SARS-CoV-2 Omicron Variations Reveal Mechanisms Controlling Cell Entry Dynamics and Antibody Neutralization
Enya Qing, Julisa Salgado, Alexandria Wilcox, Tom Gallagher.
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is adapting to continuous presence in humans. Transitions to endemic infection patterns are associated with changes in the spike (S) proteins that direct virus-cell entry. These changes generate antigenic drift and thereby allow virus maintenance in the face of prevalent human antiviral antibodies. These changes also fine tune virus-cell entry dynamics in ways that optimize transmission and infection into human cells. Focusing on the latter aspect, we evaluated the effects of several S protein substitutions on virus-cell membrane fusion, an essential final step in enveloped virus-cell entry.
Introduction
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been continuously adapting to human hosts since its emergence in late 2019. Most of these adaptations reside in the spike (S) proteins that direct virus-cell entry. D614G, the first S adaptation, increased virus stability and viral transmission, enabling subsequent adaptations. Over time, variants of concern (VOCs) arose and replaced one another through increasingly effective transmissions. While the initial VOCs contained only 8~10 S adaptations, the latest Omicron strains had over 30 each, with all strains encompassing over 80 S adaptations in total.
Materials and Methods:
To obtain purified viral particles, clarified VLP-containing FBS-free DMEM was subjected to either size-exclusion chromatography (SEC) or density ultracentrifugation. For SEC, samples were first concentrated 100-fold by ultrafiltration (Amicon, 100 kDa) before SEC (qEV original, Izon, Inc., following manufacturer protocols). VLPs were eluted from columns into 2x FBS-free DMEM. Peak VLP fractions were identified after lysis of VLPs by adding Passive Lysis Buffer (Promega, cat: E1941) and LgBiT and measuring complemented Nluc in a luminometer.
Discussion
The past five years of SARS-CoV-2 evolution has now generated an assemblage of Omicron lineages competing for continuous transmission and infection in humans. In this Omicron collection there are more than 80 deletions and substitutions in the adaptable entry-facilitating SARS-CoV-2 S proteins. While many of these variations confer escape from pre-existing antibodies, others have more enigmatic effects on virus entry functions. Entry requires extensive S protein conformational dynamics.
Acknowledgments
We thank Matteo Porotto and Anne Moscona (Columbia University) for the antiviral HR2 peptides used in this study. We thank Balaji Manicassamy (University of Iowa) for providing the ΔS-luc-GFP Replicon.
Citation: Qing E, Salgado J, Wilcox A, Gallagher T (2024) SARS-CoV-2 Omicron variations reveal mechanisms controlling cell entry dynamics and antibody neutralization. PLoS Pathog 20(12): e1012757. https://doi.org/10.1371/journal.ppat.1012757
Editor: Bart L. Haagmans, Erasmus Medical Center, NETHERLANDS, KINGDOM OF THE
Received: August 12, 2024; Accepted: November 17, 2024; Published: December 2, 2024.
Copyright: © 2024 Qing et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All data underlying the findings are fully available without restriction. All data are in the manuscript and/or supporting information files.
Funding: This research was supported by the National Institutes of Health (R21 AI 178391 to TG). The funders had no role in study design, data collection and interpretation, decision to submit the work for publication or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
