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A Metagenomic Perspective on Ecology, Biosecurity, and Public Health – Joshua Batson


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A presentation by Joshua Batson of the Chan-Zuckerberg Biohub on "A Metagenomic Perspective on Ecology, Biosecurity, and Public Health."

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A Metagenomic Perspective on Ecology, Biosecurity, and Public Health – Joshua Batson

  1. 1. A metagenomic perspective on ecology, biosecurity, and public health Joshua Batson Chan Zuckerberg Biohub Catalyst Conference February 22, 2020
  2. 2. Case Study 1: California
  3. 3. Characters... ● Alameda County, CA ● The tree of life ● Public databases ● Citizen science ● Viral evolution ● Wuhan, China ● Balloons ● Mosquitoes
  4. 4. Mosquitoes vector disease West Nile Virus Malaria parasite (Plasmodium falc.)
  5. 5. Mosquito control in the Bay Area
  6. 6. Mosquito control in the Bay Area
  7. 7. Homogenize, extract RNA, and sequence 52 million reads per mosquito
  8. 8. What do the sequences mean?
  9. 9. What do the sequences mean? Orthomyxovirus
  10. 10. Every mosquito contains multitudes
  11. 11. Including evidence of their blood meals
  12. 12. ...and of the blood meal’s pathogens
  13. 13. Citizen scientist observations confirm sequence
  14. 14. A complete viral genome can be assembled from just 100 reads from one mosquito
  15. 15. Metagenomics is quickly revealing the virome Li et al, eLife, 2015
  16. 16. Our one study had 50 novel viral genomes
  17. 17. Wuhan Mosquito Virus 6 - discovered in 2015
  18. 18. Wuhan Mosquito Virus 6 - recent sweep?
  19. 19. Where is it? Where is it going? ? ?
  20. 20. Can viruses be used to track mosquitos?
  21. 21. Metagenomics is a powerful tool for the detection and surveillance of living things. Who gets to use it? To what end?
  22. 22. Compare facial recognition
  23. 23. Case Study 2: Dhaka
  24. 24. Diagnosing Encephalitis in Dhaka
  25. 25. Chikungunya detected in cerebrospinal fluid
  26. 26. Contributors Peter Kim Joe DeRisi Steve Quake Maira Phelps Cristina Tato Amy Kistler Kalani Ratnasiri Annie Lo Hanna Retallack Calla Martyn Natalie Whitis Norma Neff Rene Sit Michelle Tan Josh Batson Gytis Dudas Amy Kistler Lucy Li Phoenix Logan Rebecca Egger Mark Zhang Charles De Bourcey Yun-Fang Juan Eric Haas-Stapleton @thebasepoint
  27. 27. What are the potential benefits of widespread metagenomic sequencing for your community? What are the risks?
  28. 28. Bonus: Dark Matter