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

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

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

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)

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

N. Cox CDC

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

North America CURRENT AND UPCOMING PROJECTS Mexico Yucatan Cameroon Influenza A Influenza B Italy Australia Hong Kong Hong Kong New Zealand Avian -Human Kenya Australia Italy Alaska Nigeria, Niger Cote D’Ivoire Avian H5N1 Canada Egypt H5N1 Vietnam H5N1 Afganisan H5N1 New York

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