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Human Virome and Emerging Viruses: Characterization, Interactions, and Molecular Insights
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Human Virome and Emerging Viruses: Characterization, Interactions, and Molecular Insights

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 1611

Special Issue Editors

Dr. Luigi Rosa

E-Mail Website
Guest Editor
Laboratory of Virology and Laboratories of Biosafety, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
Interests: arboviruses; emerging pathogens; viral-host interactions; functional virology; human virome
Special Issues, Collections and Topics in MDPI journals
Dr. Pietro Giorgio Spezia

E-Mail Website
Guest Editor
Laboratory of Virology and Laboratories of Biosafety, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy
Interests: human virome; viral metagenomics; molecular virology; genomic surveillance; viral diversity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human virome constitutes a dynamic and integral component of the host ecosystem, continuously interacting with both the immune system and the microbiota. These interactions influence immune regulation, inflammation, and overall physiological homeostasis.

Recent advances in molecular and metagenomic technologies, together with functional virology and systems biology approaches, are providing unprecedented insights into the composition, evolution, and biological activity of viral communities.

This Special Issue is supervised by Dr. Luigi Rosa, Dr. Pietro Giorgio Spezia and assisted by Davide Mariotti. This Special Issue aims to collect high-quality studies that explore the molecular and functional characterization of the human virome and its emerging components. We particularly welcome contributions that elucidate mechanistic virome–host and virome–microbiota interactions, immune-modulatory pathways, and functional assays that validate omics-based discoveries.

By integrating metagenomic profiling, molecular immunology, and experimental virology, this Special Issue seeks to advance a comprehensive understanding of viral dynamics and their impact on human health and disease.

Topics of Interest:

  • Molecular and metagenomic characterization of the human virome;
  • Functional analysis of virome–host and virome–microbiota interactions;
  • Molecular mechanisms of immune modulation and signaling;
  • Application of omics and bioinformatics to functional virology;
  • Experimental models for studying viral persistence and host response;
  • Pseudovirus and cell-based assays for mechanistic investigations;
  • Molecular evaluation and screening of antiviral compounds;
  • Integration of molecular, genomic, and immunological data in virome studies.

Dr. Luigi Rosa
Dr. Pietro Giorgio Spezia
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • human virome
  • molecular virology
  • functional virology
  • metagenomics
  • virus–host interactions
  • immune modulation
  • pseudovirus assays
  • antiviral screening
  • omics integration
  • molecular immunology

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

14 pages, 1833 KB  
Article
Prevalence of Circulating Autoantibodies Against G-Protein-Coupled Receptors as Potential Biomarkers for Long COVID: Preliminary Investigations
by Marta Camici, Marta Franco, Lorenzo Talamanca, Jessica Paulicelli, Liliana Scarnecchia, Manuela Petino, Valentina Mazzotta, Ilaria Mastrorosa, Eleonora Cimini, Eleonora Tartaglia, Stefania Notari, Paolo Zuppi, Roberto Baldelli, Maria Grazia Bocci, Fabrizio Maggi, Enrico Girardi and Andrea Antinori
Int. J. Mol. Sci. 2026, 27(4), 1787; https://doi.org/10.3390/ijms27041787 - 13 Feb 2026
Viewed by 833
Abstract
This prospective, single-center, case-control study investigated circulating autoantibodies (AAbs) targeting G protein-coupled receptors (GPCRs) in Long COVID (LC) patients to identify potential diagnostic biomarkers and therapeutic targets. Fifteen participants were enrolled at the LC clinic in Rome: eleven with severe LC—defined as >4 [...] Read more.
This prospective, single-center, case-control study investigated circulating autoantibodies (AAbs) targeting G protein-coupled receptors (GPCRs) in Long COVID (LC) patients to identify potential diagnostic biomarkers and therapeutic targets. Fifteen participants were enrolled at the LC clinic in Rome: eleven with severe LC—defined as >4 persistent symptoms (fatigue, cognitive impairment, poor exercise tolerance, dyspnea, arthralgia, or dysautonomic manifestations) >3 months post-infection—and four asymptomatic post-COVID (APC) individuals. Fatigue was assessed using the Fatigue Assessment Scale (FAS ≥ 22; severe ≥ 35). Auto-Abs against AT1R, endothelin receptor A, adrenergic (α1, α2, β1, β2), and muscarinic (M1–M5) receptors were quantified, along with blood cortisol and ACTH levels. SARS-CoV-2-specific T-cell responses to Spike and Nucleocapsid proteins were evaluated by ELISpot assay. In our small cohort, LC patients were younger, had fewer comorbidities (p = 0.03), fewer vaccine doses (p = 0.03), and higher FAS scores (33 vs. 12; p = 0.001). Mean GPCR AAbs levels were higher in LC than in APC (8.88 vs. 5.45 Units/mL; p = 0.17), indicating a coherent autoimmune signature in LC that correlates with symptom development. Morning cortisol was lower in LC (12.7 vs. 17 mg/dL; p = 0.01), and T-cell responses tended to be weaker. These findings suggest GPCR AAbs may serve as biomarkers and therapeutic targets for a subset of patients, guiding diagnosis and treatments with IV immunoglobulin or immunoadsorption. Full article
(This article belongs to the Special Issue Human Virome and Emerging Viruses: Characterization, Interactions, and Molecular Insights)
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9 pages, 1389 KB  
Article
Real-Time and Nanoplate-Based Digital PCR Assays for the Detection and Absolute Quantification of Borealpox Virus
by Fabrizio Carletti, Francesca Colavita, Eliana Specchiarello, Valeria Ferraioli, Silvia Meschi, Enrico Girardi and Fabrizio Maggi
Int. J. Mol. Sci. 2026, 27(3), 1302; https://doi.org/10.3390/ijms27031302 - 28 Jan 2026
Viewed by 459
Abstract
Borealpox virus (Alaskapox virus, BRPV), a neglected zoonotic Orthopoxvirus (OPXV), has been reported only in Alaska, usually causing mild infections. A recent fatal case in the Kenai Peninsula has raised concerns about its public health impact. Like other OPXVs, BRPV diagnosis relies on [...] Read more.
Borealpox virus (Alaskapox virus, BRPV), a neglected zoonotic Orthopoxvirus (OPXV), has been reported only in Alaska, usually causing mild infections. A recent fatal case in the Kenai Peninsula has raised concerns about its public health impact. Like other OPXVs, BRPV diagnosis relies on molecular tools, making species-specific assays essential. In this study, we developed and validated two BRPV-specific molecular assays: a TaqMan-based real-time PCR (rtPCR) and a droplet digital PCR (ddPCR) using the QIAcuity platform. Both target the viral CC-chemokines inhibitor (vCCI) gene, showing high sensitivity (limit of detection ~0.3–0.5 copies/μL), excellent specificity (no cross-reactivity with other OPXVs or rash-causing viruses), and strong reproducibility. While rtPCR is ideal for routine diagnostics, ddPCR offers absolute quantification without standard curves, enhancing the detection of low viral loads. Although the lack of clinical BRPV-positive samples limits full validation, both assays show strong potential for improving BRPV detection, helping to distinguish it from other OPXVs and supporting the early identification of emerging orthopoxvirus threats. Full article
(This article belongs to the Special Issue Human Virome and Emerging Viruses: Characterization, Interactions, and Molecular Insights)
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