We're hard at work on a complete set of case studies to guide your intepretation of genomic epidemiological data.
In the meantime, we recommend the following resources to get started.
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Visual explanation of how viral mutations and spread are related: https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html
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Introduction to interpreting phylogenetic trees: https://nextstrain.org/narratives/trees-background/
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How to interact with auspice (the engine for viewing trees): https://neherlab.org/201901_krisp_auspice.html
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Overview of genomic epidemiology (older, but still relevant and clear): http://evolve.zoo.ox.ac.uk/Evolve/Oliver_Pybus_files/EvolAnalysisOfDynamicsOfViruses.pdf
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UCSF-led analysis of genomic epi in California: https://science.sciencemag.org/content/early/2020/06/05/science.abb9263
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UK analysis of hospital-acquired infections: https://www.medrxiv.org/content/10.1101/2020.05.08.20095687v1
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UK's analysis of coronavirus introductions: https://virological.org/t/preliminary-analysis-of-sars-cov-2-importation-establishment-of-uk-transmission-lineages/507
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Australia cluster detection: https://www.medrxiv.org/content/10.1101/2020.05.12.20099929v1
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Nextstrain situation reports: https://nextstrain.org/ncov-sit-reps/