HIV

Link to edit presentation:

https://docs.google.com/presentation/d/1-VMSxEXQ6y45AHJFndRcmcdrFxSXxYMoJWRpuv2AbPM/edit?usp=sharing

Group

• Molly ([email protected])
• Joe ([email protected])
• Florencia,
• Katie ([email protected])
• Jim ([email protected])

Notes

Questions:

1. Which parts of the immune system are regulating pathogens populations? How many strains are there?

• 2 species HIV 1 and 2

• 4 groups M (major), N, O, and P

• M has at least 11 subtypes (A, B, C, D, E, F, G, H, I, J, K)

• HIV Evolutionary Dynamics Within and Among Hosts (Lemey 2006)

• Show viral load and CD4 counts first

• Show difference inter host and intra host phylogenetic tree

• Innate immunity

• Attacks CD4 T cells

• CD8 T cells

• NK cells

• Glycan shield masks HIV surface protein from immune antibody recognition

• Autoreactive B cells

• Founder virus more adapted to HLA type leads to higher viral loads (Carlson 2016)

2. What explains patterns of genetic diversity?

3. What explains population dynamics?

• Figure 1 of Perelson et al.
• So far, we have been discussing compartmental models on a population scale, but here we are focusing on within-host viral dynamics resulting in a compartmental model where compartments are infected cells within the patient.
• These types of models have helped explain phases in viral decay, which helps explain continued mutation even under treatment, potentially providing a mechanism for antiretroviral resistance.

4. What's an outstanding question for your system? How would you conduct a study to address this and how would you analyze data from this study?

Outline - molly's notes

HIV life cycle

• Retrovirus

HIV phylogeny

• Tree of within host vs between hosts
• 2 groups, HIV-1 and HIV-2
  • 2 major groups with HIV-1 (M & N)
    • 8 subgroups
      • 60 different epidemic strains
        • A lot of intra-host diversity
          • Timing of intra-host diversity

HIV immunity

• Which parts of the immune system are regulating pathogens populations? How many strains are there?
• Break up into different parts of immune response

HIV within-host progression

• Timeline of clinical presentation (acute stage, peak viremia, establishing latent pool, long term consequences)
• Genetic diversity within host
  • during acute vs. chronic infection

Resources

Useful HIV pdf: https://www.stemcell.com/media/files/wallchart/WA10015-Immune_Response_HIV.pdf