1. Analysis of Recombination in the HIV-1pol Gene Richard Myers Division of Infection and Immunity University College London

2. HIV-1 Recombination HIV-1 sequence classification: 3 groups (M, N and O) and 9 subtypes (A-H, J and K). Recombination by superinfection / co-infection. There are ~16 HIV-1 CRFs – most common CRF01 (AE) and CRF02 (AG). Intra-subtype recombination exists, but is harder to detect and studied less extensively.

3. Detecting Recombination in pol Seq Data: 10,545 HIV pol Sequences STAR Rec-PSSM Rec-Triplet (all data/pure subtypes) Subtypes Inter- subtypes Non-Recombinant Subtypes History analysis for each recombinant by Phylogenetic Trees etc Intra- subtypes LOHA

4. STAR High throughput subtyping tool that uses Position Specific Scoring Matrices (PSSMs). Myers, R. E., Clarke, C., Khan, A., Kellam, P., Tedder, R. (2006). Genotyping Hepatitis B Virus from whole and sub-genomic fragments using position specific scoring matrices in STAR-HBV. J. Gen Virol. (In Press). Myers, R. E., Gale, C. V., Harrison, A., Takeuchi, Y. & Kellam, P. (2005). A statistical model for HIV-1 sequence classification using the subtype analyser (STAR). Bioinformatics 21, 3535-40. Gale, C. V., Myers, R., Tedder, R. S., Williams, I. G. & Kellam, P. (2004). Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London. AIDS Res Hum Retroviruses 20, 457-64. http://www.vgb.ucl.ac.uk/starn.shtml

5. Subtyping Concordance 10545 sequences from the UK National Resistance Database

6. STAR and Rec-PSSM Results Subtype Frequency n.=10545 Distribution of Recombinant Architectures

7. CRF 03

8. CRF 04

9. Detection of CRF’s

10. Conclusions Large number of HIV-1 non-B subtypes in the UK (32.6%). The UK epidemic contains HIV-1 subtype recombinants (11%). Evidence for recombination outside of established CRFs. Only ~10% of recombinant sequences appear to be established CRF’s (excluding CRF01/02 General mixing of HIV-1 sequences and breakdown of subtype classification.

11. HIV-1 Subtype Evolution? Rambaut et al 2005; Nature Reviews Genetics

12. Acknowledgements Paul Kellam Yasu Takeuchi Catherine Gale Robert Gifford Arshad Kahn MRC / UCL Centre for Medical Molecular Virology

13. Detecting Recombination in pol Detecting Recombination in HIV-1 pol is a 3 step process. 1. Separate “pure subtype” sequences from putative recombinant sequences (Subtype Analyser – STAR, Rec-PSSM). 2. Analyse putative recombinant sequences using a high throughput screen for inter-subtype recombination (Rec-PSSM). 3. Analyse pure subtype sequences for intra-subtype recombination (Triplet-Rec).

14. STAR and Rec-PSSM Results Subtype Frequency n.=10545 Distribution of Recombinant Architectures