ssRNA negative strand Orthomyxoviridae: Influenza A Filoviridae: Ebola, Marburg
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Viral Genomics: Strength in Numbers David Spiro Assistant Investigator J. Craig Venter Institute [email protected]
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Viral Genomics: Strength in Numbers David Spiro Assistant Investigator J. Craig Venter Institute [email protected]. RNA viruses make up the majority of emerging diseases. ssRNA negative strand Orthomyxoviridae: Influenza A Filoviridae: Ebola, Marburg - PowerPoint PPT Presentation
Transcript of ssRNA negative strand Orthomyxoviridae: Influenza A Filoviridae: Ebola, Marburg
Viral Genomics: Strength in Numbers
David SpiroAssistant Investigator J. Craig Venter Institute
• ssRNA negative strandOrthomyxoviridae: Influenza AFiloviridae: Ebola, MarburgBunyaviridae: Hanta virus, California encephalitis virus
• ssRNA positive strandCoronaviridae: SARS/CovFlaviviridae: Dengue, Yellow Fever Virus, West NileHerpeviridae: Hepatitis E
RNA viruses make up the RNA viruses make up the majoritymajority of emerging diseases of emerging diseases
Viral Genomics For Better Preparedness
1 Large datasets to track virus evolution and host shifts (Surveillance programs, Molecular Evolution)
2 Whole genomics approach to detect mutations in entire viral genomes (Focusing beyond surface proteins)
3 New tools for high throughput sequencing and analysis (Laboratory and Computational)
4 Data in public genomic and epidemiological databases (Reporting genetic and phenotypic links)
Influenza A Genome Sequencing Project
• Family Orthomyxoviridae• Segmented single-stranded negative RNA genome
HA, NA, NP, M, PB1, PB2, PA, NS
Antigenic drift: High mutation rateHA and NASelection by host immune system
Masters of Host Adaptation:Rapid viral adaptation requires yearly vaccine development
Antigenic shift: Viral meosis- mixing of segments due to coinfection with multiple strains
Fields Virology. Third edition. Lippincott Williams and Wilkins, Philadelphia
N. Cox CDC
Seg1 (PB2)Seg2 (PB1)Seg3 (PA)Seg4 (HA)Seg5 (NP)Seg6 (NA)Seg7 (M)Seg8 (NS)
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Closure
AssemblyTrackingValidation
NCBI
Collections
RNA preparation
PrimerDesign
RT-PCR
Sequencing
150 genomes/month
North America1986-2005
CURRENT AND UPCOMING PROJECTS
Mexico Yucatan
Cameroon Influenza A
Influenza B1986-2006
Italy1986-2005
Australia2002-2005
Hong Kong1989-2005Hong
Kong2007-2008
New Zealand2002-2006
-Avian-Human
Kenya 2003-2005
Australia1978-2006
Italy1999-2004
Alaska2006-2007
Nigeria, Niger Cote D’IvoireAvian H5N1
Canada2006-2007
EgyptH5N1
VietnamH5N1
AfganisanH5N1
New York2002-2006
Animal Coronavirus Genome Project
Emerging viral threats
Transmission from animal reservoirs to humans
What genomic changes occur when virus changes hosts?
SARS/CoV
