Phenotypic Evolution of SARS-CoV-2 Spike During the COVID-19 Pandemic

Overview

Journal Nat Microbiol

Specialties Microbiology
Parasitology

Date 2025 Jan 3

PMID 39753670

Authors

Wilhelm Furnon

Vanessa M Cowton

Giuditta De Lorenzo

Richard Orton

Vanessa Herder

Diego Cantoni

Georgios Ilia

Diogo Correa Mendonca

Karen Kerr

Jay Allan

Nicole Upfold

Gavin R Meehan

Siddharth Bakshi

Udeet Ranjan Das

Sergi Molina Arias

Marion McElwee

Sarah Little

Nicola Logan

Kirsty Kwok

Katherine Smollett

Brian J Willett

Ana da Silva Filipe

David L Robertson

Joe Grove

Arvind H Patel

Massimo Palmarini

Affiliations

Soon will be listed here.

Abstract

SARS-CoV-2 variants are mainly defined by mutations in their spike. It is therefore critical to understand how the evolutionary trajectories of spike affect virus phenotypes. So far, it has been challenging to comprehensively compare the many spikes that emerged during the pandemic in a single experimental platform. Here we generated a panel of recombinant viruses carrying different spike proteins from 27 variants circulating between 2020 and 2024 in the same genomic background. We then assessed several of their phenotypic traits both in vitro and in vivo. We found distinct phenotypic trajectories of spike among and between variants circulating before and after the emergence of Omicron variants. Spike of post-Omicron variants maintained enhanced tropism for the nasal epithelium and large airways but displayed, over time, several phenotypic traits typical of the pre-Omicron variants. Hence, spike with phenotypic features of both pre- and post-Omicron variants may continue to emerge in the future.

Citing Articles

Clinical Characteristics During and After COVID-19 Infection Among Healthcare Workers During the First Wave of Omicron in Chongqing, China.

Tang H, Chen Z, Huang T, Yu P, Tang Q, Qiu Y Immun Inflamm Dis. 2025; 13(1):e70141.

PMID: 39871525 PMC: 11772718. DOI: 10.1002/iid3.70141.

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