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Pathogens
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Emerging/Re-Emerging Viruses and Antiviral Drug Design
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Emerging/Re-Emerging Viruses and Antiviral Drug Design

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 15517

Special Issue Editors

Dr. Dongxiao Liu

E-Mail Website
Guest Editor
U.S. Food and Drug Administration, Hyattsville, MD, USA
Interests: antiviral design; host-targeted antiviral; emerging pathogens
Dr. Zhiqing Zhang

E-Mail Website
Guest Editor
Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
Interests: antiviral design; host-targeted antiviral; emerging pathogens
Dr. Ishita Roy Chowdhury

E-Mail Website
Guest Editor
VA-MD Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
Interests: low pathogenicity avian influenza
Dr. Pawel Zmora

E-Mail Website
Guest Editor
Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland
Interests: influenza A virus; emerging viruses; virus–host cell interactions; virus entry; antivirals
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The emergence and re-emergence of various viral diseases, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Zika virus (ZIKV), and Dengue virus, as well as the prevalence of contagious viral diseases such as Enterovirus and human immunodeficiency virus (HIV), pose significant threats to human health. This has led to an increased demand for innovative antiviral strategies.

The development of antiviral drugs primarily follows two strategies: virus-targeted antivirals (VTAs) and host-targeted antivirals (HTAs). On the one hand, VTAs target viral components, offering high specificity and minimal harm to the host. However, they may not immediately apply to emerging viruses and are prone to drug resistance issues due to long-term usage. On the other, HTAs target host factors essential for viral replication, providing advantages in overcoming drug resistance and effectively combating a wide range of viruses, including newly emerging ones. In recent years, extensive research has been conducted on discovering and developing HTAs. There are also several other potential HTAs in the pipelines in various stages of development for different viral infections.

This Special Issue of Pathogens highlights recent advances in fundamental and applied research related to antiviral design and development, either VTAs or HTAs, targeting a broad spectrum of viral infectious diseases, including but not limited to infections due to coronavirus, flaviviruses, and enteroviruses. These efforts will provide the basis for enhancing our capabilities to fight potential upcoming infectious diseases.

Dr. Dongxiao Liu
Dr. Zhiqing Zhang
Dr. Ishita Roy Chowdhury
Dr. Pawel Zmora
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 250 words) can be sent to the Editorial Office for assessment.

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. Pathogens 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 2200 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

  • emerging viruses
  • influenza viruses
  • coronavirus
  • flaviviruses
  • enteroviruses
  • antiviral design

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Published Papers (4 papers)

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Research

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24 pages, 11367 KB  
Article
Potential Activity of 6-Pentyl-α-pyrone as an Antiviral for Bovine Coronavirus
by Luca Del Sorbo, Rosa Giugliano, Clementina Acconcia, Maria Michela Salvatore, Alessia Staropoli, Violetta Iris Vasinioti, Maria Stella Lucente, Paolo Capozza, Francesco Vinale, Annamaria Pratelli, Luigi Russo, Rosa Iacovino and Filomena Fiorito
Pathogens 2026, 15(3), 332; https://doi.org/10.3390/pathogens15030332 - 20 Mar 2026
Viewed by 510
Abstract
During infection in vitro with the strain 438/06 of bovine coronavirus (BCoV), a β-coronavirus similar to severe acute respiratory syndrome (SARS) CoV-2, treatment with 6-pentyl-α-pyrone (6PP), a fungal metabolite obtained from Trichoderma atroviride, was recently shown to influence viral load by reducing [...] Read more.
During infection in vitro with the strain 438/06 of bovine coronavirus (BCoV), a β-coronavirus similar to severe acute respiratory syndrome (SARS) CoV-2, treatment with 6-pentyl-α-pyrone (6PP), a fungal metabolite obtained from Trichoderma atroviride, was recently shown to influence viral load by reducing viral entry. Herein, the ability of 6PP to counteract the BCoV infection was further investigated both in vitro and in silico. Following the BCoV (strain 282/23) infection in bovine (MDBK) cells, the 6PP in co-treatment increased cell viability, reduced morphological signs of cell death, and significantly inhibited viral yield, by lessening the expression of the viral spike (S) protein, as well as the gene transcription of the viral nucleocapsid (NP) protein. In addition, a noticeable down-regulation in the expression of aryl hydrocarbon receptor (AhR) signaling, a strategic modulator of CoVs infection, was found. Molecular docking studies were performed to evaluate the potential interaction between 6PP and AhR involved in the BCoV infection. The docking 3D structural model showed that 6PP fits into a binding pocket positioned between the PASB and TAD domains of bovine AhR (bAhR), where the ligand is stabilized through hydrophobic interactions. In addition, the obtained computational data strongly suggest that the bAhR binding mechanism of 6PP is principally mediated by a well-conserved hydrophobic cavity playing a key role in the modulation of the receptor functions. Overall, our findings showed an antiviral action of 6PP versus BCoV infection in vitro and in silico. Full article
(This article belongs to the Special Issue Emerging/Re-Emerging Viruses and Antiviral Drug Design)
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14 pages, 1083 KB  
Article
Recent HIV Infections in Italy: Data from the HIV National Surveillance System, 2012–2023
by Barbara Suligoi, Vincenza Regine, Lucia Pugliese and Claudio Galli
Pathogens 2025, 14(9), 835; https://doi.org/10.3390/pathogens14090835 - 22 Aug 2025
Cited by 1 | Viewed by 3982
Abstract
The identification of recent HIV infections among newly diagnosed HIV cases is relevant to both implementing targeted prevention measures and estimating HIV incidence. We analyzed data on new HIV diagnoses in Italy from 2012 to 2023. We selected cases that were tested by [...] Read more.
The identification of recent HIV infections among newly diagnosed HIV cases is relevant to both implementing targeted prevention measures and estimating HIV incidence. We analyzed data on new HIV diagnoses in Italy from 2012 to 2023. We selected cases that were tested by at least one of three criteria (test for HIV recency, data on HIV seroconversion, clinical signs of acute HIV infection) to assess the rate of recent (<1 year) HIV infections. We analyzed these cases by gender, age group, nationality, and mode of transmission, and revaluated cases that were initially scored as a late diagnosis but then classified as a recent infection. Out of 36,289 new HIV diagnoses, 17,558 (48.8%) were tested for recent infection by at least one criterion and 3772 (21.5%) were classified as recent. At multivariate analysis, the probability of being recently infected was significantly higher among males, people aged 15–44 years, Italians, individuals diagnosed in Northern and Central Italy, heterosexual males, MSM, and people with a CD4 count ≥ 350 cells/uL at diagnosis. Of 8658 cases initially classified as late diagnoses, 979 (11.3%) were reclassified as recent by the aforementioned criteria. Monitoring recent infections among new HIV diagnoses is beneficial to individuals—because it motivates recently infected people to comply with antiretroviral treatment (which is more effective if started early) and to collaborate to partner notification, and to public health, as it provides evidence of epidemiological changes and stresses the need for targeted prevention in well-defined populations at risk. Full article
(This article belongs to the Special Issue Emerging/Re-Emerging Viruses and Antiviral Drug Design)
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Review

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42 pages, 3072 KB  
Review
Mumps Virus: Replication, Immune Response, and the Changing Landscape of Vaccine Effectiveness
by Jacquline Risalvato
Pathogens 2026, 15(1), 72; https://doi.org/10.3390/pathogens15010072 - 9 Jan 2026
Viewed by 1707
Abstract
Mumps virus (MuV) is a single-stranded, negative-sense RNA virus of the Family Paramyxoviridae. MuV is a highly contagious human pathogen that causes primarily mild symptoms, including hallmark swelling of the parotid glands. Severe cases can occur, leading to neurological complications, including deafness, [...] Read more.
Mumps virus (MuV) is a single-stranded, negative-sense RNA virus of the Family Paramyxoviridae. MuV is a highly contagious human pathogen that causes primarily mild symptoms, including hallmark swelling of the parotid glands. Severe cases can occur, leading to neurological complications, including deafness, meningitis, and encephalitis. The mumps vaccine, now included in combination with measles and rubella vaccines (MMR), was first made available in the 1960s. After its introduction, mumps incidence dropped dramatically to less than 500 cases annually in the US. However, even with long-standing vaccination programs, MuV continues to challenge the landscape of public health due to a resurgence of cases in the past several decades and a still present lack of approved antiviral drugs and treatments available for the disease. This review will explore the biology of MuV, focusing on how MuV replicates and interacts with the host immune system. Recent studies have also shed light on the role of protein phosphorylation in regulating viral RNA synthesis—particularly the dynamic interactions between the nucleoprotein (NP) and phosphoprotein (P)—offering new insights into how the virus controls its replication machinery both mechanistically and through utilizing host cell advantages. We also examine how the immune system responds to mumps infection and vaccination, and how those responses may vary across viral genotypes. Although the Jeryl Lynn vaccine strain has played a key role in controlling mumps for decades, outbreaks among vaccinated individuals have raised questions about the present vaccine’s efficacy against circulating and emerging genotypes and if novel strategies will be required to prevent future outbreaks. We review current epidemiological data, highlighting shifts in MuV transmission and genotype distribution, and discuss the need for updated or genotype-matched vaccines. By connecting molecular virology with real-world trends in disease spread and vaccine performance, this review aims to support ongoing efforts to strengthen mumps control strategies and inform the development of next-generation vaccines. Full article
(This article belongs to the Special Issue Emerging/Re-Emerging Viruses and Antiviral Drug Design)
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15 pages, 1189 KB  
Review
Epidemiology, Clinical Significance, and Diagnosis of Respiratory Viruses and Their Co-Infections in the Post-COVID Era
by Kaia M. Contes and Benjamin M. Liu
Pathogens 2025, 14(3), 262; https://doi.org/10.3390/pathogens14030262 - 7 Mar 2025
Cited by 63 | Viewed by 8331
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, emerged in late 2019 and rapidly evolved into a pandemic around the world. The coronavirus disease (COVID-19) pandemic has dramatically changed the epidemiology and seasonality of other traditional respiratory viruses, e.g., influenza, [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, emerged in late 2019 and rapidly evolved into a pandemic around the world. The coronavirus disease (COVID-19) pandemic has dramatically changed the epidemiology and seasonality of other traditional respiratory viruses, e.g., influenza, respiratory syncytial virus, enterovirus, etc. These traditional respiratory viruses have transmission mode and clinical symptoms similar to SARS-CoV-2 but may differ in clinical outcomes and management. Co-infection between SARS-CoV-2 and one or more traditional respiratory viruses have been reported in the literature but have shown mixed evidence in clinical outcomes. With SARS-CoV-2 evolving into mild Omicron variants, it is believed that SARS-CoV-2 co-circulates with other respiratory viruses, which in turn affect the epidemiology and clinical course of respiratory viral infections. In response to these changes, multiplex molecular tests for SARS-CoV-2 and one or more traditional respiratory viruses are attracting more attention in the field and have been developed into a variety of testing modalities. In this review, we describe the seasonality (i.e., in the Northern Hemisphere), epidemiology, and clinical significance of traditional respiratory viruses and their co-infection with SARS-CoV-2 in the post-COVID era. Furthermore, we review commonly used multiplex molecular tests and their applications for the detection of respiratory viruses and their co-infections. Altogether, this review not only sheds light on the epidemiology and clinical significance of respiratory viral infections and co-infections in the post-COVID era, and but also provides insights into the laboratory-based diagnoses of respiratory viral infections using multiplex molecular testing. Full article
(This article belongs to the Special Issue Emerging/Re-Emerging Viruses and Antiviral Drug Design)
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