1. Virulence and disease What can evolution tell us about disease and medicine?

2. Outline: virulence and disease I.Pathogen evolution A.Origins of novel pathogens B.Causes of virulence (esp. trade-off) C.Evolution of antibiotic resistance II.Evolution and human health A.Disorders due to changes in environment B.Diseases as defenses C.Disorders due to sexual conflict

3. I. Pathogen evolution: eluding the immune system - influenza Do amino acid substitutions occur at antigenic sites? Sample flu lineages from 1968 to 1987. SurvivingExtinct Antigenic sites3331 Non-antigenic sites1035 Neuroaminidase (NA): cell exit Hemagglutinin (HA): cell entry

4. Evolution of antigenic sites What kind of substitution in hemagglutinin? 18 codons with excess replacement (dN > dS): Figure 13.4

5. IB: Origins of novel pathogens - influenza Three types of influenza viruses: –A and B have 8 RNA strands, C has 7 –type A and B encode HA and NA, C does not –A and B can be severe, C generally mild Hosts: –type A: humans, swine, horses, waterfowl, gulls –type B: humans and seals –type C: humans and swine Flu A viruses are classified by HA type (1-15) and NA type (1-9) –only H1, H2, H3 and N1, N2 in humans (until recently)

6. Flu pandemics 1918Spanish flu (40m deaths)H1N1 1957Asian (1m deaths)H2N2 1968Hong KongH3N2 1977RussianH1N1 1997Avian (22 deaths)H5N1

7. Where do pandemics come from? Phylogeny of nucleoprotein gene of influenza A.

8. A role for pigs? Sialic acid – galactose on epithelial cell surface key to infection – binding site for hemagglutinin (HA) Can bind two different ways. Avian 2-3. Human 2-6.

9. H3 1968 from birds Phylogeny of flu A hemagglutinin genes

10. IC. What causes virulence? High virulence = rapid growth rate of virus Low virulence = slow growth rate of virus leads to slow development of illness or little effect on host leads to severe host illness and/or death Virulence: : tendency to reduce survival or reproductive capacity of host

11. Why doesn’t HIV evolve to become more virulent? With high virulence you get: many virions/ml blood rapid illness and death of host decreased # copulations before death of host Cost to virus Benefit to virus increased chance of transmission at each copulation

12. Evolution of Virulence: Australia’s plague of rabbits 13 wild introduced in 1858. 9 years later, 50 km spread. 1870s: 150 km / yr

13. Myxoma virus

14. Effect of myxoma virus on rabbits – 1951-1953

15. Virulence of field strains Class Survival time Fatality rate Year I <13 99% II 13-16 95- 99% III 17-28 70- 95% IV 29-50 50- 70% V - <50 1950-199 1951-233501700 1952-34137490 1953-416255090 1954-516 42260 Tests carried out on domestic rabbits

16. Trade-off hypothesis of virulence

17. Rabbit resistance evolves

18. What is the optimal level of virulence? But why is there a different balance in different pathogens--why are some more virulent than others? Why don’t some pathogens seem to become less virulent?

19. What is the optimal level of virulence? Water-borne diseases

20. What is the optimal level of virulence? Vector-borne diseases

21. Second virulence hypothesis: short-sighted evolution

22. Third virulence hypothesis: coincidental

23. I-D. Evolution of antibiotic resistance 70% of bacterial infections requiring hospitalization are resistant to some antibiotic Sepsis (infected blood / tissue) rates tripled in US from 1979 to 2000

24. Acquisition of anti-biotic resistance? Time to resistance? DrugIntroductionResistance Penicillin19431946 Streptomycin19451959 Tetracycline19481953 Vancomycin19561988 Methicillin19601961 Cefataxime19851988

25. Modes of resistance Drugactionresistance Tetracycline: blocks translationribosome mutation cellular pumps upregulated Penicillinblocks cell wallsbeta-lactamase digests drug cipro DNA packingmutation to enzymes (fluoroquinolones)(inhibits topoisomerase)

26. Efflux pumps

27. Experimental test of cost of resistance: Schrag (1997)

28. Initial competition without antibiotics Time (generations)

29. After many generations in the lab?

31. An evolutionary mystery: vancomycin resistance Vancomycin: 32 years before resistance seen. 500K staph infections per year in hospitals. By 1990s, commonly resistant to other antibiotics. Until recently, the last-resort antibiotic when other resistant. Mechanism: blocks cell-wall biosynthesis by forming complex with peptidoglycans Cross-linker: D-alanine D-alanine di-peptide Gram-positive bacteria

32. Mechanism of resistance

33. Vancomycin resistance

34. Origins of vancomycin resistance: comparison of amino acid sequences Numbers above: sequence similarity to VanA from E. foecium. Below: GC%.

35. Source of resistance

36. Antibiotic resistance summary

37. Hypotheses to explain human disorders Always deleterious: Sometimes deleterious: Only seem deleterious, actually a defense

38. Test: Barrow, Alaska G x E: Myopia (near-sightedness) Hypothesis: myopia is environment dependent Test in 1970 (35 years later) Age:MyopicNot myopic% 6-3514620242 35+ 8152 5

39. “nausea and vomiting of pregnancy”, or NVP About 2/3 of all pregnant women worldwide affected All hours (not just morning) Affects healthy mothers, who have healthy babies seems negative: reduced food intake, reduced activity level why persistent and common? II. Diseases are really defenses: “Morning sickness”

40. Post-menstrual week of pregnancy Proportion with NVP Sensitive Fetal organ Prediction 1: NVP most severe when need for protection greatest Diseases are really defenses: “Morning sickness” Sherman and Flaxman 2002

41. Study Percentage of pregnancies with miscarriage **Prediction 2: NVP should be associated with positive pregnancy outcomes Diseases are really defenses: “Morning sickness” Sherman and Flaxman 2002

42. Evolution of menopause 7 million oogonia at fifth fetal month 2 million oocytes at birth: meiotic prophase 400,000 at puberty –400 lost to ovulation –remainder degenerate (atresia)– why? –when few remain, menopause Hypotheses: –proximate: mitochondrial damage leads to apoptosis (but why aren’t there more to start with?) –adaptive??

43. Study questions 1.If you compare the pattern of mutations in a virus over time, what would indicate neutral evolution? What would indicate that selection was at work? 2.The hypothesis is that the 1918 flu virus incorporated many avian flu elements. Two hypotheses could be formulated: the 1918 flu involved recombination between human and avian flu strains, or the 1918 flu involved an avian strain shifting to humans. Imagine that you had access to flu sequences from 1900, 1905, 1910, and 1918 for ducks and humans and that you built two phylogenies, one for nucleoprotein and one for hemagglutinin. Sketch what the phylogenies would need to look like to support each hypothesis. 3.Explain why virulence rapidly declined for myxomatosis in Australian rabbits using the requirements of natural selection. 4.The 1918-1920 flu epidemic killed 40 million people. Formulate three hypotheses for why this virus did not continue killing humans at such high rates.

44. Study questions 5.Why do some pathogens evolve to become less virulent but not others? Explain why some of the key variables include mode of transmission and primary hosts. 6.Consider two diseases. In one case, hosts are infected by a single strain at a time. In the other case, hosts are infected by multiple strains at one time. How would you predict this difference to affect the evolution of virulence? 7.You are investigating the hypothesis that antibiotic resistance in a bacterial infection originated via horizontal gene transfer. Explain how you would use phylogenies to assess this.

45. References Frank, Steven A. 2002. Immunology and evolution of infectious disease. Princeton University Press. Guardabassi, L. et al. 2005. Glycopeptide VanA Operons in Paenobacillus strains isolated from soil. Antimicrobrial agents and chemotherapy 49:4227-4233. Hay, A. J. et al. 2001. The evolution of human influenza viruses. Philosophical transactions of the Royal Society Series B 356:1861-1870. Hurtado, A. M. et al. 1999. The evolution ecology of childhood asthma. In Trevathan, W. R. et al., eds. Evolutionary medicine. Oxford University Press. Launay, A. et al. 2006. Transfer of vancomycin resistance transposon Tn1549 from Clostridium symbiosum to Enterococcus spp. in the gut in gnotobiotic mice. Antimicrobial agents and chemotherapy 50:1054-1062. Lewis, D. 2006. Avian flu to human influenza. Annual review of medicine 57:139- 154. Nesse, R. M. and Williams, G. C. 1996. Why we get sick: the new science of Darwinian medicine. Random House, New York. Sherman and Flaxman. 2002. Nausea and vomiting of pregnancy in an evolutionary perspective. American Jr of Ostetrics and Gynecology 186: S190- S197. Stearns, S. and Ebert, D. 2001. Evolution in health and disease: a work in progress. Quarterly review of biology 76:417-432. Walsh, C. T. et al. 1996. Bacterial resistance to vancomycin: five genes and one missing hydrogen bond tell the story. Current biology 3:21-28. White, D. G. et al., eds. 2005. Frontiers in Antimicrobial Resitance. American Society for Microbiology.