1. Immunology and disease: parasite antigenic diversity

2. Today: Benefits and mechanisms of antigenic variation
Antigenic variation that allows pathogens to persist in the individual host they’ve infected
Antigenic variation that allows pathogens to infect hosts with prior exposure

3. Benefits of antigenic variation
Persist in infected host
Let’s look at some experimental results…

4. Experimental evolution
Manipulates the environment of a population and then looks at the resulting patterns of evolutionary change
Allows for the direct study of the selective forces that shape antigenic diversity
We’ll focus on CTL escape, which gets us down to the level of single amino acids changes that can mean life or death for both hosts and parasites

5. Review
Figure 1-27
The two main classes of MHC molecules present antigen from cytosol (MHC class I) and vesicles (MHC class II)

6. MHC class I molecule presenting an epitope
Figure 3-23

7. Figure 1-30

8. CTL escape
CTL pressure favors “escape mutants”, pathogens with amino acid substitutions in their epitopes that make them escape recognition. Substitutions can lead to escape in three ways.
They can interfere with processing and transport of peptides.
They can reduce binding to MHC molecules.
And they can reduce the affinity of TCR receptor binding.

10. CTL escape: interfering with processing/transport
A study of murine leukemia virus showed that a single amino acid substitution in a viral peptide can alter the cleavage pattern, and hence epitope presentation, and hence CTL response
MuLV is an oncogenic retrovirus
There are two main types (MCF and FMR)
Both types are controlled in large part by CTL responses, but with different immunodominant epitopes
The immunodominant CTL epitope for MCF is KSPWFTTL

11. CTL escape: interfering with processing/transport
mcf
fmr

12. CTL escape: interfering with processing/transport
Proteasomes are hollow multiprotein complexes. They are like meat-grinders for pathogen proteins found in the cytosol
Cellular proteasomes continuously chop up proteins into smaller peptides, for presentation by MHC
Proteasomal cleavage patterns determine which bits of pathogen peptides get to the cell surface

13. CTL escape: interfering with processing/transport
Changing KSPWFTTL to RSPWFTTL introduces a new cleavage site (the proteasome likes to chop after R)
Viruses with RSPWFTTL are cleaved right within what would otherwise be a great epitope, leading to a huge reduction in the abundance of the R-containing epitope available for MHC presentation
Inspection of the nucleotides reveals that this escape is mediated by a single point mutation!
End result: that epitope is unavailable to MHC and the CTL response to FMR type is weak

14. CTL escape: reducing MHC binding
Several studies report mutations that reduce peptide-MHC binding
This can either prevent MHC from dragging the peptide successfully to the cell surface, or from holding on to it once there

16. CTL escape: reducing MHC binding
Lymphocytic choriomeningitis virus (LCMV) is an RNA virus that naturally infects mice
Infection can be controlled or eliminated by a strong CTL response
Puglielli et al. used an LCMV system with transgenic mice that expressed an MHC molecule that binds a particular epitope of LCMV (GP33-43)
After infection, an initial viremia was beaten down by CTL pressure

17. CTL escape: reducing MHC binding
Later, virus titers increased. Were escape mutants to blame?
The late viruses indeed had a V to A substitution at the 3rd site of the epitope.
This substitution nearly abolished binding to the MHC molecule expressed by the mice

19. CTL escape: reducing MHC binding
SIV/macaques is used as a model system for HIV since you can’t experimentally infect humans to study the arms race between HIV and humans
Escape from CTLs appears to be a key component of the dynamics and persistence of infection within hosts
Allen et al. (2000) studied 18 rhesus macaques infected with SIV

20. CTL escape: reducing MHC binding
Ten of the monkeys expressed a particular MHC, and these all made CTLs to an epitope in the Tat protein in the acute phase of infection
Shortly after, the frequency of these Tat-specific CTLs dropped off
Sequencing showed that a majority of these animals had mutations in the Tat viral epitope that destroyed binding to the MHC
There was little variation outside of the epitope
End result: positive selection to block MHC binding

21. CTL escape: reducing TCR binding
The LCMV system also shows examples of single amino acid changes that can lead to a decline in affinity for the TCR
Tissot et al (2000) showed that a Y to F substitution in one immunodominant epitope obtained during experimental evolution in vivo caused a 100-fold reduction in affinity for the TCR
End result: escape mutation that destroys the immune system’s ability to see that epitope

22. 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 cross-reactivity (e.g. measles virus)

23. Figure 11-1 part 1 of 3
In the simplest case, each antigenic variant acts like a separate parasite that doesn’t cross-react with other variants

24. Figure 11-1 part 2 of 3

25. Figure 11-1 part 3 of 3

26. 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

27. Figure 11-2 part 1 of 2

28. Figure 11-2 part 2 of 2

29. 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!)

30. 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.

31. Benefits of antigenic variation
Why, fundamentally, is it of benefit to a parasite to extend the length of infection or re-infect hosts with prior exposure?