Virus EvolutionMolecular Epidemiology of Viral Infections

Jen-Ren Wang, Ph. D.王貞仁

Dept. of Medical Laboratory Science and Biotechnology

National Cheng Kung University

Virus evolution

• Virus evolution： constant change of a viral population in the face of selection pressures

• Virus populations display diversity.

• The sources of diversity：mutation (genetic drift), recombination, natural selection (adaptation, fitness)

Replicating viruses produce large numbers of mutant genomes

• RNA virus： Error rate- 1 in 104 or 105

• DNA virus： lower error rate – 1 in 107 or 108

- error-correcting DNA polymeras

e

- latent infection

RNA viruses and quasispecies

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

• Polymorphism

Viruses exchange information

• Recombination

- polymerase changes templates (copy choice) during replication (RNA virus)

- nucleic acid segments are broken and rejoined (DNA virus)

• Reassortment

Molecular studies are useful in

• Epidemiological investigation

• Real-time surveillance

• Make predictions about future developments

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

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

Implications of sequence information

• Maintain effective diagnostics, treatment, and prophylaxis– Strain-specific treatment: HIV, HCV, HBV, CMV– HCV： indicator of susceptibility to specific

treatments eg. Genotype 1 is resistant to interferon therapy

– Detection of mutation that confer antiviral resistance– HIV：monitor emergence of drug resistance

• Distinguish between more or less pathogenic strains– Avian influenza ： HAPI or LAPI– HCV： differ in the in tendency to cause liver damage– Attenuated vaccine strains

Methods for molecular epidemiological analysis

• Oligonucleotide fingerprinting: Rnase T1Recognize relationship between isolates se

parate from ancestral infection by no more than 3 to 5 years

• Monoclonal antibody characterization of viral epitopes

• Nucleic acid analysisNucleic acid hybridizationPCR-RFLPPCR-SSCPPCR-sequencing

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

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

•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

Influenza viruses

Virus 1968 1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996A/Hong Kong/1/68A/England/42/72A/Port Chalmers/1/73A/Scotland/840/74A/Victoria/3/75A/Texas/1/77A/Bangkok/1/79A/Philippines/2/82A/Christchurch/4/85- A/Mississippi/1/85A/Leningrad/360/86A/Sichuan/2/87A/Shanghai/11/87A/Guizhou/54/89A/Beijing/353/89A/Beijing/32/92A/Shangdong/9/93A/Johnannesburg/33/94A/Wuhan/359/95A/Sydney/5/97A/Moscow/10/99

A/USSR/90/77A/Brazil/11/78A/Chile/1/83A/Singapore/6/86A/Bayern/7/95A/Beijing/262/95A/New Caledonia/20/99

B/Victoria/98926/70B/Hong Kong/5/72B/Singapore/222/79B/USSR/100/83B/Ann Arbor/1/86B/Beijing/1/87B/Yamagata/16/88 or B/Panama/45/90B/Panama/45/90B/Beijing/184/93B/Shangdong/7/97

*Formal WHO recommendations first issued in 1973; beginning 1999 there have been two recommendations per year, one for the northern hemisphere (N) and the other for the southern hemisphere (S).

Viruses recommended in the influenza vaccines, 1968-

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 year’s

virus.

Plotkin et al. PNAS 99:6263-6268, 2002

• 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

cluster’s 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 99： 6362-6268, 2002

Predicting evolutionary change in the influenza A virus

Neil M. Ferguson and Roy M. AndersonNature Medicine 8:562-563, 2002

Ferguson and Anderson. Nature Medicine 8:562, 2002

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).

Fitch et al. PNAS 94: 7712, 1997

•The thick line running from the lower left to the upper right (open square) is called the trunk and represents the successful H3N2 lineage.

Bush et al. Science 286: 1921, 1999

• 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

• Positive selection is defined as a significant excess of nucleotide substitutions that result in amino acid replacements.

•Evolution isn’t 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 don’t learn about evolution, they can’t possibly understand modern biology or medicine. David M. Hillis. Predictive Evolution. Science 286: 1866, 1999.