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Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.

Published version
Peer-reviewed

Change log

Authors

Meng, Bo 
Abdullahi, Adam 
Ferreira, Isabella ATM 
Goonawardane, Niluka 
Saito, Akatsuki 

Abstract

The SARS-CoV-2 Omicron BA.1 variant emerged in 20211 and has multiple mutations in its spike protein2. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways3 demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.

Description

Keywords

Adult, Aged, Aged, 80 and over, Angiotensin-Converting Enzyme 2, Animals, Antibodies, Neutralizing, Antibodies, Viral, COVID-19, COVID-19 Vaccines, Cell Line, Cell Membrane, Chlorocebus aethiops, Convalescence, Female, Humans, Immune Sera, Intestines, Lung, Male, Membrane Fusion, Middle Aged, Mutation, Nasal Mucosa, SARS-CoV-2, Serine Endopeptidases, Spike Glycoprotein, Coronavirus, Tissue Culture Techniques, Virulence, Virus Internalization, Virus Replication

Journal Title

Nature

Conference Name

Journal ISSN

0028-0836
1476-4687

Volume Title

603

Publisher

Springer Science and Business Media LLC
Sponsorship
Wellcome Trust (108082/A/15/Z)
Wellcome Trust (207498/Z/17/Z)
Medical Research Council (MC_PC_17230)
MRC (via Imperial College London) (MR/W005611/1)
Medical Research Council (MR/P008801/1)
MRC (MR/T032413/1)
Wellcome Trust (107633/Z/15/Z)
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