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SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells
Open accessAbstract
The novel SARS-CoV-2 Omicron variant (B.1.1.529), first found in early November 2021, has sparked considerable global concern and it has >50 mutations, many of which are known to affect transmissibility or cause immune escape. In this study, we sought to investigate the virological characteristics of the Omicron variant and compared it with the Delta variant which has dominated the world since mid-2021. Omicron variant replicated more slowly than the Delta variant in transmembrane serine protease 2 (TMPRSS2)-overexpressing VeroE6 (VeroE6/TMPRSS2) cells. Notably, the Delta variant replicated well in Calu3 cell line which has robust TMPRSS2 expression, while the Omicron variant replicated poorly in this cell line. Competition assay showed that Delta variant outcompeted Omicron variant in VeroE6/TMPRSS2 and Calu3 cells. To confirm the difference in entry pathway between the Omicron and Delta variants, we assessed the antiviral effect of bafilomycin A1, chloroquine (inhibiting endocytic pathway), and camostat (inhibiting TMPRSS2 pathway). Camostat potently inhibited the Delta variant but not the Omicron variant, while bafilomycin A1 and chloroquine could inhibit both Omicron and Delta variants. Moreover, the Omicron variant also showed weaker cell-cell fusion activity when compared with Delta variant in VeroE6/TMPRSS2 cells. Collectively, our results suggest that Omicron variant infection is not enhanced by TMPRSS2 but is largely mediated via the endocytic pathway. The difference in entry pathway between Omicron and Delta variants may have an implication on the clinical manifestations or disease severity.
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“suggesting entry selectivity of variants is associated with clinical manifestation [67].”
From Insights of Endocytosis Signaling in Health and Disease (2023) · cites this paper as [67]
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“Current evidence suggests that pharmacological inhibition of endocytic pathways potentially regressed replication of novel SARS-CoV-2 lineage B.1.1.529 (Omicron variant) in VeroE6/TMPRSS2 cell, suggesting entry selectivity of variants is associated with clinical manifestation [67].”
From Insights of Endocytosis Signaling in Health and Disease (2023) · cites this paper as [67]
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Ivanova, T., Mariienko, Y., Mehterov, N. H., Kazakova, M., Sbirkov, Y., Todorova, K. O., Hayrabedyan, S., & Sarafian, V. S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24097734 · Cited by 18
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“Notably, reports on current 69 circulating SARS-CoV-2 variants of concern demonstrate that Omicron infection is not 70 enhanced by TMPRSS2 but is largely mediated via the endocytic pathway (12, 13).”
BackgroundHost factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects
Zhang, Y., Chen, S., Tian, Y., & Fu, X. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1407261 · Cited by 16
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SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19
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“In this respect, variations that have been reported across VOCs in the remodeling of the binding site [6], the cleavage at the S1/S2 cleavage site [34], the fusion with the host cell membrane [26,35] and the endocytotic pathways [36] could also interfere with their spreading and infectivity capacities.”
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“…of SARS‐CoV‐2 enters cells in a TMPRSS2‐ independent manner via the endosomal route (Meng et al., 2022; Peacock et al., 2022; Willett et al., 2022; H. Zhao et al., 2022), which is in good correlation with the reduced cell entry efficiency into TMPRSS2‐ expressing cells for Omicron in comparison…”
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“Transduction was performed in the presence of E64d to shut off the endosomal route in which S is activated by cathepsin B/L instead of cell surface proteases (27).”
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“2 panel E) as expected [18], thus confirming that Omicron has a decreased replicative fitness, at least in Vero E6 cells.”
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“The reduced severity of Omicron as compared to Delta is consistent with early laboratory evidence that there is a reduction in lower lung infectivity, deficient cell entry, and syncytium formation likely due to diminished mediation of plasma membrane fusion by the modified spike protein [97,98].”
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Shin, D., Smith, D. M., & Choi, J. Y. (2022) · Yonsei Medical Journal · doi:10.3349/ymj.2022.0383 · Cited by 13
“One in vitro study from Hong Kong found that the omicron variant replication was lower and had weak fusion activity in VeroE6/TMPRSS2 cells compared to delta variants, indicating that the omicron variant is less dependent on the TMPRSS2 pathway.(16) Furthermore, Hui, et al.”
BackgroundKim, T., Kim, J.-Y., Kwon, H., Jeon, S., Lee, S. J., Jung, H.-S., Kim, S.-H., Jang, D., & Lee, C. J. (2022) · Antiviral Research · doi:10.1016/j.antiviral.2022.105428 · Cited by 11
“Of note, chloroquine showed relatively poor inhibitory activity against Omicron, which was consistent with a previous report (Zhao et al., 2022).”
Mutation T9I in Envelope confers autophagy resistance to SARS-CoV-2 Omicron
Klute, S., Nchioua, R., Cordsmeier, A., Vishwakarma, J., Koepke, L., Alshammary, H., Jung, C., Hirschenberger, M., Hoenigsperger, H., Fischer, J.-R., et al. (2025) · iScience · doi:10.1016/j.isci.2025.112974 · Cited by 9
SARS-CoV-2 variants divergently infect and damage cardiomyocytes in vitro and in vivo
Mok, B. W.-Y., Kwok, M., Li, H. S., Ling, L., Lai, A., Yan, B., Law, C. T., Yeung, C. H., Zhang, J., Tam, R. C.-Y., et al. (2024) · Cell & Bioscience · doi:10.1186/s13578-024-01280-y · Cited by 9
“While earlier variants such as Delta require the transmembrane serine protease 2 (TMPRSS2) for activation, Omicron infection can occur independently of this protein, allowing Omicron to infect cells that lack TMPRSS2 [4–6, 8, 9].”
BackgroundInfluentialSelf-citationSARS-CoV-2 genomics and impact on clinical care for COVID-19
Lorenzo-Redondo, R., Carvalho, A. M. D. S., Hultquist, J. F., & Ozer, E. A. (2023) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkad309 · Cited by 12
Mahajan, N., Kesarwani, S., Salunke, C., Kumbhar, P., Yenkure, P., Shaikh, J., Shikhare, S., Mahale, S., Sachdeva, G., & Gajbhiye, R. (2022) · International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics · doi:10.1002/ijgo.14348 · Cited by 10
Keeping up with the COVID's—Could siRNA‐based antivirals be a part of the answer?
Forgham, H., Käkinen, A., Qiao, R., & Davis, T. P. (2022) · Exploration · doi:10.1002/exp.20220012 · Cited by 18
Yang, S., Tong, Y., Chen, L., & Yu, W. (2022) · Molecular Biomedicine · doi:10.1186/s43556-022-00077-0 · Cited by 10
Self-citationKinoshita, H., Yamamoto, T., Kuroda, Y., Inoue, Y., Miyazaki, K., Ohmagari, N., Tokita, D., Nguyen, P. H. A., Yamada, S., Harada, S., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-75038-4 · Cited by 9
“However, the omicron variant replicates more slowly than the Delta variant (B.1.617.2 lineage first identified in October 2020) in these cells 14 , suggesting that this line is less effective as a means of isolating omicron variants.”
BackgroundInfluentialKongsomros, S., Boonyarattanasoonthorn, T., Phongphaew, W., Kasorndorkbua, C., Sunyakumthorn, P., Im‐Erbsin, R., Lugo‐Roman, L. A., Kongratanapasert, T., Paha, J., Manopwisedjaroen, S., et al. (2024) · Journal of Traditional and Complementary Medicine · doi:10.1016/j.jtcme.2024.05.004 · Cited by 10
Purwono, P. B., Vacharathit, V., Manopwisedjaroen, S., Ludowyke, N., Suksatu, A., & Thitithanyanont, A. (2024) · PLoS ONE · doi:10.1371/journal.pone.0301330 · Cited by 12
What makes SARS‐CoV‐2 unique? Focusing on the spike protein
Qian, J., Zhang, S.-C., Wang, F., Li, J., & Zhang, J. (2024) · Cell Biology International · doi:10.1002/cbin.12130 · Cited by 16
“For example, the replication rate of Omicron in TMPRSS2 ‐ overexpressing cells is significantly slower than that of Delta because Omicron infection of host cells is mainly mediated through the endocytic pathway (H. Zhao et al., 2022).”
BackgroundBose, T., Wasimuddin, Acharya, V., Pinna, N. K., Kaur, H., Ranjan, M., Saikrishna, J., Nagabandi, T., Varma, B., Tallapaka, K. B., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1238829 · Cited by 9
“The delta and omicron variants have been observed to utilize different entry pathways for infection (Menni et al., 2022; Zhao et al., 2022), and it is likely that during this migration, the resident microbiota can get altered and any inclusion of the pathobionts may aggravate the disease outcome.”
BackgroundEvaluation of Nafamostat as Chemoprophylaxis for SARS-CoV-2 Infection in Hamsters
Neary, M., Sharp, J., Gallardo-Toledo, E., Herriott, J., Kijak, E., Bramwell, C., Cox, H., Tatham, L. M., Box, H., Curley, P., et al. (2023) · Viruses · doi:10.3390/v15081744 · Cited by 9
Use of remdesivir for COVID-19 in patients with hematologic cancer
Martin‐Onraët, A., Barrientos-Flores, C. D. J., Vilar‐Compte, D., Pérez‐Jimenez, C., & Alatorre-Fernández, P. (2022) · Clinical and Experimental Medicine · doi:10.1007/s10238-022-00964-4 · Cited by 9
Zhao, H., Zhang, C., Lam, H., Meng, X., Peng, Z., Yeung, M. L., Chan, J. F., To, K. K., & Yuen, K. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01138-0 · Cited by 8
Self-citationOtaki, J., Nakasone, W., & Nakamura, M. (2022) · bioRxiv · doi:10.1101/2021.12.30.474613 · Cited by 9
“Several studies have pointed out slow replication and cellular infection processes for less virulence [29,30].”
BackgroundDu, Q., Liang, R., Wu, M., Yang, M., Xie, Y., Liu, Q., Tang, K., Lin, X., Yuan, S., & Shen, J. (2023) · Journal of Advanced Research · doi:10.1016/j.jare.2023.10.002 · Cited by 10
“Cellular serine protease TMPRSS2 is also an essential mediator for S protein priming [63–65].”
BackgroundPoniedziałek, B., Rzymski, P., Zarębska‐Michaluk, D., Rogalska, M., Rorat, M., Czupryna, P., Kozielewicz, D., Hawro, M., Kowalska, J. D., Jaroszewicz, J., et al. (2023) · Journal of Medical Virology · doi:10.1002/jmv.28962 · Cited by 9
Hu, C. (2023) · Clinical Complementary Medicine and Pharmacology · doi:10.1016/j.ccmp.2023.100089 · Cited by 11
“In addition, follow-up after hospital discharge (Luo, 2020) is still important to those cases who are asymptomatic (Zhao et al., 2021; Brandal et al., 2021; Kumar et al., 2021).”
BackgroundDo SARS-CoV-2 Variants Differ in Their Neuropathogenicity?
Bauer, L., & van Riel, D. A. J. (2023) · mBio · doi:10.1128/mbio.02920-22 · Cited by 9
Attenuation and Degeneration of SARS-CoV-2 Despite Adaptive Evolution
Liu, Y. (2023) · Cureus · doi:10.7759/cureus.33316 · Cited by 5
“The difference between the Delta variant and the Omicron variant was greater when they were compared in Vero E6 cells expressing TMPRSS2 and it was found that Omicron lost its ability to use TMPRSS2 for cell entry [40].”
BackgroundMurillo-Zamora, E., Guzmán-Esquivel, J., Bricio-Barrios, J. A., & Mendoza-Cano, O. (2022) · Public Health · doi:10.1016/j.puhe.2022.10.014 · Cited by 8
“This latter results from 97 the specific entry pathway of the Omicron variant, which is endocytic rather than through the 98 transmembrane serine protease 2 (TMPRSS2) [7].”
BackgroundMurari, T. B., Fonseca, L. M. D. S., Pereira, H. B. D. B., Filho, A. S. N., Saba, H. C., Scorza, F. A., de Almeida, A.-C. G., Maciel, E. L. N., Mendes, J. F. F., Filho, T. M. R., et al. (2022) · Vaccines · doi:10.3390/vaccines10091504 · Cited by 8
“This can be attributed to the fact that the various mutations in the viral genome potentially attenuated its virulence by affecting its replication and fusion efficiency with the host cell, which may partially explain these findings [48].”
BackgroundCharacteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates
Feng, X., Yu, D., Zhang, M., Li, X., Zou, Q., Ma, W., Han, J.-B., Xu, L., Yang, C., Qu, W., et al. (2022) · Virologica Sinica · doi:10.1016/j.virs.2022.09.007 · Cited by 7
Palladino, R., Mercogliano, M., Fiorilla, C., Frangiosa, A., Iodice, S., Zamparelli, S. S., Montella, E., Triassi, M., & Sanduzzi, A. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph19159670 · Cited by 9
“may have poorer replication in the lungs when compared with the Delta variant [11] and attenuated replication in lower respiratory tissues [12].”
BackgroundYe, Z., Fan, Y., Tang, K., Ong, C. P., Luo, C., Chung, H.-L., Leong, T.-L., Liang, R., Lui, W., Zhou, R., et al. (2022) · International Journal of Biological Sciences · doi:10.7150/ijbs.72109 · Cited by 8
“Emerging evidence suggests that the Omicron variant is highly transmissible, highly immuneevasive but less pathogenic [12], resulting in a high rate of generally mild reinfection and breakthrough infection [11-18].”
BackgroundSelf-citationTahsin, A., Ahmed, R., Bhattacharjee, P., Adiba, M., Saba, A. A., Yasmin, T., Chakraborty, S., Hasan, A. K. M. M., & Nabi, A. N. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105903 · Cited by 9
“An earlier report has suggested the Delta variant outcompetes the Omicron BA.1 variant in infecting TMPRSS2 overexpressing VeroE6 cells in culture [78].”
Zheng, Y., & Wang, Y. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph19116404 · Cited by 8
de Souza, A. S., Amorim, V. M. D. F., de Souza, R. F., & Guzzo, C. R. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2142296 · Cited by 9
“SARS-CoV-2 BA.1 is mainly dependent on the endocytic pathway but not TMPRSS2 pathway for viral replication (Zhao et al., 2022).”
BackgroundAlenquer, M., Silva, T. M., Akpogheneta, O., Ferreira, F., Vale-Costa, S., Medina-Lopes, M., Batista, F., Garcia, A. M., Barreto, V. M., Paulino, C., et al. (2021) · medRxiv · doi:10.1371/journal.pone.0268388 · Cited by 8
Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant
Jule, Z., Roemer, C., Hossen, T., Sviridchik, V., Reedoy, K., Ganga, Y., Silangwe, S., Jackson, L., Norman, A., Karim, F., et al. (2026) · Virus Evolution · doi:10.1093/ve/veag011 · Cited by 10
“BA.3.2 and LP.8.1 showed similar replication, which was higher than that of D614G, as expected in cells that are predominantly infected through the endocytic pathway (Meng et al. 2022, Willett et al. 2022, Zhao et al. 2022).”
InfluentialImmune evasion, infectivity, and membrane fusion of the SARS-CoV-2 JN.1 variant
Tang, H., Zhuo, Y., Chen, J., Zhang, R., Zheng, M., Huang, X., Chen, Y., Huang, M., Zeng, Z., Huang, X., et al. (2025) · Virology Journal · doi:10.1186/s12985-025-02737-3 · Cited by 7
“Previous studies have shown that SARS-CoV-2 spike protein-mediated fusogenicity is closely related to viral infectivity [4, 37, 38].”
Pathak, R., Eliscovich, C., Mena, I., Cupic, A., Rutkowska, M., Chandran, K., Jangra, R., García-Sastre, A., Singer, R., & Kalpana, G. (2024) · Viruses · doi:10.3390/v16020262 · Cited by 7
“It has been reported that Omicron variants exhibit slower replication kinetics at early time points (12 and 24 h p.i.) [33–35].”
BackgroundXu, J., Song, J., Xie, Z., Yang, J. W., Wu, D., Liu, F., Zhao, Y., Zang, H., & Zhao, Y. (2023) · Medicine · doi:10.1097/md.0000000000036714 · Cited by 30
“[29] TMPRSS2 mediated the activation of spike protein to induce ACE2-mediated endocytosis, and then initiated fusion pore formation.”
BackgroundHaars, J., Palanisamy, N., Wallin, F., Mölling, P., Lindh, J., Sundqvist, M., Ellström, P., Kaden, R., & Lennerstrand, J. (2023) · Microorganisms · doi:10.3390/microorganisms11102417 · Cited by 7
“Further, the Delta and Omicron variants differ in entry pathways [36].”
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Kuzmina, A., Korovin, D., Cohen-Lass, I., Atari, N., Ottolenghi, A., Hu, P., Mandelboim, M., Rosental, B., Rosenberg, E., Diaz‐Griffero, F., et al. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e16750 · Cited by 8
Metadata
- Authors
- Zhao, H., Lu, L., Peng, Z., Chen, L.-L., Meng, X., Zhang, C., Ip, J. D., Chan, W.-M., Chu, A. W.-H., Chan, K.-H., Jin, D.-Y., Chen, H., Yuen, K.-Y., & To, K. K.-W.
- Affiliations
- University of Hong Kong (HK)
- Queen Mary Hospital (CN)
- Corresponding author
- Zhao, Hanjun
- To, Kelvin Kai-Wang
- ORCID
- Venue
- Emerging Microbes & Infections
- Publisher
- Informa UK Limited
- Published
- 2022-01-19
- Volume
- 11
- Issue
- 1
- Pages
- 277-283
- ISSN
- 2222-1751 (ISSN-L)
- PMC
- PMC8774049
- OpenAlex
- W4200625712
- Cited by
- 413
- References
- 25
- Citations by year
- 2026: 12 · 2025: 29 · 2024: 68 · 2023: 104 · 2022: 197
- FWCI
- 29.38
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Emerging Microbes & Infections (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Theme-Based Research Scheme (T11-709/21-N)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Keywords
- Omicron variant, Delta variant, viral entry pathways, TMPRSS2, endocytic pathway, viral replication, cell-cell fusion, camostat, bafilomycin A1, chloroquine, competition assay
- MeSH terms
- Whole Genome Sequencing, COVID-19, SARS-CoV-2, Animals, Carcinoma, Non-Small-Cell Lung, Chlorocebus aethiops, Chloroquine, Endocytosis, Esters, Guanidines, Humans, Lung Neoplasms, Recombinant Proteins, Serine Endopeptidases, Vero Cells, Virus Cultivation, Virus Replication, Macrolides, Cell Line, Tumor, Virus Internalization, Immune Evasion
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