SARS-CoV-2 Stem loop 2 motif (s2m) structure, dynamics, and thermodynamics

Coronaviruses are responsible for infections ranging from the common cold to Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS) and the current novel coronavirus (COVID-19) epidemics. The coronaviral genomes are large at nearly 30 kilobases. Viruses like SARS-CoV-2, responsible for COVID-19, continuously evolve as changes in the genetic code (caused by genetic mutations or viral recombination) occur during replication of the genome. However, a small section (41 nts) define the stem loop 2 motif (s2m) which is highly conserved in the RNA genomes of several viral families, including coronaviruses, suggesting an evolutionary selective advantage or role in the lifecycle independent of the host. We have witnessed great success with vaccine development, but antiviral development continues to lag. Key to antivirials is the identification of structure-function relationships in these highly conserved sequences. Our molecular dynamics simulations build understanding of the structural and dynamical underpinnings of these differences and provide a basis for investigating the s2m structure-function connection. We report four separate efforts that distinguish: (1) SARS-CoV from SARS-CoV-2 s2m characterized by the U5C and G31U mutations, (2) U5C and G31U individual impact as single mutants, (3) SARS-CoV-2 and Delta s2m which differ by an additional G15U mutation, and (4) the indeletion of s2m in Omicron SARS-CoV-2. Principal component analysis was used to identify s2m conformational substates, and a quasiharmonic approximation was used to estimate the relative entropy between each model to quantitate the structural and dynamical consequences on thermodynamics. Understanding the structure and function of conserved viral structures like the s2m is essential for developing potent antivirals resistant to “immune escape” when a new viral variant appears.