Evaluating the Potential for Immune Escape: How Likely is an Antibody to Protect Against a Specific SARS-CoV-2 Variant

In this activity, provided by Digital World Biology, students use free, online biotechnology resources to investigate how well different commercial antibodies might work against SARS-CoV-2 variants. Students will first use NextStrain.org to locate and detect the spike proteins of emerging SARS-CoV-2 variants. Next, they will "use iCn3D and BLAST to align the sequence of the variant spike protein to a sequence of a spike protein that is bound to a commercial antibody." After identifying mutations in the antibody binding site, students will then compare "chemical bonds that would be formed between the original amino acid and the antibody with the predicted bonds that could be formed by the variant amino acid and predict whether their antibody will be effective against their variant."

Included is a 3-page instructor guide detailing each step of the activity, a 2-page student instructional sheet, activity materials, such as data spreadsheets, and an informational video on using NextStrain.org, BLAST, and iCn3D.