An Interdisciplinary Approach to Virology Research

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

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 16299

Special Issue Editor

Graduate School of Medicine, Nagoya University, Nagoya, Japan
Interests: Epstein-Barr virus;extracellular vesicles;fate of infected cells

Special Issue Information

Dear Colleagues,

Interdisciplinary research by teams that integrates information, data, techniques, tools, and/or theories from two or more research fields advances fundamental understanding and solves problems in biology. The current COVID-19 pandemic boosted virus research through collaborations with various specialists in conjunction with recent advances in technology, highlighting the importance of interdisciplinary research in virology that is beyond the scope of the traditional field.

In this Special Issue of Viruses, we will focus on virus research performed by researchers from two or more disciplines. We welcome original research articles and reviews across a broad range of virus research from virus molecular biology and pathogenesis to antiviral agents and therapy.

Dr. Yoshitaka Sato
Guest Editor

Manuscript Submission Information

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Keywords

  • virus–host interactions
  • pathogenicity
  • omics approach
  • in silico simulation
  • virome
  • antivirals
  • big data biology

Published Papers (5 papers)

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Research

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14 pages, 4335 KiB  
Article
Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences
by Qiao Du, Fang Peng, Qing Xiong, Kejin Xu, Kevin Yi Yang, Mingqiang Wang, Zhitian Wu, Shanying Li, Xiaorui Cheng, Xinjie Rao, Yuyouye Wang, Stephen Kwok-Wing Tsui and Xi Zeng
Viruses 2023, 15(4), 909; https://0-doi-org.brum.beds.ac.uk/10.3390/v15040909 - 31 Mar 2023
Viewed by 1364
Abstract
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 [...] Read more.
Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus. Full article
(This article belongs to the Special Issue An Interdisciplinary Approach to Virology Research)
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11 pages, 2588 KiB  
Article
Organic Electrochemical Transistors as Versatile Tool for Real-Time and Automatized Viral Cytopathic Effect Evaluation
by Francesco Decataldo, Catia Giovannini, Laura Grumiro, Maria Michela Marino, Francesca Faccin, Martina Brandolini, Giorgio Dirani, Francesca Taddei, Davide Lelli, Marta Tessarolo, Maria Calienni, Carla Cacciotto, Alessandra Mistral De Pascali, Antonio Lavazza, Beatrice Fraboni, Vittorio Sambri and Alessandra Scagliarini
Viruses 2022, 14(6), 1155; https://0-doi-org.brum.beds.ac.uk/10.3390/v14061155 - 26 May 2022
Cited by 1 | Viewed by 1764
Abstract
In-vitro viral studies are still fundamental for biomedical research since studying the virus kinetics on cells is crucial for the determination of the biological properties of viruses and for screening the inhibitors of infections. Moreover, testing potential viral contaminants is often mandatory for [...] Read more.
In-vitro viral studies are still fundamental for biomedical research since studying the virus kinetics on cells is crucial for the determination of the biological properties of viruses and for screening the inhibitors of infections. Moreover, testing potential viral contaminants is often mandatory for safety evaluation. Nowadays, viral cytopathic effects are mainly evaluated through end-point assays requiring dye-staining combined with optical evaluation. Recently, optical-based automatized equipment has been marketed, aimed at the real-time screening of cell-layer status and obtaining further insights, which are unavailable with end-point assays. However, these technologies present two huge limitations, namely, high costs and the possibility to study only cytopathic viruses, whose effects lead to plaque formation and layer disruption. Here, we employed poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (Pedot:Pss) organic electrochemical transistors (OECTs) for the real-time, electrical monitoring of the infection of cytolytic viruses, i.e., encephalomyocarditis virus (EMCV), and non-cytolytic viruses, i.e., bovine coronavirus (B-CoV), on cells. OECT data on EMCV were validated using a commercially-available optical-based technology, which, however, failed in the B-CoV titration analysis, as expected. The OECTs proved to be reliable, fast, and versatile devices for viral infection monitoring, which could be scaled up at low cost, reducing the operator workload and speeding up in-vitro assays in the biomedical research field. Full article
(This article belongs to the Special Issue An Interdisciplinary Approach to Virology Research)
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19 pages, 4375 KiB  
Article
Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions
by Puja Adhikari, Bahaa Jawad, Praveen Rao, Rudolf Podgornik and Wai-Yim Ching
Viruses 2022, 14(3), 465; https://0-doi-org.brum.beds.ac.uk/10.3390/v14030465 - 24 Feb 2022
Cited by 8 | Viewed by 2252
Abstract
The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an increased [...] Read more.
The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an increased efficiency. In particular, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain, including the effect of double mutation, and compare the results with the wild type. We have recently developed a method of calculating the amino-acid–amino-acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant finding is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations. Full article
(This article belongs to the Special Issue An Interdisciplinary Approach to Virology Research)
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Review

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20 pages, 1413 KiB  
Review
Molecular Basis of Epstein–Barr Virus Latency Establishment and Lytic Reactivation
by Takayuki Murata, Atsuko Sugimoto, Tomoki Inagaki, Yusuke Yanagi, Takahiro Watanabe, Yoshitaka Sato and Hiroshi Kimura
Viruses 2021, 13(12), 2344; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122344 - 23 Nov 2021
Cited by 61 | Viewed by 7674
Abstract
Epstein–Barr virus (EBV) is a causative agent of infectious mononucleosis and several types of cancer. Like other herpesviruses, it establishes an asymptomatic, life-long latent infection, with occasional reactivation and shedding of progeny viruses. During latency, EBV expresses a small number of viral genes, [...] Read more.
Epstein–Barr virus (EBV) is a causative agent of infectious mononucleosis and several types of cancer. Like other herpesviruses, it establishes an asymptomatic, life-long latent infection, with occasional reactivation and shedding of progeny viruses. During latency, EBV expresses a small number of viral genes, and exists as an episome in the host–cell nucleus. Expression patterns of latency genes are dependent on the cell type, time after infection, and milieu of the cell (e.g., germinal center or peripheral blood). Upon lytic induction, expression of the viral immediate-early genes, BZLF1 and BRLF1, are induced, followed by early gene expression, viral DNA replication, late gene expression, and maturation and egress of progeny virions. Furthermore, EBV reactivation involves more than just progeny production. The EBV life cycle is regulated by signal transduction, transcription factors, promoter sequences, epigenetics, and the 3D structure of the genome. In this article, the molecular basis of EBV latency establishment and reactivation is summarized. Full article
(This article belongs to the Special Issue An Interdisciplinary Approach to Virology Research)
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Other

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14 pages, 5878 KiB  
Brief Report
In Silico Analysis and Synthesis of Nafamostat Derivatives and Evaluation of Their Anti-SARS-CoV-2 Activity
by Kazuhiro J. Fujimoto, Daniel C. F. Hobbs, Miki Umeda, Akihiro Nagata, Rie Yamaguchi, Yoshitaka Sato, Ayato Sato, Kohsuke Ohmatsu, Takashi Ooi, Takeshi Yanai, Hiroshi Kimura and Takayuki Murata
Viruses 2022, 14(2), 389; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020389 - 14 Feb 2022
Cited by 2 | Viewed by 2376
Abstract
Inhibition of transmembrane serine protease 2 (TMPRSS2) is expected to block the spike protein-mediated fusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nafamostat, a potent TMPRSS2 inhibitor as well as a candidate for anti-SARS-CoV-2 drug, possesses the same acyl substructure as camostat, [...] Read more.
Inhibition of transmembrane serine protease 2 (TMPRSS2) is expected to block the spike protein-mediated fusion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nafamostat, a potent TMPRSS2 inhibitor as well as a candidate for anti-SARS-CoV-2 drug, possesses the same acyl substructure as camostat, but is known to have a greater antiviral effect. A unique aspect of the molecular binding of nafamostat has been recently reported to be the formation of a covalent bond between its acyl substructure and Ser441 in TMPRSS2. In this study, we investigated crucial elements that cause the difference in anti-SARS-CoV-2 activity of nafamostat and camostat. In silico analysis showed that Asp435 significantly contributes to the binding of nafamostat and camostat to TMPRSS2, while Glu299 interacts strongly only with nafamostat. The estimated binding affinity for each compound with TMPRSS2 was actually consistent with the higher activity of nafamostat; however, the evaluation of the newly synthesized nafamostat derivatives revealed that the predicted binding affinity did not correlate with their anti-SARS-CoV-2 activity measured by the cytopathic effect (CPE) inhibition assay. It was further shown that the substitution of the ester bond with amide bond in nafamostat resulted in significantly weakened anti-SARS-CoV-2 activity. These results strongly indicate that the ease of covalent bond formation with Ser441 in TMPRSS2 possibly plays a major role in the anti-SARS-CoV-2 effect of nafamostat and its derivatives. Full article
(This article belongs to the Special Issue An Interdisciplinary Approach to Virology Research)
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