Incorporate molecular assay / structural information about mutations/variants

[flaneuse]

• ACE2 binding
• Immune evasion maps
• Incorporate vaccination information? CDC NYT
• Incorporate as flag for mutation tracker -- if there's an increase in lineage/cases in a place with high levels of immunity through vaccination and/or high levels of previous cases --> immediate flag as suggestive of immune evasion (e.g. P.1/P.2 in Brazil, B.1.526 in NY)

[flaneuse]

Therapeutic Escape

• https://opendata.ncats.nih.gov/variant/activity

Antibody Escape Screens

• https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/
• https://www.biorxiv.org/content/10.1101/2021.01.27.428529v2
• https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(20)30624-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312820306247%3Fshowall%3Dtrue
• https://www.biorxiv.org/content/10.1101/2021.03.17.435863v1
• https://science.sciencemag.org/content/371/6531/850
• https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(21)00071-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2666379121000719%3Fshowall%3Dtrue
• https://www.biorxiv.org/content/10.1101/2021.04.06.438709v1
• https://www.biorxiv.org/content/10.1101/2021.04.07.438818v1
• https://www.biorxiv.org/content/10.1101/2020.11.06.372037v2
• https://science.sciencemag.org/content/371/6531/823

ACE2 Binding

• https://linkinghub.elsevier.com/retrieve/pii/S0092867420310035

Structural data

• https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_entity_source_organism.taxonomy_lineage.name%22%2C%22operator%22%3A%22exact_match%22%2C%22value%22%3A%22SARS-CoV-2%22%7D%2C%22service%22%3A%22text%22%2C%22type%22%3A%22terminal%22%2C%22node_id%22%3A0%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22pager%22%3A%7B%22start%22%3A0%2C%22rows%22%3A100%7D%2C%22scoring_strategy%22%3A%22combined%22%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%7D%2C%22request_info%22%3A%7B%22src%22%3A%22ui%22%2C%22query_id%22%3A%22d9596462957a07a7197450e452b05f5d%22%7D%7D

Epitopes

• https://www.iedb.org/result_v3.php?cookie_id=d5b85c

Seroprevalence

• https://covid19serohub.nih.gov/

Vaccination rates

• https://covid.cdc.gov/covid-data-tracker/#vaccinations
• https://ourworldindata.org/covid-vaccinations