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

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Author(s)
Meng, Bo
Abdullahi, Adam
Ferreira, Isabella ATM
Goonawardane, Niluka
Saito, Akatsuki
Kimura, Izumi
Yamasoba, Daichi
Gerber, Pehuén Pereyra
Fatihi, Saman
Rathore, Surabhi
Zepeda, Samantha K
Papa, Guido
Kemp, Steven A
Ikeda, Terumasa
Toyoda, Mako
et al.
Griffith University Author(s)
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2022
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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.

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Nature

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603

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7902

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© The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Medical infection agents (incl. prions)

Biomedical and clinical sciences

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Meng, B; Abdullahi, A; Ferreira, IATM; Goonawardane, N; Saito, A; Kimura, I; Yamasoba, D; Gerber, PP; Fatihi, S; Rathore, S; Zepeda, SK; Papa, G; Kemp, SA; Ikeda, T; Toyoda, M; et al., Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity, Nature, 2022, 603 (7902), pp. 706-714

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