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Viral Genomics Workshop
A Viral Genomics Outbreak Mystery
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Viral Genomics Workshop
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Welcome to the Mystery Outbreak Workshop!
Background
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We begin…
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Discussion One: What kind of pathogen are we dealing with?
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Identifying Patterns in the Outbreak
Sample Collection Part I
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Fuchsia City begins collecting…
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What Data Should We Collect?
Sample Collection Part II
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Genomic Specialists
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Samples Collected for Testing and Sequencing
Beginning the Investigation
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The investigation begins:
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Example Forms for Field Investigation:
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Employing Field Epidemiology:
Pathogen Identification
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Who’s that pathogen?!
Pathogen Isolation
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The Novel Pathogen
Source Tracing
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The hidden source:
Sequencing and Bioinformatics
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Uncovering the Source
Genome Assembly QC
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QC Checks
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Quality Control and Sequence Alignments
Genomic Epidemiology
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Understanding the Technical Concepts Underlying Genomic Analysis
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Phylogenetic Tree Interpretation Cheat Sheet
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Results of Genomic Analysis
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What Can the Phylogenetic Tree Tell Us?
Public Health Implementation
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Public Health Action
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What Comes Next?
Containing the Epidemic
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Conclusion:
To the readers
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Author’s Notes
Viral Genomics Workshop
Mystery Outbreak Exercise
Author
Steph M. Lunn, MPH, MS
Published
April 10, 2024
Modified
today
This is a book!
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Welcome to the Mystery Outbreak Workshop!
