIDS pandemic, the Democratic Republic of Congo (DRC), exhibit a substructure more similar to group O than to global-group M. Conclusions: The substructure present within groups O and M is quantifiably different. The well defined clades, the subtypes that characterize group M diversification, are not present in group O or amongst group M strains from the DRC. The group M subtypes are thus unique and a signature of pandemic HIV-1.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Robertson, Professor David
• Authors: Archer, J., and Robertson, D. L.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: AIDS
• Publisher: Lippincott, Williams and Wilkins
• ISSN: 0269-9370
• ISSN (Online): 1473-5571