Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition)

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Coronaviruses".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 15759

Special Issue Editors


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Guest Editor
1. National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
2. The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
Interests: virology; ASFV; viral entry; emerging viruses; virus discovery; infectious diseases; coronavirus
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
College of Life Sciences, Hebei Agricultural University, Baoding, China
Interests: influenza; COVID-19; HIV; antivirals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Based on the success of the first volume (https://www.mdpi.com/journal/viruses/special_issues/coronavirues_pathogenesis_immunity_antivirals), we are pleased to reopen the second volume to continue collecting high-quality Special Issue articles.

The Coronaviridae family includes a large number of viruses affecting humans, farm animals, pets, wildlife, and birds. Since coronaviruses have a broad host range and tropism, there is a continuous emergence of new coronaviruses, new serotypes, and variants of the currently known coronaviruses. Some of them might cross the species barrier and infect humans, such as the ongoing SARS-CoV-2 epidemic. Thus, it is important to study the pathogenesis and immunity of coronaviruses to develop antiviral drugs and vaccines. In this Special Issue of Viruses, we invite the submission of original research papers and review articles spanning all aspects of coronaviruses including molecular mechanisms mediating virus virulence, molecular basis of virus replication, virus pathogenesis, virus diagnosis, animal models, host immune response involved in protection against infection, development of vaccines and antiviral drugs and coronaviruses in wildlife.

Prof. Dr. Wentao Li
Prof. Dr. Fei Yu
Guest Editors

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Keywords

  • coronavirus
  • pathogenesis
  • molecular
  • vaccines
  • evolution
  • immunity
  • antivirals

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Related Special Issue

Published Papers (10 papers)

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Research

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18 pages, 5071 KB  
Article
The Introduction of a HuR-Binding Site in the 3′ UTR and the CD47 Cytoplasmic Tail Enhances SARS-CoV-2 S-Protein Expression in Cells
by Ivan M. Pereverzev, Irina A. Bakhno, Kristina I. Yakovleva, Ilya S. Dovydenko and Evgeniya E. Burkova
Viruses 2026, 18(1), 137; https://doi.org/10.3390/v18010137 - 21 Jan 2026
Viewed by 182
Abstract
In this study, we constructed plasmids to increase the overall expression level of the SARS-CoV-2 S-protein and its presentation on the cell surface. To this end, we designed a series of plasmid constructs encoding the SARS-CoV-2 S-protein with modifications to its cytoplasmic domain [...] Read more.
In this study, we constructed plasmids to increase the overall expression level of the SARS-CoV-2 S-protein and its presentation on the cell surface. To this end, we designed a series of plasmid constructs encoding the SARS-CoV-2 S-protein with modifications to its cytoplasmic domain and containing various 5′ and 3′ untranslated regions. Our results confirmed the critical role of the S-protein cytoplasmic domain in limiting its localization to the cell surface. We confirmed that deletion of the 19 C-terminal amino acids, which contain an endoplasmic reticulum retrieval signal, significantly increased S-protein presentation on the cell surface. Furthermore, introducing the HuR-binding site from the CD47 3′ untranslated region and replacing the 19 C-terminal amino acids of the S-protein with the CD47 cytoplasmic tail significantly enhanced total S-protein expression compared to the wild-type S-protein and constructs with the 19-amino-acid deletion. Unfortunately, for the plasmid constructs bearing CD47 elements, their higher surface expression compared to the wild-type S-protein correlated with a high total protein expression level. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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15 pages, 1588 KB  
Article
Cytokine and Antibody Isotype Responses in Vaccinated Healthcare Workers with SARS-CoV-2 Breakthrough Infections
by Miguel Ángel Fernández-Rojas, Tanya Plett-Torres, Guillermina Ávila, Mirza Romero-Valdovinos, Ana María Salazar, Monserrat Sordo, Mariana Chávez-Vargas, Cesar Josué Coeto Ángeles, Mayra Cruz-Rivera, Carlos Santiago-Olivares, Juan Pablo Ramírez Hinojosa, Pablo Maravilla, Patricia Ostrosky-Wegman, Fela Mendlovic and Ana Flisser
Viruses 2025, 17(11), 1517; https://doi.org/10.3390/v17111517 - 19 Nov 2025
Viewed by 1161
Abstract
Background: Healthcare workers (HCWs) are at high risk of breakthrough SARS-CoV-2 infections despite complete vaccination schedules. There are gaps in our understanding of the specific antibody isotypes and cytokine profiles produced during an infection following vaccination. In this study, we evaluated SARS-CoV-2 [...] Read more.
Background: Healthcare workers (HCWs) are at high risk of breakthrough SARS-CoV-2 infections despite complete vaccination schedules. There are gaps in our understanding of the specific antibody isotypes and cytokine profiles produced during an infection following vaccination. In this study, we evaluated SARS-CoV-2specific antibody isotypes and their association with cytokine production in HCWs with breakthrough infections. Methods: Serum samples from 114 HCWs were analyzed for antibody isotypes against the nucleoprotein (NCP) and the receptor binding domain (RBD) of the spike protein, as well as for a panel of 13 cytokines. Results: Vaccinated SARS-CoV-2+ HCWs showed a higher prevalence of anti-SARS-CoV-2 antibodies against NCP (IgM = 93.8%, IgG = 93.8%, IgA = 28.1%) and RBD (IgM = 46.9%, IgG = 100%, IgA = 90.6%). A specific IgM response to NCP was more frequent in vaccinated SARS-CoV-2+ individuals, whereas IgA responses were predominantly specific for RBD. Both pro- and anti-inflammatory cytokines were elevated in vaccinated HCWs with breakthrough infections compared with unvaccinated and uninfected individuals. Interestingly, infected IgG+ HCWs with IgM specific for both NCP and RBD exhibited significantly higher IL-8, IL-6, TNF-α, IFN-γ, IL-2, IL-10, and TGF-β concentrations. Conclusion. Our data show that breakthrough infections in vaccinated HCWs induce a robust pro-and anti-inflammatory cytokine profile, which is associated with a broader IgM response directed against both NCP and RBD. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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19 pages, 4709 KB  
Article
The Tetraspanin CD9 Facilitates SARS-CoV-2 Infection and Brings Together Different Host Proteins Involved in SARS-CoV-2 Attachment and Entry into Host Cells
by Vanessa Rivero, María Laura Saiz, Daniel Torralba, Carlos López-Larrea, Beatriz Suarez-Alvarez and Marta L. DeDiego
Viruses 2025, 17(8), 1141; https://doi.org/10.3390/v17081141 - 20 Aug 2025
Cited by 1 | Viewed by 4189
Abstract
CD9 protein belongs to a family of proteins called tetraspanins, so named for their four-transmembrane-spanning architectures. These proteins are located in domains in the plasmatic membrane, called tetraspanin-enriched microdomains (TEMs). Several proteases and cellular receptors for virus entry cluster into TEMs, suggesting that [...] Read more.
CD9 protein belongs to a family of proteins called tetraspanins, so named for their four-transmembrane-spanning architectures. These proteins are located in domains in the plasmatic membrane, called tetraspanin-enriched microdomains (TEMs). Several proteases and cellular receptors for virus entry cluster into TEMs, suggesting that TEMs are preferred virus entry portals. Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates virus attachment and entry into cells by binding to human angiotensin-converting enzyme 2 (ACE-2). In addition, the secretory, type-I membrane-bound SARS-CoV-2 S protein is synthesized as a precursor (proS) that undergoes posttranslational cleavages by host cell proteases, such as furin and TMPRSS2. Moreover, it has been shown that neuropilin-1 (NRP1), which is known to bind furin-cleaved substrates, potentiates SARS-CoV-2 infectivity. Our results indicate that CD9 facilitates SARS-CoV-2 infection. In addition, we show how knocking out CD9 leads to a decrease in the expression of NRP1, a protein that improves SARS-CoV-2 infection. Furthermore, we show that CD9 colocalizes with ACE-2, NRP1, furin, and TMPRSS2 at the plasma membrane; that the absence of CD9 decreases the expression of these proteins on the plasma membrane CD9-enriched microdomains, and that CD9 interacts with ACE2. In conclusion, our data suggest that CD9 facilitates SARS-CoV-2 infection and that CD9 brings together different host proteins involved in SARS-CoV-2 attachment and entry into host cells, such as ACE2, NRP1, furin, and TMPRSS2. Importantly, the fact that a blocking antibody targeting CD9 can effectively reduce SARS-CoV-2 titers highlights not only the mechanistic role of CD9 in viral entry but also offers translational potential, suggesting that tetraspanin-targeting antibodies could be developed as therapeutic agents against SARS-CoV-2 and possibly other coronaviruses, with meaningful implications for clinical intervention. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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17 pages, 4093 KB  
Article
4-Hydroxychalcone Inhibits Human Coronavirus HCoV-OC43 by Targeting EGFR/AKT/ERK1/2 Signaling Pathway
by Yuanyuan Huang, Jieyu Li, Qiting Luo, Yuexiang Dai, Xinyi Luo, Jiapeng Xu, Wei Ye, Xinrui Zhou, Jiayi Diao, Zhe Ren, Ge Liu, Zhendan He, Zhiping Wang, Yifei Wang and Qinchang Zhu
Viruses 2025, 17(8), 1028; https://doi.org/10.3390/v17081028 - 23 Jul 2025
Viewed by 1104
Abstract
Human coronaviruses are a group of viruses that continue to threaten human health. In this study, we investigated the antiviral activity of 4-hydroxychalcone (4HCH), a chalcone derivative, against human coronavirus HCoV-OC43. We found that 4HCH significantly inhibited the cytopathic effect, reduced viral protein [...] Read more.
Human coronaviruses are a group of viruses that continue to threaten human health. In this study, we investigated the antiviral activity of 4-hydroxychalcone (4HCH), a chalcone derivative, against human coronavirus HCoV-OC43. We found that 4HCH significantly inhibited the cytopathic effect, reduced viral protein and RNA levels in infected cells, and increased the survival rate of HCoV-OC43-infected suckling mice. Mechanistically, 4HCH targets the early stages of viral infection by binding to the epidermal growth factor receptor (EGFR) and inhibiting the EGFR/AKT/ERK1/2 signaling pathway, thereby suppressing viral replication. Additionally, 4HCH significantly reduced the production of pro-inflammatory cytokines and chemokines in both HCoV-OC43-infected RD cells and a suckling mouse model. Our findings demonstrate that 4HCH exhibits potent antiviral activity both in vitro and in vivo, suggesting its potential as a therapeutic agent against human coronaviruses. This study highlights EGFR as a promising host target for antiviral drug development and positions 4HCH as a candidate for further investigation in the treatment of coronavirus infections. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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27 pages, 4886 KB  
Article
A Novel Toolkit of SARS-CoV-2 Sub-Genomic Replicons for Efficient Antiviral Screening
by Maximilian Erdmann, Peter A. C. Wing, Isobel Webb, Maia Kavanagh Williamson, Tuksin Jearanaiwitayakul, Edward Sullivan, James Bazire, Iart Luca Shytaj, Jane A. McKeating, David A. Matthews and Andrew D. Davidson
Viruses 2025, 17(5), 597; https://doi.org/10.3390/v17050597 - 23 Apr 2025
Viewed by 1736
Abstract
SARS-CoV-2 is classified as a containment level 3 (CL3) pathogen, limiting research access and antiviral testing. To address this, we developed a non-infectious viral surrogate system using reverse genetics to generate sub-genomic replicons. These replicons contained the nsp1 mutations K164A and H165A and [...] Read more.
SARS-CoV-2 is classified as a containment level 3 (CL3) pathogen, limiting research access and antiviral testing. To address this, we developed a non-infectious viral surrogate system using reverse genetics to generate sub-genomic replicons. These replicons contained the nsp1 mutations K164A and H165A and had the spike, membrane, ORF6, and ORF7a coding sequences replaced with various reporter and selectable marker genes. Replicons based on the ancestral Wuhan Hu-1 strain and the Delta variant of concern were replication-competent in multiple cell lines, as assessed by Renilla luciferase activity, fluorescence, immunofluorescence staining, and single-molecule fluorescent in situ hybridization. Antiviral assays using transient replicon expression showed that remdesivir effectively inhibited both replicon and viral replication. Ritonavir and cobicistat inhibited Delta variant replicons similarly to wild-type virus but did not inhibit Wuhan Hu-1 replicon replication. To further investigate the impact of nsp1 mutations, we generated a recombinant SARS-CoV-2 virus carrying the K164A and H165A mutations. The virus exhibited attenuated replication across a range of mammalian cell lines, was restricted by the type I interferon response, and showed reduced cytopathic effects. These findings highlight the utility of sub-genomic replicons as reliable CL2-compatible surrogates for studying SARS-CoV-2 replication and drug activity mechanisms. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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17 pages, 3690 KB  
Article
An In-Depth Characterization of SARS-CoV-2 Omicron Lineages and Clinical Presentation in Adult Population Distinguished by Immune Status
by Greta Marchegiani, Luca Carioti, Luigi Coppola, Marco Iannetta, Leonardo Alborghetti, Vincenzo Malagnino, Livia Benedetti, Maria Mercedes Santoro, Massimo Andreoni, Loredana Sarmati, Claudia Alteri, Francesca Ceccherini-Silberstein and Maria Concetta Bellocchi
Viruses 2025, 17(4), 540; https://doi.org/10.3390/v17040540 - 8 Apr 2025
Viewed by 1098
Abstract
This retrospective study analyzed SARS-CoV-2 Omicron variability since its emergence, focusing on immunocompromised (IPs) and non-immunocompromised adult people (NIPs). Phylogenetic analysis identified at least five major Omicron lineage groups circulating in Central Italy, from December 2021 to December 2023: (a) BA.1 (34.0%), (b) [...] Read more.
This retrospective study analyzed SARS-CoV-2 Omicron variability since its emergence, focusing on immunocompromised (IPs) and non-immunocompromised adult people (NIPs). Phylogenetic analysis identified at least five major Omicron lineage groups circulating in Central Italy, from December 2021 to December 2023: (a) BA.1 (34.0%), (b) BA.2 + BA.4 (25.8%), (c) BA.5 + BF (10.8%), (d) BQ + BE + EF (9.2%), and (e) Recombinants (20.2%). The BA.2 + BA.4 lineages were more common in IPs compared to NIPs (30.9% vs. 17.8%, respectively; p = 0.011); conversely, Recombinants were less prevalent in IPs than in NIPs (16.0% vs. 27.1%, respectively; p = 0.018). High-abundant single nucleotide polymorphisms (SNPs; prevalence ≥ 40%) and non-synonymous SNPs (prevalence ≥ 20%) increased during the emergence of new variants, rising from BA.1 to Recombinants (54 to 92, and 43 to 70, respectively, both p < 0.001). Evaluating the genetic variability, 109 SNPs were identified as being involved in significant positive or negative associations in pairs (phi > 0.70, p < 0.001), with 19 SNPs associated in 3 distinct clusters (bootstrap > 0.96). Multivariate regression analysis showed that hospitalization was positively associated with one specific cluster, including S686R and A694S in Spike and L221F in Nucleocapsid (AOR: 2.74 [95% CI: 1.13–6.64, p = 0.025]), and with increased age (AOR:1.03 [95% CI: 1.00–1.06], p = 0.028). Conversely, negative associations with hospitalization were observed for female gender and previous vaccination status (AORs: 0.34 [95% CI: 0.14–0.83], p = 0.017 and 0.19 (95% CI: 0.06–0.63, p = 0.006, respectively). Interestingly, the S686R SNP located in a furin cleavage site suggests its potential pathogenetic role. The results show how Omicron genetic diversification significantly influences disease severity and hospitalization, together with age, sex, and vaccination status as key factors. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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26 pages, 8825 KB  
Article
Biochemical Screening of Phytochemicals and Identification of Scopoletin as a Potential Inhibitor of SARS-CoV-2 Mpro, Revealing Its Biophysical Impact on Structural Stability
by Sarika Bano, Jyotishna Singh, Zainy Zehra, Md Nayab Sulaimani, Taj Mohammad, Seemasundari Yumlembam, Md Imtaiyaz Hassan, Asimul Islam and Sanjay Kumar Dey
Viruses 2025, 17(3), 402; https://doi.org/10.3390/v17030402 - 12 Mar 2025
Cited by 3 | Viewed by 1830
Abstract
The main protease (Mpro or 3CLpro or nsp5) of SARS-CoV-2 is crucial to the life cycle and pathogenesis of SARS-CoV-2, making it an attractive drug target to develop antivirals. This study employed the virtual screening of a few phytochemicals, and the [...] Read more.
The main protease (Mpro or 3CLpro or nsp5) of SARS-CoV-2 is crucial to the life cycle and pathogenesis of SARS-CoV-2, making it an attractive drug target to develop antivirals. This study employed the virtual screening of a few phytochemicals, and the resultant best compound, Scopoletin, was further investigated by a FRET-based enzymatic assay, revealing an experimental IC50 of 15.75 µM. The impact of Scopoletin on Mpro was further investigated by biophysical and MD simulation studies. Fluorescence spectroscopy identified a strong binding constant of 3.17 × 104 M⁻1 for Scopoletin binding to Mpro, as demonstrated by its effective fluorescence quenching of Mpro. Additionally, CD spectroscopy showed a significant reduction in the helical content of Mpro upon interaction with Scopoletin. The findings of thermodynamic measurements using isothermal titration calorimetry (ITC) supported the spectroscopic data, indicating a tight binding of Scopoletin to Mpro with a KA of 2.36 × 103 M−1. Similarly, interaction studies have also revealed that Scopoletin forms hydrogen bonds with the amino acids nearest to the active site, and this has been further supported by molecular dynamics simulation studies. These findings indicate that Scopoletin may be developed as a potential antiviral treatment for SARS-CoV-2 by targeting Mpro. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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14 pages, 2996 KB  
Article
Structures of HCoV-OC43 HR1 Domain in Complex with Cognate HR2 or Analogue EK1 Peptide
by Xiuxiu He, Huanzhen Liu, Guang Yang and Lei Yan
Viruses 2025, 17(3), 343; https://doi.org/10.3390/v17030343 - 28 Feb 2025
Viewed by 1133
Abstract
Human coronavirus OC43 (HCoV-OC43) is usually associated with common colds, but also related to severe disease in the frail. Its envelope glycoproteins spike (S) is responsible for host-cell attachment and membrane fusion. To understand the molecular basis of membrane fusion of HCoV-OC43, we [...] Read more.
Human coronavirus OC43 (HCoV-OC43) is usually associated with common colds, but also related to severe disease in the frail. Its envelope glycoproteins spike (S) is responsible for host-cell attachment and membrane fusion. To understand the molecular basis of membrane fusion of HCoV-OC43, we solved the 3.34 Å crystal structure of the post-fusion state formed by two heptad repeat domains (HR1P and HR2P) of OC43-S. This fusion core comprises a parallel trimeric coiled coil of three HR1 helices with 61 Å at length, around which three HR2 helices are entwined in an antiparallel manner, as anticipated. Moreover, a pan-CoV fusion inhibitor EK1 derived from OC43-HR2P was also crystalized with OC43-HR1P in the resolution of 2.71 Å. Parallel comparisons rationalize the design of EK1, maintaining various hydrophobic and charged or hydrophilic interactions formed in the initial fusion core to stabilize the overall conformation. Together, our results not only reveal the critical intrahelical and interhelical interactions underlying the mechanism of action of OC43-S fusion, but also help our understanding on the mechanism of HCoV-OC43 inhibition by analogue HR2 mimic peptide. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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Review

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26 pages, 3262 KB  
Review
A Review of Receptor Recognition Mechanisms in Coronaviruses
by Jie Liu, Wenjing Luo, Jianming Li, Bingyi Cai, Zhiwei Lei, Shiyun Lin, Zhuohong Chen, Zhaoyang Yue, Xulin Chen, Yongkui Li, Zhen Luo, Qiwei Zhang and Xin Chen
Viruses 2025, 17(12), 1628; https://doi.org/10.3390/v17121628 - 16 Dec 2025
Viewed by 607
Abstract
Cellular receptor recognition exerts fundamental roles during coronavirus infection. Clarifying the regulatory mechanism of virus receptor helps to better understand viral infection, transmission and pathogenesis; predict potential host and how viral escape from immune system; prevent coronavirus infection or develop treatment therapy. Herein, [...] Read more.
Cellular receptor recognition exerts fundamental roles during coronavirus infection. Clarifying the regulatory mechanism of virus receptor helps to better understand viral infection, transmission and pathogenesis; predict potential host and how viral escape from immune system; prevent coronavirus infection or develop treatment therapy. Herein, we summarize current understanding of host receptor recognition mechanisms in the different genera of coronavirus family. And we also review diverse methodologies of identification and clarification of virus receptors. The integration of structural biology, multi-omics, computational predictions, synthetic biology and artificially engineered viral receptors, provide a powerful framework for elucidating coronavirus–receptor interactions. This also supports the development of broad-spectrum antiviral agents, smart biosensors, and intervention strategies against emerging coronaviruses. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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27 pages, 951 KB  
Review
Mechanisms of Cell–Cell Fusion in SARS-CoV-2: An Evolving Strategy for Transmission and Immune Evasion
by Kate Chander Chiang, Cheng En Nicole Chiu, Mazharul Altaf, Mark Tsz Kin Cheng and Ravindra K. Gupta
Viruses 2025, 17(11), 1405; https://doi.org/10.3390/v17111405 - 22 Oct 2025
Cited by 1 | Viewed by 1760
Abstract
Early studies on the evolution of SARS-CoV-2 revealed mutations that favored host transmission of the virus and more efficient viral entry. However, cell-free virus spread is vulnerable to host-neutralizing antibodies. As population immunity developed, mutations that confer escape from neutralization were selected. Notably, [...] Read more.
Early studies on the evolution of SARS-CoV-2 revealed mutations that favored host transmission of the virus and more efficient viral entry. However, cell-free virus spread is vulnerable to host-neutralizing antibodies. As population immunity developed, mutations that confer escape from neutralization were selected. Notably, cell syncytia formation wherein an infected cell fuses with a noninfected cell is a more efficient route of transmission that bypasses humoral immunity. Cell syncytia formation has been implicated in the pathogenicity of SARS-CoV-2 infection whilst compromising host transmission due to impaired whole virion release. Therefore, understanding the mechanisms of virus-mediated cell–cell fusion will aid in identifying and targeting more pathogenic strains of SARS-CoV-2. Whilst the general kinetics of cell–cell fusion have been known for decades, the specific mechanisms by which SARS-CoV-2 induces fusion are beginning to be elucidated. This is partially due to emergence of more reliable, high throughput methods of quantifying and comparing fusion efficiency in experimental models. Moreover, the ongoing inflammatory response and emerging health burden of long COVID may point to cell–cell fusion in the pathogenesis. In this review, we synthesize current understanding of SARS-CoV-2-mediated cell–cell fusion and its consequences on immune escape, viral persistence, and the innate immune response. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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