Post on 06-Oct-2020
Quasispecies dynamics and antiviral designs
Esteban Domingo
Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco (Madrid)
edomingo@cbm.uam.es
Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz (Madrid)
Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona
CONSENSUS
MUTANT SPECTRUM
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- Viral quasispecies constitute reservoirs of genotypic and phenotypic variants (drug resistance, etc.)
- Intra-mutant spectrum interactions (complementation or interference) can promote or suppress dominance of specific variants
- Replication rate, viral load, genetic heterogeneity and viral fitness are interconnected parameters
- Quasispecies dynamics can affect long-term virus evolution [memory, chance shedding of particular variants, rapid evolution related to pandemic potential (norovirus, enterovirus 71)]
Domingo, E., Sheldon, J., Perales, C., MMBR, 2012
Domingo, E., Sheldon, J., Perales, C., MMBR, 2012
Underlying influences High mutation rates 10-3 to 10-5 subst./nt ~106-fold higher than for cellular DNA
Principles of Darwinian evolution Reproduction with genetic variation Competition Selection
Bottleneck events
Combination therapy (i.e. HAART for AIDS)
Splitting into an induction and maintenance regimen
Targeting of cellular functions
Combined use of immunotherapy and chemotherapy
Lethal mutagenesis
Major strategies developed to overcome the adaptive potential conferred by high mutation rates and quasispecies dynamics
Resistance mutations may jeopardize the efficacy of these strategies
Domingo, E., Sheldon, J., Perales, C., MMBR, 2012
Low viral load and low fitness favor extinction
Transition towards extinction involves a 102- to 103- fold decrease of specific infectivity
No change of the consensus sequence of the population
Rapid movement towards regions of sequence space with biased base composition (A,U- rich genomes upon ribavirin treatment)
Selection of mutagen-resistant mutants can jeopardize extinction
Extinction by lethal mutagenesis
Fitness landscape (Sewall Wright)
Can a virus be trapped in a pit of low fitness?
FMDV genome
L VP4 VP2 VP3 2A 2B 2C VP1 3A 3C 3D
VPg(s)
poly A
A U G A U G
Lab Lb
O
OH OH
HO
N N
N
O
NH2
Ribavirin, mutagenic for FMDV
Guanidine hydrochloride, inhibitor of FMDV replication
H N - C - NH HCl 2 2 . NH
Advantage of sequential inhibitor-mutagen administration
Guanidine prevents interference
Perales C. et al., 2009 PLoS Pathog 5: e1000658
Mutagen removed at different passages
Effect of increasing amount of inhibitor
Different administrations of inhibitor and mutagen
A simple theoretical model (S. Manrubia)
Main features: WT, D, sensitive and resistant to the inhibitor (I) w = mutation rate µ = rate of generation of I-resistant individuals R, r = number of progeny genomes by WT, D Number of infected cells, infectious cycles per cell
Perales C. et al., 2009 PLoS Pathog 5: e1000658
[ I ]
[ I ]
[ I ]
Jc1 GNN
105
104
103
102
10
Vira
l tite
r (TC
ID50
/ml)
106
107
108
… … … p15 p30 p45…
p60 … p80…
p100Jc1
0 10 20 30 40 50 60 70 9080 100
Passage number
p0
105
104
103
102
10
RN
A (m
olec
ules
/ng)
106
107108
0 10 20 30 40 50 60 70 9080 100
C Gluc NS2 NS3 NS4a NS4b NS5a NS5b E1 p7 E2 5’UTR 3’UTR
J6 JFH-1
HCV Jc1, genotype 2a (Charles Rice)
Passage number
RN
A (m
olec
ules
/ng)
Vi
ral t
iter (
TCID
50/
ml)
Combination Sequential
Combination Sequential
Sequential versus combination treatment
Iranzo J. et al., 2011 P.N.A.S. 108(38): 16008-13
I+Mut.
+I +Mut.
+I
+Mut.
I+Mut.
Perales C. et al., 2009 PLoS Pathog 5: e1000658
Therapy involving mutagens and inhibitors
• A mutagen can increase the frequency of inhibitor resistant mutants
• An inhibitor can prevent replication of interfering mutants that contribute to lethal defection
• The mutant spectrum can suppress inhibitor-resistant mutants that affect a trans-complementable protein
• A mutagenized mutant spectrum can suppress high fitness genomes
González-López, et al., 2004 J. Virol. 78: 3319-24 Crowder and Kirkegaard, 2005 Nature Genetics 37: 701-9 Perales et al., 2007 J. Mol. Biol. 369: 985-1000
Thus, a number of interconnected parameters (mutation rate, intensity of inhibition, target of the inhibitor, etc.) must be considered in antiviral designs
Combined
Dose dependant Combined
MUTAGEN M
UTA
GEN
INHIBITOR
INH
IBIT
OR
Mutagen dose In
hibi
tor d
ose
C S
Ext
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Drug 2 D
rug
1
Perales C. et al., submitted
Case of FMDV with guanidine and ribavirin
Domingo, E., Sheldon, J., Perales, C., MMBR, 2012
Experiments with animal models are needed • Possible tests of inhibitor-mutagen administration in
non-responder patients
Precedents: 5-Fluorouracil prevented the establishment of a persistent LCMV infection in mice (C. Ruiz_Jarabo et al. 2003) The mutagenic pyrimidine analogue KP1461 mutagenized HIV-1 in a clinical assay (J.I. Mullins et al. 2011) In some cases the antiviral action of ribavirin might be exerted in part through lethal mutagenesis (Arenavirus, HCV ?)
Will lethal mutagenesis find a clinical application?
Prospects
Conclusions
Effective antiviral therapies must consider the adaptive potential of viral quasispecies and internal interactions within mutant spectra Lethal mutagenesis aims at extinguishing viruses through an excess of mutations, a process that can be viewed as an irreversible loss of viral fitness When an inhibitor and a mutagenic agent participate in therapy a sequential inhibitor-mutagen administration may have an advantage over the corresponding combination Such an advantage has been documented with several viruses, and it is probably a consequence of the dynamics of selection of inhibitor-escape mutants and of the need of defector genomes to replicate to exert their interfering activity
Julie Sheldon Celia Perales Ana M. Ortega Nathan Beach
Susanna Manrubia Jaime Iranzo
Ana Isabel de Ávila Isabel Gallego María Eugenia Soria
Josep Quer F. Rodríguez-Frías Juan I. Esteban Carlos Briones Jordi Gómez
Charles Rice