Virtual Seminars on Genomics and Bioinformatics

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Virtual Seminars on Genomics and
Bioinformatics Sharing Knowledge with the
World www.VirtualGenomics.Org
Genomic Footprinting of Encephalic and
Hemorrhagic Viruses Willy Valdivia-Granda Orion
Integrated Biosciences www.orionbiosciences.com
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Genomic Footprinting of Encephalic and
Hemorrhagic Viruses
Willy A. Valdivia-Granda Orion Integrated
Biosciences, Inc. Willy.Valdivia_at_orionbiosciences.
com
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Dissemination of Infectious Diseases
BioScience, May 2003 One million tons of dust
may contain 10 quadrillion microbes (USGS).
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Encephalic and Hemorrhagic Viruses
Arenaviridae Argentine, Bolivian, and Venezuelan
hemorrhagic fevers Lassa fevers
Bunyaviridae Hantavirus, the Congo-Crimean, Rift
Valley fever virus
Flaviviridae Hepatitis, Dengue, Yellow fever,
Japanese encephalitis and West Nile viruses
Filoviridae Ebola and Marburg viruses
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Viral Encephalic Fevers
West Nile virus (WNV) has a wide distribution in
Africa, West Asia, and the Middle East.
In 2001, WNV caused 18 deaths and sickened 131
other people.
For 2002, state health departments in 48 states
reported 4,156 cases of West Nile virus in
people, resulting in 284 deaths.
Genetic studies indicates that the Mexican WNV
strain was likely introduced from the central US
(Estrada-Franco, 2003).
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West Nile Virus Summer 2003
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West Nile Virus Surveillance 2004
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West Nile Virus in Animals
In 2002 West Nile virus cost equine owners in
Colorado and Nebraska more than 1.25 million
Prevention costs for WNV vaccinations likely
exceeded an additional 2.75 million.
The fatality rate among the WNV cases that had
been vaccinated was 20.3 while 36.6 of
unvaccinated animals had died or were
euthanatized.
http//www.combs.colostate.edu/aphi/finalrevisions
.doc
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Dengue fever
Dengue fever is a flavivirus infection
transmitted by the mosquito Aedes aegypti
After an incubation period of 7-10 days, a
flu-like illness develops with high fevers,
chills, myalgia and headaches.
Yearly, dengue causes more than 50 million cases
of infection, 24,000 deaths and 500,000
hemorrhagic cases
There are four antigenically distinct, but
related, dengue virus serotypes, DENV-1, DENV-2,
DENV-3 and DENV-4
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Seroprevalence of Flaviviruses in Animals
J Commun Dis. 1995 27(4)242-246. Micro-haemagglu
tination inhibition (HI) test
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Preventive Measures for Encephalic and
Hemorrhagic Viruses
Accurate identification Infected patients
isolation and/or evacuation Vaccine
development providing immunity Control of vectors
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Molecular Detection Methods for Viruses
Sub- Species
Family
Genus
Species
Strain
DNA Sequencing
DNA-DNA reassociation
RT-PCR
Degenerated-PCR
Immunology
Microarray
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Viral Sequence Recovery Using DNA Microarrays
Viral sequences were physically scraped,
amplified, cloned, and sequenced
Prototypical Coronavirus Genome Structure
D. Wang and J. DeRisi et al.
2003 PLoS Biology Volume 1 Issue 2
http//biology.plosjournals.org
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Overview Genomic Footprinting Flavivirus
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Biological Assumptions for the Genomic
Footprinting
Flaviviridae Family
Hepaciviruses (9.4 Kb)
5 UTR CAP
E2
C
NS2
E1
NS3
NS4
NS4B
NS5B
NS5A
3 UTR
Pestiviruses ( 12Kb)
5 UTR IRE
C
NS2-3
E
E2
NS4A
NS4B
NS5A
NS5B
3 UTR
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Biological Assumptions for the Genomic
Footprinting
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Computational Assumptions for the Genomic
Footprinting
3340 aminoacids
Why Aminoacid?
Information Content 31
Nucleotide substitution 10-3 per site per year
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Computational Assumptions for the Genomic
Footprinting
CLUSTAL-W
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Computational Assumptions for the Genomic
Footprinting
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Ungapped Whole Genomic Footprinting
Flavivirus ( 11Kb)
20 Genomes
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Ungapped Whole Genomic Footprinting
Flavivirus ( 11Kb)
20 Genomes
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Ungapped Whole Genomic Footprinting
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Ungapped Whole Genomic Footprinting
Profile Generation
Genomic Footprinting
9-12 Aminoacids
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Genomic Signature Duplications
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Genomic Signature Count
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Ungapped Whole Genomic Footprinting
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Genomic Signatures Distribution in the Genomic
Catalog
Analysis of genomic sigantures using 33872
sequences of the family Flaviviridae established
that genomic signatures are specific for the
Flavivirus genus
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NS5 Flaviviridae Genomic Catalog (79 viral
species)
1574 Sequences for NS5 protein
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Flavivirus Genomic Signature NS5
Population expansion Selective
sweeps Deleterious regions
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Flavivirus Genomic Signature OIB-NS5-20
Means of the
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Preferential Aminoacid Usage in 116 Flavivirus
Sequences
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Preferential Aminoacid Usage for NS5 Genomic
Signature
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NS5 Genomic Signature Phylogenic Incongruence
Homologous Recombination Regions - Natural
selection - Mechanistic/ecological - Genome
segment reassortment
J. Virol., April 1, 2004 78(7) 3319 - 3324. J.
Virol., February 15, 2004 78(4) 2114 - 2120.
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Arising Biological Questions About Genomic
Signatures
Are genomic signatures relevant for pathogen
replication?
Enhancers of polymerase activity
Silencing of host genes. MHC?
Competitive advantage over other viral serotypes
Role in virus recombination and the generation of
new variability
Are some genomic signatures duplications defining
host range and are related with vector
transmission?
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Human Major Histocompatibility Complex
THE MHC SEQUENCING CONSORTIUM Nature 401, 921 -
923 (1999) doi10.1038/44853
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Genomic Footprinting and Biological Complexity
100,000X
123,000X
25 Å
4 Å
Kuhn RJ et al. (2002). Cell 8108(5)717-25.
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Genomic Footprinting Overview
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Genomic Footprinting of Encephalic and
Hemorrhagic Viruses
Willy A. Valdivia-Granda Orion Integrated
Biosciences, Inc.
Willy.Valdivia_at_orionbiosciences.com