Molecule of the Month: SARS-CoV-2 Nucleocapsid and Home Tests

Soon after the COVID19 pandemic began, the research community mobilized to find ways to fight it. Thanks to these efforts, we have many effective methods for stopping the spread of the virus. Vaccines protect us against infection and nirmatrelvir (the anti-viral active ingredient in Pfizer's Paxlovid) can be used to help treat people who get infected. But perhaps most importantly, many easy-to-use home test kits are widely available to see if we are infected. This is a central tool in the fight against SARS-CoV-2, since it allows us to test ourselves any time and quarantine if we’re infected, thus giving us greater confidence in the safety of social situations.

Most home test kits look for the presence of nucleocapsid in the sample that we collect. Nucleocapsid has the job of packaging the viral genome inside virions. It is made in large quantities in cells infected by SARS-CoV-2, so it provides an effective target for testing. The tests typically use a “flow-through” technology. A small sample is placed in a small well and the molecules flow through an area that has antibodies that recognize nucleocapsid. Then the antibody-bound nucleocapsid flows further and is captured in the distinctive line of a positive test. These tests also include a control that tests for a common molecule, such as our own antibodies, just to make sure the sample was collected correctly.

Nucleocapsid is a complex molecule with many functional parts. One section folds into an RNA-binding domain (PDB ID 7act), with a groove that grips a short segment of the viral genomic RNA. Another section folds into a dimerization domain (6wji) that brings two nucleocapsid molecules together. The rest of the protein is intrinsically disordered, forming tails at each end of the protein chain and a flexible linker that connects the two structured domains. These disordered regions assist with RNA binding and orchestrate association of nucleocapsid dimers into larger assemblies that package the RNA in the small space inside virions.

SARS-CoV-2 home test kits rely on antibodies that specifically recognize nucleocapsid within the complex mix of biomolecules found in a nasal sample. Different brands of these kits use different antibodies that recognize different portions of the molecule. This is not surprising, since the immune system is very effective at developing antibodies that probe all aspects of a target molecule, so developers of tests have many choices for the antibodies they use. For example, the illustration shown here superimposes three structures of antibodies bound to different faces of the RNA-binding domain of nucleocapsid, from PDB ID 7cr5, 7n3c, and 7sts.