This resource introduces students to the use of Nextstrain and Nextclade to visualize the phylogeny of SARS-CoV-2 variants of concern and variants of interest. Terminology and an introduction to the Nextclade resource are provided in a 4-part worksheet.

This case was written in Spring 2020 during the COVID-19 pandemic. It focuses on understanding the structure and interaction of the SARS-Cov-2 viral spike protein that facilitates infection in human cells.

The Life Lab Revisions team has piloted a Canvas-based approach to building scientific competencies in labs.

In March 2020, institutions underwent a massive transition to distance learning as a result of the COVID-19 pandemic. With so little time to devise new materials to maximize learning in the new virtual environment, instructors devised a variety of innovative strategies for completing the Spring 2020 semester. While highly disruptive, the pandemic also brought mainstream attention to a wide array of scientific concepts and provided an opportunity to teach students about science in real-time. Teaching topics related to COVID-19 can be approached from many different disciplines such as virology, immunology, biochemistry, genetics, public health, pharmacology, systems biology, and synthetic biology. By bringing together lessons devised by each of the authors on their own, we offer a series of curriculum modules that can be used either collectively or in parts to provide students with a multidisciplinary look at the virus and to answer their own curiosity about the disease that will define their generation.

Primary image: 360-degree view of COVID-19. The primary image depicts a SARS-CoV-2 virion surrounded by the fields of study that are featured in our pedagogical activities.

Critically reading and evaluating claims made in the primary literature are vital skills for the future professional and personal lives of undergraduate students. However, the formal presentation of intricate content in primary research articles presents a challenge to inexperienced readers. During the fall 2020 semester, I introduced a Collaborative Annotation Project (CAP) into my online 400-level developmental neurobiology course to help students critically read eight research papers. During CAP, students used collaborative annotation software asynchronously to add clarifying comments, descriptions of and links to appropriate websites, and pose and answer questions on assigned papers. Student work was guided and assessed using a CAP grading rubric. Responses to anonymous surveys revealed students found CAP helpful for reading the primary literature and the rubric clarified expectations for the project. Here, I describe how I introduced, used, and assessed CAP in my online class, and I share the detailed CAP instructions and rubric.

Primary image: A moment of levity while annotating primary literature. Sample student annotations from the Collaborative Annotation Project. Student #1 compares immunofluorescence data to Christmas lights, an observation appreciated by student #2. Student names have been removed.

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four assignments that use open-source, online molecular visualization and bioinformatics tools to examine the interaction between the SARS-CoV-2 spike protein and the ACE2 receptor. The interaction between these two proteins initiates SARS-CoV-2 infection of human host cells and is the cause of COVID-19. In assignment I, students identify sequences with homology to the SARS-CoV-2 spike protein and use them to build a primary sequence alignment. Students make connections to a linked primary research article as an example of how scientists use molecular and phylogenetic analysis to explore the origins of a novel virus. Assignments II through IV teach students to use an online molecular visualization tool for analysis of secondary, tertiary, and quaternary structure. Emphasis is placed on identification of noncovalent interactions that stabilize the SARS-CoV-2 spike protein and mediate its interaction with ACE2. We assigned this project to upper-level undergraduate biochemistry students at a public university and liberal arts college. Students in our courses completed the project as individual homework assignments. However, we can easily envision implementation of this project during multiple in-class sessions or in a biochemistry laboratory using in-person or remote learning. We share this project as a resource for instructors who aim to teach protein structure and function using inquiry-based molecular visualization activities.

Primary image: Exploration of SARS-CoV-2 spike protein: student generated data from assignments I - IV. Includes examples of figures submitted by students, including a sequence alignment and representations of 3D protein structure generated using UCSF Chimera. The primary image includes student generated data and a cartoon from Pixabay, an online repository of copyright free art.