SARS-CoV-2 Delta and Omicron variants resist spike cleavage by human airway trypsin-like protease
Wenyan Ren, … , Shuaiyao Lu, Xiawei Wei
Wenyan Ren, … , Shuaiyao Lu, Xiawei Wei
Published September 17, 2024
Citation Information: J Clin Invest. 2024;134(18):e174304. https://doi.org/10.1172/JCI174304.
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Research Article COVID-19

SARS-CoV-2 Delta and Omicron variants resist spike cleavage by human airway trypsin-like protease

Abstract

Soluble host factors in the upper respiratory tract can serve as the first line of defense against SARS-CoV-2 infection. In this study, we described the identification and function of a human airway trypsin–like protease (HAT), capable of reducing the infectivity of ancestral SARS-CoV-2. Further, in mouse models, HAT analogue expression was upregulated by SARS-CoV-2 infection. The antiviral activity of HAT functioned through the cleavage of the SARS-CoV-2 spike glycoprotein at R682. This cleavage resulted in inhibition of the attachment of ancestral spike proteins to host cells, which inhibited the cell-cell membrane fusion process. Importantly, exogenous addition of HAT notably reduced the infectivity of ancestral SARS-CoV-2 in vivo. However, HAT was ineffective against the Delta variant and most circulating Omicron variants, including the BQ.1.1 and XBB.1.5 subvariants. We demonstrate that the P681R mutation in Delta and P681H mutation in the Omicron variants, adjacent to the R682 cleavage site, contributed to HAT resistance. Our study reports what we believe to be a novel soluble defense factor against SARS-CoV-2 and resistance of its actions in the Delta and Omicron variants.

Authors

Wenyan Ren, Weiqi Hong, Jingyun Yang, Jun Zou, Li Chen, Yanan Zhou, Hong Lei, Aqu Alu, Haiying Que, Yanqiu Gong, Zhenfei Bi, Cai He, Minyang Fu, Dandan Peng, Yun Yang, Wenhai Yu, Cong Tang, Qing Huang, Mengli Yang, Bai Li, Jingmei Li, Junbin Wang, Xuelei Ma, Hongbo Hu, Wei Cheng, Haohao Dong, Jian Lei, Lu Chen, Xikun Zhou, Jiong Li, Wei Wang, Guangwen Lu, Guobo Shen, Li Yang, Jinliang Yang, Zhenling Wang, Guowen Jia, Zhaoming Su, Bin Shao, Hanpei Miao, Johnson Yiu-Nam Lau, Yuquan Wei, Kang Zhang, Lunzhi Dai, Shuaiyao Lu, Xiawei Wei

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Figure 1

Defense-related component existing in the respiratory tract inhibits infection of ancestral SARS-CoV-2 but not Delta and Omicron variants.

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Defense-related component existing in the respiratory tract inhibits inf...
(A–C) Infectivity of WT (A), Delta (B), and Omicron BA.1 (C) pseudoviruses pretreated with nasal wash samples (NW) from young (20–30 years) and old (55–70 years) participants (n = 10). (D) Infectivity of WT pseudovirus with respiratory tract proteases or proteins (n = 3). (E) WT pseudovirus treated with NW, with or without HAT inhibitors aprotinin and soybean trypsin inhibitor (STI) (n = 10). (F) HAT (2 μg/mL) pretreated with spike proteins, incubated with WT pseudovirus, determined infectivity (n = 3). (G and H) Representative images (G) and quantification (H) of CPE in Vero E6 cells infected with live ancestral viruses, with or without HAT (0.5–5 μg/mL) (n = 3). (I and J) Cell lysates collected 48 hours after infection with live viruses for gRNA (I) and sgRNA (J) assays (n = 3). (K) The mRNA levels of tmprss11d in trachea (left) and lung (right) tissues in mice infected with SARS-CoV-2 on day 3 after infection (n = 3 mice each group). (L and M) The representative images displayed conjugates (arrow) formed with SARS-CoV-2 spike protein (green) and released trypsin-like protease (red) in bronchial tissues of infected mice (L) and primates (M). (N) The images indicated SARS-CoV-2 particles (green) trapped by filamentous HAT (red) in the sputum of patients with COVID-19. The inset shows magnified conjugates in merged images. Data are representative (D, F, G–J, and K) of 2 independent experiments with 3 replicates each. Unpaired, 2-tailed Student’s t test was performed in D and K, and 1-way ANOVA analysis followed by Tukey’s multiple comparison post hoc test was conducted in A–C, E, F, and H–J. Scale bars: 200 μm in G; 4 μm in L and M; and 10 μm in N. Data are presented as mean values ± SEM in A–K. *P <0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.