Applying Nextstrain and iCn3D to modify and expand an existing activity for undergraduate students characterizing potential binding of antibodies to mutations in the pathogens Influenza, Respiratory Syncytial Virus (RSV), or Enterovirus D68

Antibodies are proteins that can protect against disease using a variety of mechanisms, including binding to pathogens and targeting them for destruction. Structural modeling of antibody binding to the SARS-Cov-2 spike protein and how mutations might allow viruses to escape antibody neutralization has been previously investigated in Antibody Engineering Hackathons. The procedure for investigating immune escape can be used for students in affordable and accessible Course-Based Undergraduate Research Experiences (CUREs). In this work, we adapted and expanded the SARS-Cov-2 protocol to address new pathogens, including hookworms, Respiratory Syncytial Virus (RSV), Influenza, and Enterovirus D68. We found each presented unique challenges; however, these challenges present opportunities for student research. We describe how modifications to the SARS-Cov-2 protocol designed for SARS-CoV-2 could allow students to investigate the impact of mutations in each of these pathogens when binding to antibodies.