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SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression

Authors :
Daniela Niemeyer
Saskia Stenzel
Talitha Veith
Simon Schroeder
Kirstin Friedmann
Friderike Weege
Jakob Trimpert
Julian Heinze
Anja Richter
Jenny Jansen
Jackson Emanuel
Julia Kazmierski
Fabian Pott
Lara M. Jeworowski
Ruth Olmer
Mark-Christian Jaboreck
Beate Tenner
Jan Papies
Felix Walper
Marie L. Schmidt
Nicolas Heinemann
Elisabeth Möncke-Buchner
Morris Baumgardt
Karen Hoffmann
Marek Widera
Tran Thi Nhu Thao
Anita Balázs
Jessica Schulze
Christin Mache
Terry C. Jones
Markus Morkel
Sandra Ciesek
Leif G. Hanitsch
Marcus A. Mall
Andreas C. Hocke
Volker Thiel
Klaus Osterrieder
Thorsten Wolff
Ulrich Martin
Victor M. Corman
Marcel A. Müller
Christine Goffinet
Christian Drosten
Publica
Source :
Niemeyer, Daniela; Stenzel, Saskia; Veith, Talitha; Schroeder, Simon; Friedmann, Kirstin; Weege, Friderike; Trimpert, Jakob; Heinze, Julian; Richter, Anja; Jansen, Jenny; Emanuel, Jackson; Kazmierski, Julia; Pott, Fabian; Jeworowski, Lara M.; Olmer, Ruth; Jaboreck, Mark-Christian; Tenner, Beate; Papies, Jan; Walper, Felix; Schmidt, Marie L.; ... (2022). SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression. PLoS biology, 20(11), e3001871. Public Library of Science 10.1371/journal.pbio.3001871
Publication Year :
2021

Abstract

Epidemiological data demonstrate that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) Alpha and Delta are more transmissible, infectious, and pathogenic than previous variants. Phenotypic properties of VOC remain understudied. Here, we provide an extensive functional study of VOC Alpha replication and cell entry phenotypes assisted by reverse genetics, mutational mapping of spike in lentiviral pseudotypes, viral and cellular gene expression studies, and infectivity stability assays in an enhanced range of cell and epithelial culture models. In almost all models, VOC Alpha spread less or equally efficiently as ancestral (B.1) SARS-CoV-2. B.1. and VOC Alpha shared similar susceptibility to serum neutralization. Despite increased relative abundance of specific sgRNAs in the context of VOC Alpha infection, immune gene expression in infected cells did not differ between VOC Alpha and B.1. However, inferior spreading and entry efficiencies of VOC Alpha corresponded to lower abundance of proteolytically cleaved spike products presumably linked to the T716I mutation. In addition, we identified a bronchial cell line, NCI-H1299, which supported 24-fold increased growth of VOC Alpha and is to our knowledge the only cell line to recapitulate the fitness advantage of VOC Alpha compared to B.1. Interestingly, also VOC Delta showed a strong (595-fold) fitness advantage over B.1 in these cells. Comparative analysis of chimeric viruses expressing VOC Alpha spike in the backbone of B.1, and vice versa, showed that the specific replication phenotype of VOC Alpha in NCI-H1299 cells is largely determined by its spike protein. Despite undetectable ACE2 protein expression in NCI-H1299 cells, CRISPR/Cas9 knock-out and antibody-mediated blocking experiments revealed that multicycle spread of B.1 and VOC Alpha required ACE2 expression. Interestingly, entry of VOC Alpha, as opposed to B.1 virions, was largely unaffected by treatment with exogenous trypsin or saliva prior to infection, suggesting enhanced resistance of VOC Alpha spike to premature proteolytic cleavage in the extracellular environment of the human respiratory tract. This property may result in delayed degradation of VOC Alpha particle infectivity in conditions typical of mucosal fluids of the upper respiratory tract that may be recapitulated in NCI-H1299 cells closer than in highly ACE2-expressing cell lines and models. Our study highlights the importance of cell model evaluation and comparison for in-depth characterization of virus variant-specific phenotypes and uncovers a fine-tuned interrelationship between VOC Alpha- and host cell-specific determinants that may underlie the increased and prolonged virus shedding detected in patients infected with VOC Alpha.

Details

ISSN :
15457885
Volume :
20
Issue :
11
Database :
OpenAIRE
Journal :
PLoS biology
Accession number :
edsair.doi.dedup.....65c3293ea12289a5a44136329bcbe57e
Full Text :
https://doi.org/10.1371/journal.pbio.3001871