1. Evolution and transmission in HIV Steve Paterson Review; Rambaut 2004 Nature Reviews Genetics 5: 52-61 ‘The causes and consequences of HIV evolution’

2. Use phylogenies to follow infection HIV is an RNA virus, with a high mutation rate mutates over course of infection

3. HIV

4. HIV Gag gene polymorphism

6. Phylogenetic tree should mirror contact structure of infection

7. Molecular epidemiology of HIV in Edinburgh HIV mutates as passes from one individual to next Use substitutions to build phylogenies and track pattern of infection

8. HIV phylogeny Holmes et al (1994) J. Inf. Diseases 171:45-53

10. Oliveira et al (2006) Nature. 444, 836-837

13. Origins of HIV Rambaut 2004 Nature Reviews Genetics 5: 52-61 HIV-1 HIV-2

14. Origins of HIV-1

15. Within host evolution of HIV high rate of mutation –(0.2 errors/genome) high rate of replication –(gen. time = 2.5 days, 10 10 - 10 12 virions/day) natural selection –immune selection –genetic drift

16. Genetic diversity of HIV Rambaut (2004) Nature Reviews Genetics 5, 52-61

17. Evolution of drug resistance in HIV

18. env gene blue sites = +ve seln. Ross (2002) J. Virol. 76 : 11715-20 CTL escape Long-livedShort-lived Immune pressure, effective at driving amino-acid change in long-lived patients?