In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins

Abstract

The SARS-CoV-2 variant Omicron is characterized, among others, by more than 30 amino acid changes occurring on the spike glycoprotein with respect to the original SARS-CoV-2 spike protein. We report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human antibodies, obtained by modeling them into selected publicly available resolved 3D structures of spike–antibody complexes and investigating the effects of these mutations at structural level. We predict that the interactions of Omicron spike with human antibodies can be either negatively or positively affected by amino acid changes, with a predicted total loss of interactions only in a few complexes. Moreover, our analysis applied also to the spike-ACE2 interaction predicts that these amino acid changes may increase Omicron transmissibility. Our approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology and represents a model to be adopted also in the case of other variants.

Airway and Systemic Immune Responses Following the Third COVID-19 Vaccination in COPD Patients

“…[12][13][14] Since late 2021, the Omicron variant has become a variant of concern worldwide, 15 with at least 30 amino acid changes to the Spike protein compared to the wild-type strain. 16 While there is a lower risk of severe disease and death following infection with Omicron than previous SARS-CoV-2 variants, the very high levels of transmission continue to pose demands on healthcare systems and may lead to significant morbidity, particularly in vulnerable populations. 17 In this study, we prospectively evaluated the immune responses to the third COVID-19 vaccination, with a longitudinal sample collection including pre-and post-booster airway and systemic sampling.…”