Establishment and maintenance of the latent HIV-1 DNA reservoir


Richard Neher
Biozentrum, University of Basel


slides at neherlab.org/201901_StLucia.html

The people who made this happen...

  • Fabio Zanini
  • Jan Albert
  • Johanna Brodin
  • Christa Lanz
  • Göran Bratt
  • Lina Thebo
  • Vadim Puller

HIV-1 evolution within one individual



silouhette: clipartfest.com, Zanini at al, 2015. Collaboration with Jan Albert and his group

HIV-1 sequencing before and after therapy

Zanini et al, eLife, 2015; Brodin et al, eLife, 2016. Collaboration with the group of Jan Albert

Population sequencing to track all mutations above 1%

Zanini et al, eLife, 2015

Detailed time-resolved record of evolution of the entire genome (here V3 in patient 3)

Zanini et al, eLife, 2015

Frequent reversion towards the center of HIV phylogeny

  • Almost one third of all mutations are reversions (~5% expected by chance)
  • Reversions accumulate slowly throughout chronic infection
  • Reversion can explain much of the intra/inter-host evolutionary rate mismatch
Zanini et al, eLife, 2015

Divergence at increasingly conserved positions

  • Six categories from high to low conservation
  • mutation away from preferred state with rate $\mu$
  • selection against non-preferred state with strength $s$
  • variant frequency dynamics: $\frac{d x}{dt} = \mu -s x $
  • equilibrium frequency: $\bar{x} = \mu/s $
  • fitness cost: $s = \mu/\bar{x}$
  • Fit model of minor variation to categories of conservation
  • $\Rightarrow$ harmonic average fitness cost in category

Fitness landscape of HIV-1

Zanini et al, Virus Evolution, 2017

p17 sequencing from PBMCs on fully suppressive therapy

Brodin et al, eLife, 2016

Hypermutated and intact proviral p17 sequences

  • Between 0 and 43% hypermutants, median 13%
  • Between 3 and 43 unique sequences >1% read frequency, median 25
  • Majority of hypermutant sequences have stop codons
Brodin et al, eLife, 2016

Proviral DNA mostly identical to pre-therapy RNA

Brodin et al, eLife, 2016

No evidence of ongoing evolution

Brodin et al, eLife, 2016

No evidence of ongoing evolution -- hypermutated provirus

Brodin et al, eLife, 2016

Most proviral DNA originates from shortly after start of therapy

  • latent HIV → barcode of a T-cell lineage
  • all latent integrated virus derives from late infection
Brodin et al, eLife, 2016

Possible explanations for reservoir establishment time distributions

Reservoir shaped by T-cell turn-over
  • T-cell lineages are short lived w/o treatment
  • The reservoir is cleared/superseeded by subsequent infection
  • on therapy: T-cell clones live decades
  • pre-therapy state is frozen
Reservoir formation triggered by immune deactivation
Abrahams et al, bioRxiv, 2019

Summary

  • Continuous reversion to ancestral states throughout chronic infection
  • Minor diversity allows fitness cost estimates at every position in the genome
  • The latent reservoir is a snapshot of the pre-treatment population
  • No evidence of ongoing replication
  • No clear trend of diversity loss on treatment
  • Proviral DNA can serve as a T-cell lineage marker

Acknowledgments

  • Fabio Zanini
  • Jan Albert
  • Johanna Brodin
  • Christa Lanz
  • Göran Bratt
  • Lina Thebo
  • Vadim Puller