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Viral Genomics: Strength in Numbers David Spiro Assistant Investigator J. Craig Venter Institute

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Presentation on theme: "Viral Genomics: Strength in Numbers David Spiro Assistant Investigator J. Craig Venter Institute"— Presentation transcript:

1 Viral Genomics: Strength in Numbers David Spiro Assistant Investigator J. Craig Venter Institute dspiro@jcvi.org

2 ssRNA negative strand Orthomyxoviridae: Influenza A Filoviridae: Ebola, Marburg Bunyaviridae: Hanta virus, California encephalitis virus ssRNA positive strand Coronaviridae: SARS/Cov Flaviviridae: Dengue, Yellow Fever Virus, West Nile Herpeviridae: Hepatitis E RNA viruses make up the majority of emerging diseases

3 Viral Genomics For Better Preparedness 1 Large datasets to track virus evolution and host shifts (Surveillance programs, Molecular Evolution ) 2Whole genomics approach to detect mutations in entire viral genomes ( Focusing beyond surface proteins) 3New tools for high throughput sequencing and analysis ( Laboratory and Computational) 4Data in public genomic and epidemiological databases ( Reporting genetic and phenotypic links)

4 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 rate HA and NA Selection 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

5 N. Cox CDC

6 Seg1 (PB2) Seg2 (PB1) Seg3 (PA) Seg4 (HA) Seg5 (NP) Seg6 (NA) Seg7 (M) Seg8 (NS) 1 2 3 4 57 6 8 Closure Assembly Tracking Validation NCBI Collections RNA preparation Primer Design RT-PCR Sequencing 150 genomes/month

7 North America 1986-2005 CURRENT AND UPCOMING PROJECTS Mexico Yucatan Cameroon Influenza A Influenza B 1986-2006 Italy 1986-2005 Australia 2002-2005 Hong Kong 1989-2005 Hong Kong 2007-2008 New Zealand 2002-2006 -Avian -Human Kenya 2003-2005 Australia 1978-2006 Italy 1999-2004 Alaska 2006-2007 Nigeria, Niger Cote D’Ivoire Avian H5N1 Canada 2006-2007 Egypt H5N1 Vietnam H5N1 Afganisan H5N1 New York 2002-2006

8 Animal Coronavirus Genome Project  Emerging viral threats  Transmission from animal reservoirs to humans  What genomic changes occur when virus changes hosts? SARS/CoV

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