Virus Evolution Molecular Epidemiology of Viral Infections

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Virus EvolutionMolecular Epidemiology of Viral
Infections
Jen-Ren Wang, Ph. D. ??? Dept. of Medical
Laboratory Science and Biotechnology National
Cheng Kung University
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Virus evolution

• Virus evolutionconstant change of a viral
  population in the face of selection pressures
• Virus populations display diversity.
• The sources of diversitymutation (genetic
  drift), recombination, natural selection
  (adaptation, fitness)

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Replicating viruses produce large numbers of
mutant genomes

• RNA virusError rate- 1 in 104 or 105
• DNA viruslower error rate 1 in 107 or 108
• - error-correcting DNA polymerase
• - latent infection

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RNA viruses and quasispecies

• Viruses exist as dynamic distributions of non
  identical but related replicons.
• Polymorphism

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Viruses exchange information

• Recombination
• - polymerase changes templates (copy choice)
  during replication (RNA virus)
• - nucleic acid segments are broken and rejoined
  (DNA virus)
• Reassortment

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Molecular studies are useful in

• Epidemiological investigation
• Real-time surveillance
• Make predictions about future developments

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Molecular epidemiology of viral infections

• Distinguish between related strains of viruses
• Deduce the relationships between viruses from
  different outbreaks or individual patients
• Dissemination and evolution of viruses can be
  followed locally and globally

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Molecular epidemiology of viruses

• Determine the sources of imported viruses
• Monitor pathways of virus transmission
• Monitor the process of control activities
• Develop molecular reagents for rapid detection of
  viral infections

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Implications of sequence information

• Maintain effective diagnostics, treatment, and
  prophylaxis
• Strain-specific treatment HIV, HCV, HBV, CMV
• HCVindicator of susceptibility to specific
  treatments eg. Genotype 1 is resistant to
  interferon therapy
• Detection of mutation that confer antiviral
  resistance
• HIVmonitor emergence of drug resistance
• Distinguish between more or less pathogenic
  strains
• Avian influenza HAPI or LAPI
• HCVdiffer in the in tendency to cause liver
  damage
• Attenuated vaccine strains

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Methods for molecular epidemiological analysis

• Oligonucleotide fingerprinting Rnase T1
• Recognize relationship between isolates
  separate from ancestral infection by no more
  than 3 to 5 years
• Monoclonal antibody characterization of viral
  epitopes
• Nucleic acid analysis
• Nucleic acid hybridization
• PCR-RFLP
• PCR-SSCP
• PCR-sequencing

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Oligonucleotide fingerprint analysis

• Restriction enzyme- No
• Probe- No
• Basis for distinctions- Rnase T1 cleavage sites
• Level of resolution- subtypes, quasispecies
• Advantages- simple directly applicable to RNA
  viruses. Can detect point mutations
• Disadvantages- complex electrophoresis procedure

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Nucleotide sequencing

• Restriction enzyme- No
• Probe- No
• Basis for distinctions- nucleotide sequence
• Level of resolution- single genome (if cloned)
• Advantages- wide applicability, can identify
  single nucleotide mutation
• Disadvantages- Technically complex produces
  large amounts of data automated sequencing
  requires expensive equipment

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Influenza viruses

• Antigenic drift
• - Epidemics
• - increase in incidence of pneumonia and
• lower respiratory disease
• - excess rates of hospitalization or
• mortality
• Antigenic shift
• -Widespread and severe epidemics
• - Pandemic

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Viruses recommended in the influenza vaccines,
1968-
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Each year a new flu vaccine is produced, and
judging which strains to target is a tricky
business. A new study evaluating viral evolution
suggests a more systemic approach to predicting
next years virus.Plotkin et al. PNAS
996263-6268, 2002
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• They found that among the sequences within each
  of these large clusters, those sequences isolated
  in China or Hong Kong are found preferentially in
  the first half of the clusters lifetime. These
  results support the hypothesis that dominant
  viral swarms tend to originate in Asia and
  thereafter spread across the globe.

Joshua B. Plotkin et.al., PNAS 996362-6268, 2002
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Predicting evolutionary change in the influenza A
virusNeil M. Ferguson and Roy M.
AndersonNature Medicine 8562-563, 2002
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Unlike HIV, which is constantly growing in
diversity, influenza change constantly but with
limited diversity at any point in time-giving an
unusual conifer tree shape (R. Bush).
Ferguson and Anderson. Nature Medicine 8562,
2002
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• The thick line running from the lower left to the
  upper right (open square) is called the trunk and
  represents the successful H3N2 lineage.

Fitch et al. PNAS 94 7712, 1997
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• The average life-span of a nontrunk lineage is
  1.5 years, although one recent nontrunk lineage
  persisted for 5 years ().

Bush et al. Science 286 1921, 1999
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• Positive selection is defined as a significant
  excess of nucleotide substitutions that result in
  amino acid replacements.

Bush et al. Science 286 1921, 1999
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Evolution isnt just something that happened in
the past evolution can be observed in the
present, and in some cases, used to predict the
future. School boards and science educators need
to understand this simple fact If student dont
learn about evolution, they cant possibly
understand modern biology or medicine. David
M. Hillis. Predictive Evolution. Science 286
1866, 1999.