Nextstrain build for novel coronavirus SARS-CoV-2
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Guidance for interpretation

Introductory resources

  • Visual explanation of how viral mutations and spread are related: https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html

  • Introduction to interpreting phylogenetic trees: https://nextstrain.org/narratives/trees-background/

  • How to interact with auspice (the engine for viewing trees): https://neherlab.org/201901_krisp_auspice.html

  • Overview of genomic epidemiology (older, but still relevant and clear): http://evolve.zoo.ox.ac.uk/Evolve/Oliver_Pybus_files/EvolAnalysisOfDynamicsOfViruses.pdf

Case Studies

  • UCSF-led analysis of genomic epi in California: https://science.sciencemag.org/content/early/2020/06/05/science.abb9263

  • UK analysis of hospital-acquired infections: https://www.medrxiv.org/content/10.1101/2020.05.08.20095687v1

  • UK’s analysis of coronavirus introductions: https://virological.org/t/preliminary-analysis-of-sars-cov-2-importation-establishment-of-uk-transmission-lineages/507

  • Australia cluster detection: https://www.medrxiv.org/content/10.1101/2020.05.12.20099929v1

  • Nextstrain situation reports: https://nextstrain.org/ncov-sit-reps/