Multidrug Resistant HIV1 Resulting from Intrapatient Viral Recombination Barbara Weiser, MD Wadswort

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Multidrug Resistant HIV-1 Resulting from
Intrapatient Viral RecombinationBarbara Weiser,
MDWadsworth CenterNew York State Department of
HealthAlbany, New York, USA
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Acknowledgements

• Wadsworth Center
• Kimdar Sherefa Kemal
• Harold Burger
• Penelope Huggins
• UCLA
• Christina Kitchen
• Marc Suchard
• Vladimir Minin

• InPheno, Basel
• Thomas Klimkait
• François Hamy
• Katarina Petrovic
• Los Alamos Laboratory
• Brian Foley
• Boehringer Ingelheim
• Douglas Mayers
• Albert Einstein
• Kathryn Anastos

US National Institutes of Health
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Background

• Rapid evolution of HIV-1 resis-tance is known to
  result from point mutations, but evidence
  suggests that HIV-1 recombination leads to
  multidrug resistance as well.

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Background

• Recombination can lead to the acquisition of
  numerous genetic traits that confer a selective
  advantage on the new viral strain.

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Background

• Although recombination has long been postulated
  to result in multidrug resistance, such events
  have not yet been described in detail in infected
  individuals.

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Objective

• To examine the role of recombination in the
  emergence of multidrug resistance in patients.

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Methods

• We analyzed multiple HIV-1 sequences over time
  from a woman who developed drug resistance soon
  after initiating antiretroviral therapy (ART).

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Methods

• Challenge Demonstrating intrapatient
  recombination is difficult because most viral
  genomes within a single person are too similar to
  permit detection of the chimeric strains.

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Methods

• We focused on variants in the female genital
  tract and plasma because genomes in these sites
  are often compartmentalized.

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Methods

• 89 unique viral variants were obtained either by
  endpoint dilution or cloning.
• We then sequenced the protease and RT genes.

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Study Patient

• Patient 38 was an asymp-tomatic woman in the New
  York City Womens Inter-agency HIV Study (WIHS)
  who initiated AZT, 3TC, and NVP in 2000.

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• Study Patient
• We studied HIV-1 obtained at 3 time points
• May 1998, before ART
• February 2000, soon after starting ART
• July 2000, during continued treatment

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Study Patient

• Although the patient exhibited a partial response
  to ART, she displayed virologic failure in both
  the plasma and genital tract, specifically the
  cervico-vaginal lavage (CVL).

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Resistance and RC Before ART

• Plasma
  CVL .
• GENOTYPE WT WT
• PHENOTYPE WT WT
• RC, 92
  106
• RC Values gt50, fit 20-49 intermediate,
  lt20 unfit

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Resistance and RC Soon After Initiation of ART
Majority Species
Plasma
CVL . GENOTYPE K103N
A98V, G190S PHENOTYPE NVP-R
NVP-R RC, mean 53
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Resistance and RC 7 Months After Initiation of
ART Majority Species
Plasma
CVL . GENOTYPE K103N, M184V
KI03N, M184V PHENOTYPE NVP-R, 3TC-R
NVP-R, 3TC-R RC , mean 56
74
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Bayesian Analysis to Detect Recombination

• Bayesian analysis allows for varying evolutionary
  rates, selective pressures, and trees along the
  sequence alignment.
• It also provides estimates of uncertainty for
  those quantities including location and number of
  recombination events.

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Bayesian Analysis Two Specific Questions

• 1) Are there recombinants?
• 2) If so, what is the identity of the parental
  strains?

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Bayesian Analysis Demonstrating Recombination
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Bayesian Analysis Demonstrating Recombination
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Summary

• 1. By analyzing individual HIV-1 variants in the
  female genital tract and plasma, we documented
  that intra-patient recombination resulted in
  multi-drug resistance in an infected individual.

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Summary

• 2. Identification of HIV-1 recombinants and their
  parental strains revealed that under the
  selective pressure of ART, variants evolved in
  both sites that were fit and displayed
  high-level, multidrug resistance.

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Summary

• 3. Our findings provide new insight into the
  evolution and spread of highly resistant HIV-1.
• 4. They also draw attention to the rapid
  development of multidrug resistance that can
  occur in individuals initiating combination ART.

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• Characteristics of Patient 38
• Date Log Viral Load CD4 Count
• Plasma CVL
  .
  
• May 98 5.34 NA 120
• Feb 00 4.31 4.85
  359
• July 00 4.30 4.15
  387

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Replicative Capacity

• InPheno Basel
• RC Values
• gt50, fit 20-49 intermediate, lt20
  unfit

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• Study Patient
• The patient reported intermittent adherence to
  ART related to crack cocaine use, with positive
  urine toxicology in February 2000.