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Viruses
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Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition)
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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 2025 | Viewed by 1324

Special Issue Editors

Prof. Dr. Wentao Li

grade E-Mail Website
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
Prof. Dr. Fei Yu

E-Mail Website
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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Related Special Issue

Published Papers (4 papers)

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Research

27 pages, 4886 KiB  
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
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 KiB  
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
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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 KiB  
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
Viewed by 549
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 KiB  
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 388
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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