![Page 1: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/1.jpg)
HCV Evolution: Diversification and Convergence
Yury Khudyakov
Division of Viral HepatitisCenters for Disease Control and Prevention, Atlanta, GA
![Page 2: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/2.jpg)
Public Health
Reduction of morbidity and mortality
- Diagnostics- Treatment- Prevention
Medicine
Introduction
![Page 3: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/3.jpg)
A high rate of mutation defines rapid HCV evolution
HCV genome continuously changes
“Arms Race”
Pervasive coevolution
Opportunity for convergence
Introduction
![Page 4: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/4.jpg)
PHYLOGENETIC ANALYSISIntra-Host HCV Variants
Patient 1
Patient 2
Patient 3
Patient 4
![Page 5: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/5.jpg)
Network of coordinated substitutions in the HCV polyprotein
K-Core Decomposition of HCV Network
![Page 6: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/6.jpg)
Bayesian Network of HCV Polyprotein Site Interactions and Therapy Outcome
![Page 7: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/7.jpg)
Bayesian Network associating the HVR1 sites with IFN response and host demographic factors
HVR1-BN
![Page 8: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/8.jpg)
Intra-Host Evolution over
Many Years
![Page 9: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/9.jpg)
15.991aIDUFemaleUnknownD
15.961aUnknownMaleBlackC
18.121aIDUFemaleBlackB
8.841bTransfusionMaleWhiteA
YearsGenotypeTransmissionGenderRacePatient ID
Sentinel County HCV Follow-up Study
![Page 10: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/10.jpg)
0.0 5.0 10.0 15.0
0.00
10.00
20.00
Div
erge
nce
Time
DBA C
HCV Quasispecies Divergence During Long-Term Chronic Infection
Patients
![Page 11: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/11.jpg)
HVR1: patient A
Time-pints (Yrs)
0
8.8
2.8
7.92.3
0-2.8 yr
7.9-8.8 yr
HVR1: patient B
0
17.218.2
11.2
15.3
12.213.4
10.19.07.93.33.02.8
16.2
Time-points (Yrs) 0 - 3.3 yr
7.9-13.4
7.9-17.2
15.3-18.2
HVR1: patient DTime-points (Yrs)
0
16.0
1.5
2.52.74.8
2.3
1.62.0
11.612.114.015.0
1.5-2.7 yr
4.8-16.0 yr
HVR1: patient CTime-points (Yrs)
0
9.0
16.0
7.1
15.0
8.1
14.6
10.5
0.3
11.1
0-0.3 yr
7.1-8.1 yr
9.0-16.0 yr
HVR1 Phylogenetic Trees
![Page 12: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/12.jpg)
DBA C
0.0 5.0 10.0 15.0
0.00
0.50
1.00
1.50
2.00
dN/d
S
Time
Changes in Selection Pressures Over Time
dN/dS vs. TimeHVR1 – R=-0.58, p=0.0001NS5A – R=-0.61, p=0.0001
Titer vs. TimeR=0.585, p=0.0001
Titer vs. dN/dSR=-0.383, p=0.012
Patients
![Page 13: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/13.jpg)
![Page 14: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/14.jpg)
![Page 15: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/15.jpg)
![Page 16: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/16.jpg)
![Page 17: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/17.jpg)
![Page 18: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/18.jpg)
![Page 19: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/19.jpg)
![Page 20: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/20.jpg)
![Page 21: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/21.jpg)
![Page 22: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/22.jpg)
![Page 23: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/23.jpg)
Genetic Linkage to Viral and Host Factors
Genomic StructureQS diversity
HCV QS SEQUENCE HOST
Viral titer
dN/dS
HCV QS SEQUENCE Factors
![Page 24: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/24.jpg)
I. Molecular Epidemiologic Data• NHANESIII:
• 106 patients• 1384 HVR1 quasispecies; Genotypes 1 – 6• HVR1: positions 1491 to 1577nt (polyprotein 488 to 516)• 5’UTR: positions 127 to 340nt• NS5B: positions 8290 to 8589nt (polyprotein 2651 to 2749)
II. Quantitative Structure Relationships• Probabilistic Graphical Models:
• Bayesian Networks (BN)
III. Predictions• Causal models:
• BN classifiers
![Page 25: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/25.jpg)
Bayesian Network Model Associating Sequences of HCV HVR1 Quasispecies to Viral and Host Parameters
![Page 26: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/26.jpg)
Bayesian Network Model Associating Sequences of HCV HVR1 Quasispecies to Viral and Host Parameters
![Page 27: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/27.jpg)
Bayesian Network Model Associating Sequences of HCV HVR1 Quasispecies to Viral and Host Parameters
![Page 28: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/28.jpg)
Bayesian Network Model Associating Sequences of 3 HCV Genome Regions to Viral and Host Parameters
![Page 29: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/29.jpg)
Target classes 10-fold-CV ‡
(%) Acc.randTest †
(10-fold-CV ‡)TestSet**
Genotype 99.9% 0.3286 100%
dN/dS^^ (3-bin) (2-bin)
94.4%92.2%
0.4020 0.5120
70.3%82.7%
NQSaa-hvr1 88.0% 0.3887 70.3%
NQSnt-hvr1 87.7% 0.3978 72.4%
Viral Titer 97.2% 0.6031 52.40%
‡ Avg. accuracies† Random assignment of class labels** 10 NHANES-3 patients; 5M and 5F; Genotypes 1a and 1b; 185nt/96aa HVR1 QS^^ Based on dNdS 3 class or 2 class grouping
Quantitative Validation of Models
Predictions: Classification Modeling
![Page 30: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/30.jpg)
Five physicochemical properties (Atchley et al, 2005):
Polarity, α-helix , Size, aa frequency, Charge
Multiple sequence alignment
Euclidean distance between every pair of sequences
Visualization of distance matrix Pathfinder network (r = ∞, q = n-1)
Methods
![Page 31: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/31.jpg)
PFNET
![Page 32: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/32.jpg)
Inter-genotype convergence
Genotype 1
![Page 33: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/33.jpg)
Genotype 2
Inter-genotype convergence
![Page 34: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/34.jpg)
• 24.3% of all links are between different genotypes.
Genotype convergence
![Page 35: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/35.jpg)
• We immunized mice with 102 HVR1 peptides covering all high-density regions of the sequence space.
• We tested the reactivity of each sera against 262 peptides (in yellow), a total of 26724 reactions
Cross-reactivity experiment
![Page 36: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/36.jpg)
• There were 5039 positive reactions (blue links), which correspond to 18.85% of all tested.
![Page 37: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/37.jpg)
• Three peptides (yellow) were found that collectively reacted with all 262 antigens.
![Page 38: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/38.jpg)
Relationship between the reduction of selection pressure and cross-immunoreactivity among HCV intra-host variants
Patient Correlation between DN/DS and ACR
p-value
Patient B -0.6262 0.0166Patient C -0.9101 0.0003Patient D -0.476 0.1001
60*ACR
DN/DS
Patient C
![Page 39: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/39.jpg)
Public Health: Reduction of morbidity and mortality
- Diagnostics- Treatment- Prevention
Medicine:
Conclusion
Many viral phenotypic traits with significant medical and public healthimplications are convergent rather than ancestral
![Page 40: HCV Evolution: Diversification and Convergence Yury Khudyakov Division of Viral Hepatitis Centers for Disease Control and Prevention, Atlanta, GA](https://reader037.vdocument.in/reader037/viewer/2022110321/56649ce15503460f949ac471/html5/thumbnails/40.jpg)
Thank you!