nextstrain.org/groups/neherlab

• Started as part of the surveillance effort in Switzerland
• Most European countries -- updated twice a week
• Heavy focus on sequences from the last 4 weeks (but still subsampled in many cases)
• Administrative divisions for some countries
• Variant specific builds via CoVariants
• We sometimes include experimental features
• Moderate effort to add more -- get in touch if you have specific ideas or requests

• Frequency dynamics are skewed by sampling biases and varying incidence
• Rare sequences might represent large outbreaks in poorly sampled regions
• Sudden changes in sampling strategies might look like rapidly increasing frequencies
• Focus on specific mutations in known VoCs might miss important others
• Laboratory characterization takes time

• By Tyler Starr, Allie Greaney, Jesse Bloom and colleagues
• Systematic evaluation of all RBD mutations for escape and ACE2 binding
• Monoclonals binding to class 1,2,3,4 epitopes
• Convalescent and vaccine sera to map population escape
• Escape maps of indivual sera and antibodies by Bloom lab
• Escape calculator for retained binding by Jesse Bloom

• Escape in distinct RBD epitope classes
• RBD escape in convalescent/vaccine sera
• NTD mutations
• Other VoC associated mutations (nsp6 del)

• ACE2 binding
• Furin cleavage site mutations
• Recent growth