Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain

"To Be Vaccinated or Not to Be Vaccinated": Factors Influencing COVID-19 Vaccine Hesitancy and Future Vaccination Willingness Amongst US Women of Reproductive Age

Background & Objectives

Growing data on the impact of herd immunity and susceptibility of unvaccinated persons to chronic COVID sequelae requires deeper understanding of vaccine stigma and hesitancy to facilitate population needs. Reproductive-aged women (18-45 years) were at a "vaccine paradox" during COVID-19 - hesitant to receive the vaccine, yet at increased risk for COVID infection. In this study, we sought to: identify demographic predictors, reasons, geographic location of vaccine hesitancy, and COVID-specific attributes that predict future vaccination willingness. We hypothesized that high COVID risk perception and high COVID stress would be predictors of willingness.

Methods

Study Design: Cross-sectional survey of women across the United States. Main Outcomes and Measures: Vaccine hesitancy was defined as responding "No/Not Sure" to the question "Have you received any of the COVID-19 vaccines?" The COVID-Risk scale evaluate perceived COVID Risk, and the COVID-19 Perceived Stress Scale (PSS-10-c) evaluated COVID stress. Open ended questions inquired about participants' vaccine concerns.

Results

Of the 1,037 women who accessed the survey, 948 (91%) consented and completed. Predictors of vaccine hesitancy included younger aged parents (p=0.005), non-white race (p=0.003), and having high school or lower educational attainment (p<0.0001). Using smoking as a proxy measure of "health behavior", we found long-term smokers or quitters were more hesitant than those who never smoked (p=0.03). Geographic analyses showed the most vaccine hesitant women resided in Southeast and Midwest US. Hesitancy reasons included side effects (21%) and fertility/pregnancy concerns (4%). High COVID risk perception (p=0.0004) and high COVID stress (p=0.01) significantly predicted future willingness to get vaccinated.

Conclusions and Relevance

This research provides insights for managing the "vaccine paradox" in reproductive age women, and identifying factors that influence COVID-19 vaccine hesitancy and future vaccination willingness. Public health and policy advocates could target messaging around COVID risk and stress in Southeastern and Midwestern regions; as well as address women's concerns around fertility and other side effects.

On the Nature of the Interactions That Govern COV-2 Mutants Escape from Neutralizing Antibodies

The most fruitful prevention and treatment tools for the COVID-19 pandemic have proven to be vaccines and therapeutic antibodies, which have reduced the spread of the disease to manageable proportions. The search for the most effective antibodies against the widest set of COV-2 variants has required a long time and substantial resources. It would be desirable to have a tool that will enable us to understand the structural basis on which mutants escape at least some of the epitope-bound antibodies, a tool that may substantially reduce the time and resources invested in this effort. In this work, we applied a computational-based tool (employed previously by us to understand COV-2 spike binding to its cognate cell receptor) to the study of the effect of Delta and Omicron mutations on the escape tendencies. Our binding energy predictions agree extremely well with the experimentally observed escape tendencies. They have also allowed us to set forth a structural explanation for the results that could be used for the screening of antibodies. Lastly, our results explain the differences in molecular interactions that govern interaction of the spike variants with the receptor as opposed to those with antibodies.

SARS-CoV-2 omicron RBD forms a weaker binding affinity to hACE2 compared to Delta RBD in in-silico studies

The COVID-19 pandemic sparked an unprecedented race in biotechnology in a search for effective therapies and a preventive vaccine. The continued appearance of SARS-CoV-2 variants of concern (VoCs) further swept the world. The entry of SARS-CoV-2 into cells is mediated by binding the receptor-binding domain (RBD) of the S protein to the cell-surface receptor, human angiotensin-converting enzyme 2 (hACE2). In this study, using a coarse-grained force field to parameterize the system, we employed steered-molecular dynamics (SMD) simulations to reveal the binding of SARS-CoV-2 Delta/Omicron RBD to hACE2. Our benchmarked results demonstrate a good correlation between computed rupture force and experimental binding free energy for known protein-protein systems. Moreover, our findings show that the Omicron RBD has a weaker binding affinity to hACE2, consistent with the respective experimental results. This indicates that our method can effectively be applied to other emerging SARS-CoV-2 strains.Communicated by Ramaswamy H. Sarma.

A bivalent form of a RBD-specific synthetic antibody effectively neutralizes SARS-CoV-2 variants

Coronavirus Disease 2019 (COVID-19) pandemic is severely impacting the world, and tremendous efforts have been made to deal with it. Despite many advances in vaccines and therapeutics, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remains an intractable challenge. We present a bivalent Receptor Binding Domain (RBD)-specific synthetic antibody, specific for the RBD of wild-type (lineage A), developed from a non-antibody protein scaffold composed of LRR (Leucine-rich repeat) modules through phage display. We further reinforced the unique feature of the synthetic antibody by constructing a tandem dimeric form. The resulting bivalent form showed a broader neutralizing activity against the variants. The in vivo neutralizing efficacy of the bivalent synthetic antibody was confirmed using a human ACE2-expressing mouse model that significantly alleviated viral titer and lung infection. The present approach can be used to develop a synthetic antibody showing a broader neutralizing activity against a multitude of SARS-CoV-2 variants.