Resources

• McBroome, J., Martin, J., de Bernardi Schneider, A. et al. Identifying SARS-CoV-2 regional introductions and transmission clusters in real time. Virus Evolution v8, Issue 1 (2022). doi:10.1093/ve/veac048

• Turakhia, Y., Thornlow, B., Hinrichs, A.S. et al. Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic. Nat Genet 53, 809–816 (2021). doi.org/10.1038/s41588-021-00862-7

• Kramer AM, Sanderson T, Corbett-Detig R. Treenome Browser: co-visualization of enormous phylogenies and millions of genomes.  Bioinformatics (Oxford, England) vol. 39,Issue 1 (2023). doi: 10.1093/bioinformatics/btac772

• de Bernardi Schneider, Adriano et al. StrainHub: a phylogenetic tool to construct pathogen transmission networks. Bioinformatics (Oxford, England) vol. 36,3 (2020). doi:10.1093/bioinformatics/btz646

• Stoddard, G., Black, A., Ayscue, P. et al. Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. BMC Public Health 22, 456 (2022). doi:10.1186/s12889-022-12790-0

• Fauver, Joseph R., et al. Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States. Cell 181.5 (2020). doi:10.1016/j.cell.2020.04.021

• Lin, Chantel et al. Towards Equitable Access to Public Health Pathogen Genomics in the Western Pacific. The Lancet regional health. Western Pacific vol. 18 (2022). doi:10.1016/j.lanwpc.2021.100321

• Turakhia, Y., Thornlow, B., Hinrichs, A. et al. Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape. Nature 609, 994–997 (2022). doi.org/10.1038/s41586-022-05189-9

• Latest COVID-19 Guidance: 

https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/Guidance.aspx

• Tracking COVID-19 in California: 

https://covid19.ca.gov/state-dashboard/

• CDPH COVID Variant Tracking: 

https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-19/COVID-Variants.aspx

• Current Status of COVID-19 in Santa Cruz County: https://www.santacruzhealth.org/HSAHome/HSADivisions/PublicHealth/CommunicableDiseaseControl/CoronavirusHome.aspx

• Testing options: https://www.santacruzhealth.org/HSAHome/HSADivisions/PublicHealth/CommunicableDiseaseControl/CoronavirusHome/SAVELivesSantaCruzCounty/GetTested.aspx

• COVID-19 Genomic Epidemiology Toolkit: 

https://www.cdc.gov/amd/training/covid-19-gen-epi-toolkit.html

• Getting started with Nextstrain:

https://www.youtube.com/watch?v=aubtBo-dAhw

• Demo: Building a region-focused SARS-CoV-2 Nextstrain tree:

https://www.youtube.com/watch?v=ciGqAYT4d-4

• Nextstrain SARS-CoV-2 resources: 

https://nextstrain.org/sars-cov-2/

• Stanford University SARS-CoV-2 Variant Dashboard: 

https://covdb.stanford.edu/variants/omicron/

• Outbreak Info: 

https://outbreak.info/

• California COVID Assessment Tool: 

https://calcat.covid19.ca.gov/cacovidmodels/

• CZ GEN EPI: 

https://czgenepi.org/

• WHO - Global genomic surveillance strategy for pathogens with pandemic and epidemic potential 2022–2032: 

https://www.who.int/initiatives/genomic-surveillance-strategy

• covSPECTRUM:

https://cov-spectrum.org/explore/United%20States/AllSamples/Past6M

• Taxonium GitHub:

https://github.com/theosanderson/taxonium 

• Chronumental GitHub:

https://github.com/theosanderson/chronumental 

• Pathogen Genomics GitHub:

https://github.com/pathogen-genomics