Lecture 12. Immunology and disease: parasite antigenic diversity. and. Phylogenetic trees

Transcription

1 Lecture 12 Immunology and disease: parasite antigenic diversity and Phylogenetic trees

2 Benefits of antigenic variation 2. Infect hosts with prior exposure Hosts often maintain memory against prior infections, generating a selective pressure for parasites to vary Cross-reaction occurs when the host can use its specific recognition from a prior exposure to fight against a later, slightly different antigenic variant Good vaccines are ones that have excellent crossreactivity (e.g. measles virus)

3 In the simplest case, each antigenic variant acts like a separate parasite that Figure doesn t cross-react 11-1 with part other variants 1 of 3

4 Figure 11-1 part 2 of 3

5 Figure 11-1 part 3 of 3

6 Benefits of antigenic variation 2. Infect hosts with prior exposure A more dynamic mechanism of antigenic variation is seen in influenza virus Antigenic drift is caused by point mutations in the genes encoding surface proteins Antigenic shift is caused by reassortments leading to novel surface proteins

7 Figure 11-2 part 1 of 2

8 Figure 11-2 part 2 of 2

9 Benefits of antigenic variation 2. Infect hosts with prior exposure Antigenic drift is caused by point mutations in the hemagglutinin and neuraminidase genes, which code for surface proteins Every 2-3 years a variant arises that can evade neutralization by antibodies in the population Previously immune individuals become susceptible Most individuals still have some cross-reactivity and the ensuing epidemic tends to be relatively mild (but still kills 100s of thousands per year!)

10 Benefits of antigenic variation 2. Infect hosts with prior exposure Antigenic shift brings in an all-new hemagglutinin or neuraminidase gene to a naïve population Can lead to severe infections and massive pandemics like the Spanish flu of 1918.

11 Phylogenetics

12 Today: What is a phylogenetic tree? How are trees inferred using molecular data? How do you assess confidence in trees and clades on trees? Why do trees for different data sets sometimes conflict? What can you do with trees beyond simply inferring relatedness?

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14 Molecular epidemiology The study of HIV ushered in a new way to think about pathogen variation where the nucleotide sequence became the primary source of information Phylogenetic trees have become very important analytical tools for tracking epidemics, understanding where new pathogens came from, testing forensic hypotheses, and reconstructing demographic changes Often termed molecular epidemiology since it answers many of the same questions as traditional epidemiology

15 Origins of HIV/AIDS Where did HIV come from? Divine retribution Doesn t matter--it doesn t cause AIDS Conspiracy theories - e.g. the CIA did it Voodoo rituals Ritualistic use of monkey blood Contamination of vaccines Zoonosis (a disease communicable from animals to humans under natural conditions) How can we discriminate between these hypotheses?

16 Origins of HIV/AIDS Where did HIV come from? Divine retribution The poor homosexuals--they have declared war upon nature, and now nature is exacting an awful retribution -Pat Buchanan "With 80,000 dead of AIDS, our promiscuous homosexuals appear literally hellbent on Satanism and suicide -Pat Buchanan "AIDS is not just God's punishment for homosexuals; it is God's punishment for the society that tolerates homosexuals. -Jerry Falwell Grown men should not be having sex with prostitutes, unless they are married to them -Jerry Falwell QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture.

17 Origins of HIV/AIDS Where did HIV come from? Divine retribution The poor homosexuals--they have declared war upon nature, and now nature is exacting an awful retribution -Pat Buchanan "With 80,000 dead of AIDS, our promiscuous homosexuals appear literally hellbent on Satanism and suicide -Pat Buchanan "AIDS is not just God's punishment for homosexuals; it is God's punishment for the society that tolerates homosexuals. -Jerry Falwell Grown men should not be having sex with prostitutes, unless they are married to them -Jerry Falwell QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture.

18 Origins of HIV/AIDS Where did HIV come from? Doesn t matter--it doesn t cause AIDS

19 Origins of HIV/AIDS Where did HIV come from? Doesn t matter--it doesn t cause AIDS

20 Origins of HIV/AIDS Divine retribution Doesn t matter--it doesn t cause AIDS Conspiracy theories - e.g. the CIA did it Ritualistic use of monkey blood Zoonosis (a disease communicable from animals to man under natural conditions) Contamination of vaccines THE PLAUSIBLE HYPOTHESES ALL HAVE IN COMMON THE INCRIMINATION OF SIMIAN IMMUNODEFICIENCY VIRUSES (SIVcpz) FROM CHIMPANZEES THE KEY DISCOVERY WAS THE FINDING THAT AFRICAN PRIMATES ARE INFECTED WITH SIMILAR VIRUSES

21 Phylogenetics interlude What is this thing and why is it on all these slides?

22 Phylogenetics interlude All the phylogenetics you need to know, in 5 minutes It s all about ancestors and offspring, lineages branching The ancestor could be distant great grandmother or a human immunodeficiency virus patient 1 The ancestral form of some gene (a marker ) is inherited in two offspring lineages patient 0 patient 2 Let s assume that we re looking at virus from a patient 0 who then infects two others

23 Phylogenetics interlude Mutations happen when genetic material is copied Changes accumulate independently along each branch (within each new infectee) If one of these patients now infects two new victims, they inherit those changes

24 Phylogenetics interlude patient 0 patient 3 patient 4 Eventually, a series of branching events, plus mutations along each branch, lead to 4 current HIV infected patients Their viruses display genetic diversity that reflects their evolutionary history patient 5 patient 2 patient 6

25 Phylogenetics interlude Unfortunately, we almost never have access to that history What we can do, is go out into nature and sample genetic markers Then we work backwards to infer the most likely series of events that gave rise to what we observe

26 Phylogenetics interlude In this case, we would infer a tree that correctly recapitulated the chain of infections

27 Phylogenetics interlude

28 Phylogenetics interlude TRUE TRANSMISSION HISTORY AND SAMPLING TIMES INFERRED TREE FROM GENE SEQUENCES

29 Phylogenetics interlude

30 Phylogenetics interlude Sequences recovered from the victim Sequences recovered from the patient Sequences also recovered from other HIV-positive individuals from the same city

31 Phylogenetics interlude Human HIV The evolutionary pattern in this HIV phylogeny is just like the pattern in human mtdna In both, we see a subpopulation that has recently emerged from a more diverse source population A few years of HIV evolution = 1 million years of human mtdna evolution

32 Molecular phylogenetics fundamentals All of life is related by common ancestry. Recovering this pattern, the "Tree of Life", is one of the primary goals of evolutionary biology. Even at the population level, the phylogenetic tree is indispensable as a tool for estimating parameters of interest. Likewise at the among species level, it is indispensable for examining patterns of diversification over time. First, you need to be familiar with some tree terminology.

33 Tree terminology Internal nodes represent hypothetical ancestors; the ancestor of all the sequences that comprise the tree is the root of the tree. Edges can also be classified as internal (leading to an internal node) or external (leading to an external node). Most methods try to estimate the amount of evolution that takes place between each node on the tree, which can be represented as branch length. The branching pattern of the tree is its topology.

34 Inspect branch lengths; they speak volumes Kinshasa 1959??? Manchester 1959

35 Inspect branch lengths; they speak volumes

36 Tree styles There are many different ways of drawing trees, so it is important to know whether these different ways actually reflect differences in the kind of tree, or whether they are simply stylistic conventions. Think of the tree as a mobile:

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38 polytomies These polytomies can represent two different situations; first they may represent simultaneous divergence- all the descendants evolved at the same time (a 'hard' polytomy); alternatively, they may indicate uncertainty about phylogenetic relationships (a 'soft' polytomy).

39 Rooted and unrooted trees Cladograms and additive trees can either be rooted or unrooted. A rooted tree has a node identified as the root from which ultimately all other nodes descend, hence a rooted tree has direction. This direction corresponds to evolutionary time. Unrooted trees lack a root, and therefore do not specify evolutionary relationships in quite the same way. They do not allow the determination of ancestors and descendants. Here we have an unrooted tree for human, chimpanzee, gorilla, orang, and gibbon (B). The rooted tree (above) corresponds to the placement of the root on the branch leading to gibbon.

40 consensus trees

41 monophyletic clades

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43 Inferring phylogenies All phylogeny reconstruction methods assume you start with a set of aligned sequences. The alignment is the statement of homology, that is shared ancestry from which historical inferences are made. The alignment, then, becomes critical to reconstructing phylogenies. In some cases, the alignment is trivial. In many cases it is not.

44 Inferring phylogenies There are two fundamental ways of treating data; as distances or as discrete characters. Distance methods first convert aligned sequences into a pairwise distance matrix, then input that matrix into a tree building method Discrete methods consider each nucleotide site (or some function of each site) directly. Consider the following example:

45 Inferring phylogenies There are also two fundamental ways of finding the best phylogenetic tree Clustering methods use some algorithm to cobble together a single tree Optimality methods survey all possible trees and compare how well they fit the data Clustering methods versus optimality methods

46 Phylogeny reconstruction: maximum parsimony The data for maximum parsimony comprise individual nucleotide sites. For each site the goal is to reconstruct the evolution of that site on a tree subject to the constraint of invoking the fewest possible evolutionary changes. In parsimony we are optimizing the total number of evolutionary changes on the tree or tree length. The tree length, then, is the sum of the number of changes at each site. So, if we have k sites, each with a length of l, then the length L of the tree is given by

47 Phylogeny reconstruction: maximum likelihood The method of maximum likelihood is a contribution of RA Fisher, who first investigated its properties in Principle: evaluate all possible trees (topology and branch lengths) and substitution model parameters (TS/TV, base freq, rate heterogeneity etc.). These are the hypotheses. Choose the one that maximizes the likelihood of your data (the alignment) Likelihood: Given that the coin you re tossing just gave you 15 heads out of 100 tosses, the likelihood that it is fair is very small. Given the nature of molecular evolutionary data, where evolution has run just once, yielding one data set, maximum likelihood is a powerful framework--evaluate a bunch of different hypotheses to find the one most likely to have generated the observed data!

48 A non-biological example: coin tossing If the probability of an event X dependent on model parameters p is written P ( X p ) then we would talk about the likelihood L ( p X ) that is, the likelihood of the parameters given the data.

49 A non-biological example: coin tossing Say we toss a coin 100 times and observe 56 heads and 44 tails. Instead of assuming that p is 0.5, we want to find the MLE for p. Then we want to ask whether or not this value differs significantly from How do we do this? We find the value for p that makes the observed data most likely. p L

50 A non-biological example: coin tossing So why did we waste our time with the maximum likelihood method? In such a simple case as this, nobody would use maximum likelihood estimation to evaluate p. But not all problems are this simple!

51 Traditional versus Bayesian phylogenetics

52 Traditional versus Bayesian phylogenetics

53 Estimating confidence: Bootstrapping trees

54 What can you do with trees beyond simply inferring relatedness?

55 What can you do with trees beyond simply inferring relatedness? Chang et al. (2002) used maximum likelihood phylogenetic ancestral reconstruction methods to recreate a putative ancestral archosaur visual pigment (ca. 240 mya)

56 What can you do with trees beyond simply inferring relatedness? Chang et al. Fig 1

57 What can you do with trees beyond simply inferring relatedness? To determine if these ancestral pigments would be functionally active, the corresponding genes were chemically synthesized and then expressed in tissue culture

58 What can you do with trees beyond simply inferring relatedness? Chang et al. Fig 2

59 What can you do with trees beyond simply inferring relatedness? The expressed artificial genes were all found to yield stable photoactive pigments with max values of about 508 nm, which is slightly redshifted relative to that of extant vertebrate pigments.

60 What can you do with trees beyond simply inferring relatedness? Chang et al. Fig 3 What might you speculate about the behavior of the ancestral archosaur based on these results?

61 Origins of HIV/AIDS Back to HIV and chimpanzees SIV was discovered in 1985 in a captive Asian monkey SIVs are found naturally only in African primates x x x SIVcpz HIV-1/O SIVcpz SIVagmTAN x HIV-1/N SIVagmVER x HIV-1/M SIVmnd SIVagmGRI HIV-2/A SIVsm SIVlhoest SIVsun SIVcol HIV-2/B SIVsyk Cercocebus atys Pan troglodytes Chlorocebus aethiops Cercopithecus albogularis Cercopithecus lhoesti 0.1 Colobus guereza

62 Origins of HIV/AIDS

63 Origins of HIV/AIDS HIV-2 introduced at least 8 times from mangabeys HIV-1 introduced at least 3 times from chimps QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture. Two of these groups endemic to Cameroon Group M is pandemic

64 Origins of HIV/AIDS HIV-1 1 group M causes >99.9% of HIV infections worldwide Slightly harder to pin down its geographical origins because of spread Various clues place it at the same seen (probably Cameroon) It s s a close relative to other AIDS viruses clearly linked to Cameroon Chimpanzees themselves acquired their virus from preying on other primates How did the virus get into humans?

65 Origins of HIV/AIDS Divine retribution Doesn t matter--it doesn t cause AIDS Conspiracy theories - e.g. the CIA did it Ritualistic use of monkey blood Zoonosis (a disease communicable from animals to man under natural conditions) Contamination of vaccines THE PLAUSIBLE HYPOTHESES ALL HAVE IN COMMON THE INCRIMINATION OF SIMIAN IMMUNODEFICIENCY VIRUSES (SIVcpz) FROM CHIMPANZEES THE KEY DISCOVERY WAS THE FINDING THAT AFRICAN PRIMATES ARE INFECTED WITH SIMILAR VIRUSES

66 Origins of HIV/AIDS

67 Origins of HIV/AIDS The River: A Journey Back to the Source of HIV and AIDS by Edward Hooper. There s s an apparent correlation between oral polio vaccine (OPV) sites ( ) 1960) and earliest instances of HIV-1 1 in Democratic Republic of Congo (DRC, ex- Zaire). 350/400 chimps sacrificed in experiments at Lindi camp near Kisangani, DRC, and allegedly OPV cultured in their kidneys (Hooper 1999). This culturing process is suggested to have facilitated the transfer to humans of chimpanzee simian immunodeficiency virus (SIVcpz( SIVcpz). There s s a precedent: early polio vaccines are known to have been contaminated with the simian virus SV40.

68 Origins of HIV/AIDS

69 Origins of HIV/AIDS

70 Origins of HIV/AIDS

71 Origins of HIV/AIDS Non-invasive sampling of SIVcpz from the supposed source (and a big blank space on the map of SIVcpz distribution)

72 Origins of HIV/AIDS

73 Origins of HIV/AIDS

74 Origins of HIV/AIDS Western blot analysis of Kisangani chimpanzee urine samples gp160 gp p66 p51 gp41 p31 p24 p17

75 Origins of HIV/AIDS

76 Origins of HIV/AIDS

77 Origins of HIV/AIDS Phylogenetic position Expected for source population Phylogenetic position of Kisangani SIV Worobey et al. (2004): Nature

78 Origins of HIV/AIDS Ancestor estimated At 1930ish Vaccines used after 1957

79 Origins of HIV/AIDS Summary The SIVcpz from the alleged HIV-1 group M source region (according to OPV/AIDS theory) is not the sister lineage to group M Confirms other lines of evidence (dating, ZR59, archival vaccine testing, group N recombination, genetic diversity in Kinshasa) A new region where we can expect possible emergence of HIV- 1 Sampling is continuing to study natural history of SIVcpz in wild chimps