HIV1 fitness costs associated with mutations to escape immune pressure

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HIV-1 fitness costs associated with mutations to
escape immune pressure
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• Topics to cover in this seminar
• Brief introduction to the ex vivo method to
  measure relative viral fitness
• What is the relationship between fitness and
  disease progression?
• Does CTL escape mutations during early disease
  reduce fitness?

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How do we measure viral fitness?

• Relative fitness of viruses is measured in
  growth-competition experiments using mixed
  infections and in which the initial viruses are
  genetically and phenotypically distinguishable
  (Domingo and Holland, Annu. Rev. Microbiol. 1997
  51151-178)
• These competition experiments have been developed
  by Drs. John Holland (UCSD, La Jolla, Ca) and
  Esteban Domingo (Centro de Biologia and Molecular
  Severo Ochoa, Madrid, Spain) using a number of
  RNA viruses including VSV, FMDV, and HIV.
• However, few studies have correlated relative ex
  vivo fitness to disease progression by any virus
  OR examined the relationship between to virus
  distribution in the human population
• Several groups have now utilized the
  competition/co-infection assay to compare fitness
  of drug resistant and wild type HIV-1 isolates.
  Often differences in fitness are better
  indicators of the emergence of specific drug
  resistant isolates than level of drug resistance
  between isolates.
• e.g. the K70R HIV-1 isolate is more fit and less
  resistant to AZT than the T215Y HIV-1 isolate and
  yet K70R HIV-1 isolate emerges first in patients
  treated with AZT monotherapy (Harrigan PR et al.
  1998, J Virol.723773)

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HIV-1 lifecycle
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Measurement of viral fitness

• Relative fitness virus production in dual
  infection/proportion in the inoculum
• Fitness difference ratio of relative fitness
  values More fit/less fit

Ball et al, 2003
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Comparing total relative fitness values and viral
loads
Quinones-Mateu et al., J. Virol. 2000
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Theories on the fitness of RNA viruses
RNA viruses have been used a tool for
evolutionary studies for decades
Quasispecies is a term defined by Eigen and
describes the large population of viruses that
rapidly evolve from new infections or bottlenecks
Domingo, Holland, and other have shown in tissue
culture infections with VSV or FMDV that viral
fitness continues to increase only with
exponential increases in population size and
diversity (aka The Red Queen Hypothesis) Any
change in selection pressure or a decrease in
population size will invoke the Mullers Ratchet.
Under strong selective pressure, high mutation
frequencies will result in accumulation of
deleterious mutations and overwhelm mutations
that lead to fitness gains
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Do these evolutionary principles and fitness
theories apply in nature?
We conclude that the genetic variation in these
data sets can be explained by a predominance of
random genetic drift of neutral mutations with
brief episodes of natural selection that were
frequently masked by recombination. Shriner et
al., Genetics 2004
Shankarappa et al., J. Virol. 1999
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Samples obtained from 10 HIV-1 infected patients
spanning a three to six year period
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Replication kinetics on CCR5.CD4.U87 cells
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Troyer et al., J. Virol. 2005
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Relationship between fitness and CD4 cell counts,
viral RNA load, HIV-1 genetic diversity and
length of infection
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Correlates of ex vivo HIV-1 fitness An
intrapatient analyses
All patients
Only samples from untreated
p lt 0.05
p lt 0.01
p lt 0.01
p lt 0.01
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Conclusions
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Cellular immunity and HIV fitness
Animation courtesy of Dr. Gary Kaiser
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Cellular immunity to HIV CTLs

• CTL response is strongly associated with the
  resolution of primary HIV viremia
• Certain class I HLA alleles are associated with
  fast or slow HIV disease progression
• SIV studies in macaques
• Specific depletion / inhibition of CTLs results
  in increased viral load and rapid disease
  progression
• Schmitz et al. 1999 Science 283857-60
• Jin et al. 1999 J Exp Med 189991-8
• CTL escape occurs largely through selection of
  point mutations
• TCR interaction
• MHC binding
• Antigen processing

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CTL escape and HIV fitness I

• CTL escape is constrained by fitness costs
• SIV-macaque model
• Smith et al. J Biol Chem 2003 27844816-25
• Peyerl et al. J Virol 2004 7813901-10
• CTL escapes with fitness costs selected in vivo
• Escape variants may revert upon virus
  transmission to HLA-unmatched hosts
• SIV Friedrich et al. Nat Med 2004 10275-81
• HIV-1 Leslie et al. Nat Med 2004 10282-89
• Escape from vaccine-induced CTL response resulted
  in a crippled SIV
• Matano et al. J Exp Med 2004 121709-18
• CTL selection at the population level
• HLA alleles are associated with particular escape
  mutations
• Moore et al. Science 2002 2961439-43
• Kiepiela et al. Nature 2004 432769-74
• Leslie et al. J Exp Med 2005 201891-902

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CTL escape and HIV fitness II

• Can CTL escape selected in vivo exact a
  significant and durable fitness cost on the
  virus?
• Compensatory mutations?
• SIV Friedrich et al. J Virol 2004 782581-5
• HIV-1 Kelleher et al. J Exp Med 2001 193375-86

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• Insertion of Gag T242N into NL4-3 results in a
  reduction in fitness in MT4 cells
• NL4-3 bearing recombinant p24 from a patient
• Recombinant with 242N (escape) is less fit than
  242T (wild-type) in MT4 cells

Martinez-Picado et al. (2006) J Virol
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Seattle Primary Infection Cohort Patient 1362
(A0201/2501, B18/51, C0102/1203)
Cao et al. 2003 J Immunol 1713837-46
At least 19 different CTL escapes occurred in at
least 9 proteins
Env gp120 (5) RT (3) Gag p24 (2) Tat (2) Vpr
(2) PR (2) Nef (1) p6 (1) Vpu (1)
Strategy Generate chimeric viruses expressing
escaped and unescaped versions of env and gag
from patient 1362
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Mutations in the HIV-1 env and to a lesser
extent, gag gene are predominantly found in CTL
epitopes
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CTL escape mutations in gag CAp24 of pt1362
reduce fitness
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CTL escape mutations in env gp120 of pt1362
reduce fitness
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CTL escape mutations in env gp120 of pt1362
reduce fitness (continued.)
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Does CTL escape mutations correspond to other
clinical parameters?
Conclusions CTL escape mutations in gag epitopes
reduce fitness and appear later in infection CTL
escape mutations in env emerge early but without
a significant cost in fitness The env gene is
major target for both CTL and humoral
activity Furthermore, in untreated patients,
replicative fitness maps to the env gene and is
controlled by the efficiency of host cell entry
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Acknowledgements
University of Washington Jim Mullins Yi Liu Mark
Jensen Fred Hutchinson Cancer Research
Center Julie McElrath John McNevin Institute of
Tropical Medicine, Belgium Guido Vanham Case
Western Reserve University Ryan Troyer Randall
Krizan Awet Abraha Kalonji Collins Santiago
Avila Denis Tebit Yong Gao Michael Lobritz Dawn
Moore Erika Fraundorf