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Advanced Perspectives on Virus–Host Interactions
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Advanced Perspectives on Virus–Host Interactions

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: 20 November 2025 | Viewed by 3297

Special Issue Editor

Dr. Qibin Geng

E-Mail Website
Guest Editor
Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
Interests: virus; host; structure; biology; cells; biochemistry; protein; gene; vaccines; immunology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses possess remarkable adaptability, enabling them to infect diverse hosts ranging from bacteria to humans. These interactions underlie numerous infectious diseases, including SARS-CoV-2, influenza, AIDS, and various zoonotic illnesses, with profound societal and healthcare impacts. Despite considerable progress in virology, our understanding of the dynamic interplay between viruses and hosts remains incomplete. Elucidating these processes is critical in developing innovative strategies for prevention, diagnosis, and therapeutic intervention.

This Special Issue will provide a comprehensive platform for exploring the molecular, cellular, and systemic aspects of virus–host interactions, focusing on how viruses manipulate host cellular machinery, evade immune responses, and shape host physiology. By highlighting groundbreaking research and reviews, we aim to deepen the understanding of these mechanisms and their implications for viral pathogenesis and host health.

Scope and Key Themes:

Molecular and Cellular Interactions: Studies unveiling the mechanisms behind viral entry, and replication and the manipulation of host pathways.

Immune Evasion and Manipulation: Insights into how viruses evade innate and adaptive immune responses and exploit host immunity.

Host Signaling and Gene Regulation: Exploration of host gene expression modulation and signaling pathways in response to viral infection.

Pathogenesis and Disease Progression: Investigations linking virus–host interactions to clinical outcomes, including acute and chronic infections.

Innovative Therapeutic Strategies: Novel interventions targeting virus–host interactions in disease management.

We invite original research articles, comprehensive reviews, and methodological studies that address the intricate relationships between viruses and their hosts. For this Special Issue, we also welcome interdisciplinary approaches that bridge molecular biology, immunology, and clinical research, as well as studies highlighting implications for antiviral drug and vaccine development.

Dr. Qibin Geng
Guest Editor

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. 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

  • viral manipulation of host metabolics
  • virus–host interactions
  • host–pathogen co-evolution
  • susceptibility and resistance to viral infection
  • novel antiviral strategies

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Published Papers (4 papers)

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Research

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19 pages, 4184 KiB  
Article
Host–Virus Interface in Persistent SARS-CoV-2 Infections: Viral Characteristic Evolution and Gene Expression Profiling Analysis
by Athok Shofiudin Maarif, Yukari Nishikawa, Miyako Takata, Kyosuke Kanai, Edo Riyandani, Kengo Mukuda, Momone Mimura, Kosuke Yamaguchi, Hiroyuki Kato, Ryo Okamoto, Kensaku Okada, Tsuyoshi Kitaura, Masaki Nakamoto, Akira Yamasaki, Seiji Kageyama and Hiroki Chikumi
Int. J. Mol. Sci. 2025, 26(13), 6221; https://doi.org/10.3390/ijms26136221 - 27 Jun 2025
Viewed by 282
Abstract
Persistent SARS-CoV-2 infections involve prolonged viral replication and immune system interactions, potentially driving viral evolution and immune escape. This study examines viral characteristics and host gene expression changes in persistent infections. The nasopharyngeal samples from four patients with persistent SARS-CoV-2 infections at Tottori [...] Read more.
Persistent SARS-CoV-2 infections involve prolonged viral replication and immune system interactions, potentially driving viral evolution and immune escape. This study examines viral characteristics and host gene expression changes in persistent infections. The nasopharyngeal samples from four patients with persistent SARS-CoV-2 infections at Tottori University Hospital, Japan, were analyzed. Viral isolates were cultured, and infectivity was assessed using TCID50 assays. To investigate host responses, RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs), and Gene Ontology (GO) enrichment analysis mapped affected biological pathways. Viral genome sequencing detected mutations associated with prolonged infection. The results showed significant infectivity differences between early- and late-phase infection. Gene expression analysis revealed a strong early phase of pro-inflammatory response (IL6, TNF, IL1B, CXCL10) followed by immune suppression. GO enrichment analysis highlighted inflammation and cytokine-mediated immune pathways. Genomic sequencing identified mutations in ORF1ab and the spike (S) protein, potentially aiding immune escape. The findings underscore that SARS-CoV-2 adapts during persistent infections, altering infectivity and immune responses. These highlight the need for continued monitoring of prolonged infections to mitigate immune escape and viral evolution. Full article
(This article belongs to the Special Issue Advanced Perspectives on Virus–Host Interactions)
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14 pages, 1866 KiB  
Article
Naturally Occurring Angiotensin Peptides Enhance the SARS-CoV-2 Spike Protein Binding to Its Receptors
by Katelin X. Oliveira, Fariha E. Bablu, Emily S. Gonzales, Taisuke Izumi and Yuichiro J. Suzuki
Int. J. Mol. Sci. 2025, 26(13), 6067; https://doi.org/10.3390/ijms26136067 - 24 Jun 2025
Viewed by 337
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for Coronavirus Disease 2019 (COVID-19), utilizes its spike protein to infect host cells. In addition to angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1), AXL acts as a spike protein receptor and mediates infection, [...] Read more.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for Coronavirus Disease 2019 (COVID-19), utilizes its spike protein to infect host cells. In addition to angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1), AXL acts as a spike protein receptor and mediates infection, especially in respiratory cells with low ACE2 expression. Angiotensin II (1–8) can be cleaved into shorter peptides within the biological system. Antibody-based binding assays showed that angiotensin II causes a two-fold increase in the binding between the spike protein and AXL, but not ACE2 or NRP1. While a longer peptide, angiotensin I (1–10), did not affect the spike–AXL binding, shorter lengths of angiotensin peptides exhibited enhancing effects. The C-terminal deletions of angiotensin II to angiotensin (1–7) or angiotensin (1–6) resulted in peptides with enhanced activity toward spike–AXL binding with a similar capacity as angiotensin II. In contrast, the N-terminal deletions of angiotensin II to angiotensin III (2–8) or angiotensin IV (3–8) as well as the N-terminal deletions of angiotensin (1–7) to angiotensin (2–7) or angiotensin (5–7) produced peptides with a more potent ability to enhance spike–AXL binding (2.7-fold increase with angiotensin IV). When valine was substituted for tyrosine at position 4 in angiotensin II or when tyrosine at position 4 was phosphorylated, spike–AXL binding was increased, suggesting that modifications to tyrosine trigger enhancement. Angiotensin IV also enhances spike protein binding to ACE2 and NRP1. Thus, angiotensin peptides may contribute to COVID-19 pathogenesis by enhancing spike protein binding and thus serve as therapeutic targets. Full article
(This article belongs to the Special Issue Advanced Perspectives on Virus–Host Interactions)
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17 pages, 5153 KiB  
Article
A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms
by Ting Ye, Han Li, Du Hai, Zhima Zhaxi, Jie Duan, Yang Lin, Jiatao Xie, Jiasen Cheng, Bo Li, Tao Chen, Xiao Yu, Xueliang Lyu, Xueqiong Xiao, Yanping Fu and Daohong Jiang
Int. J. Mol. Sci. 2025, 26(8), 3853; https://doi.org/10.3390/ijms26083853 - 18 Apr 2025
Viewed by 400
Abstract
Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel [...] Read more.
Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as “bait” to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms. Full article
(This article belongs to the Special Issue Advanced Perspectives on Virus–Host Interactions)
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Review

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14 pages, 2350 KiB  
Review
Current Perspectives on Functional Involvement of Micropeptides in Virus–Host Interactions
by Haowen Sun, Rongrong Gu, Tingting Tang, Kul Raj Rai and Ji-Long Chen
Int. J. Mol. Sci. 2025, 26(8), 3651; https://doi.org/10.3390/ijms26083651 - 12 Apr 2025
Cited by 1 | Viewed by 920
Abstract
Micropeptides (miPEPs), encoded by short open reading frames (sORFs) within various genomic regions, have recently emerged as critical regulators of multiple biological processes. In particular, these small molecules are now increasingly being recognized for their role in modulating viral replication, pathogenesis, and host [...] Read more.
Micropeptides (miPEPs), encoded by short open reading frames (sORFs) within various genomic regions, have recently emerged as critical regulators of multiple biological processes. In particular, these small molecules are now increasingly being recognized for their role in modulating viral replication, pathogenesis, and host immune responses. Both host miPEPs and virus-derived miPEPs have been noted for their ability to regulate virus–host interactions through diversified mechanisms such as altering protein stability and modulating protein–protein interactions. Although thousands of sORFs have been annotated as having the potential to encode miPEPs, only a small number have been experimentally validated so far, with some directly linked to virus–host interactions and a small subset associated with immune modulation, indicating that the investigation of miPEPs is still in its infancy. The systematic identification, translational status assessment, in-depth characterization, and functional analysis of a substantial fraction of sORFs encoding miPEPs remain largely underexplored. Further studies are anticipated to uncover the intricate mechanisms underlying virus–host interactions, host immune modulation, and the broader biological functions of miPEPs. This article will review the emerging roles of miPEPs in virus–host interactions and host immunity, and discuss the challenges and future perspectives of miPEP studies. Full article
(This article belongs to the Special Issue Advanced Perspectives on Virus–Host Interactions)
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