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Viruses
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Innovative Imaging in Viral Research
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Innovative Imaging in Viral Research

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

Deadline for manuscript submissions: closed (20 February 2023) | Viewed by 16010

Special Issue Editor

Dr. Jean-Pierre Baudoin

E-Mail Website
Guest Editor
1. Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
2. IHU-Méditerranée Infection, 13005 Marseille, France
Interests: diagnostic; emerging infectious diseases; sample preparation; ultramicrotomy; electron microscopy; tomography; light microscopy; CLEM; whole-cells; cell cultures; viruses; bacteria; infective endocartidis; neuronal migration; cytoskeleton; centrosome; golgi; primary cilium; neuronal networks; mauthner cell; cell trafficking; nanoparticles

Special Issue Information

Dear Colleagues,

In the context of the current pandemic period, better imaging of viruses has never been so crucial for improving diagnostics, for monitoring viral infections and for better understanding the structure and function of viruses. The objective of this Special Issue is to bring to the virologists' community, and the whole scientific community more broadly, recent advances in the imaging of viruses.

Scientists from public and private institutions are warmly encouraged to build this Special Issue with quality articles, brief reports, technical notes, and reviews for sharing original results based on new techniques or novel approaches with existing techniques in both the diagnostic and fundamental research fields. We look for manuscripts using advanced imaging of single viruses (from purified solutions; animal/human samples) or viruses in the context of infected cells (ex vivo in animal/human tissues; in vitro in 2D/3D cultured cells). The focus of the current Special Issue will be placed on the innovative nature of the study used for virus imaging and the help that such innovation can bring for faster diagnostics, workflow automation and/or new knowledge about virus biology. Innovation may originate from sample preparation, advanced microscopy modalities/technology or image processing such as the use of artificial intelligence (AI). Finally, emphasis will be given both on the scientific breakthrough of the described methodology but also on the ease of the imaging innovation to be shared and applied worldwide in other laboratories and facilities.

 “Viruses are always speaking—the secret is to learn their language.” 

Dr. Jean-Pierre Baudoin
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. 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

  • infectious diseases
  • virus
  • viral infectious cycle
  • diagnostic
  • imaging
  • light microscopy
  • super-resolution
  • electron microscopy
  • liquid-phase electron microscopy
  • correlative light-electron-microscopy
  • cryo-microscopy
  • three-dimensional (3D) reconstructions
  • single-particle analysis
  • atomic-force microscopy
  • elemental mapping
  • sample preparation
  • automation
  • artificial intelligence

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Published Papers (5 papers)

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Research

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17 pages, 3669 KiB  
Article
Near-Native Visualization of SARS-CoV-2 Induced Membrane Remodeling and Virion Morphogenesis
by Tim Bergner, Fabian Zech, Maximilian Hirschenberger, Steffen Stenger, Konstantin M. J. Sparrer, Frank Kirchhoff and Clarissa Read
Viruses 2022, 14(12), 2786; https://doi.org/10.3390/v14122786 - 14 Dec 2022
Cited by 10 | Viewed by 4392
Abstract
Infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, leads to profound remodeling of cellular membranes, promoting viral replication and virion assembly. A full understanding of this drastic remodeling and the process of virion morphogenesis remains [...] Read more.
Infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, leads to profound remodeling of cellular membranes, promoting viral replication and virion assembly. A full understanding of this drastic remodeling and the process of virion morphogenesis remains lacking. In this study, we applied room temperature transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) tomography to visualize the SARS-CoV-2 replication factory in Vero cells, and present our results in comparison with published cryo-EM studies. We obtained cryo-EM-like clarity of the ultrastructure by employing high-pressure freezing, freeze substitution (HPF-FS) and embedding, allowing room temperature visualization of double-membrane vesicles (DMVs) in a near-native state. In addition, our data illustrate the consecutive stages of virion morphogenesis and reveal that SARS-CoV-2 ribonucleoprotein assembly and membrane curvature occur simultaneously. Finally, we show the tethering of virions to the plasma membrane in 3D, and that accumulations of virus particles lacking spike protein in large vesicles are most likely not a result of defective virion assembly at their membrane. In conclusion, this study puts forward a room-temperature EM technique providing near-native ultrastructural information about SARS-CoV-2 replication, adding to our understanding of the interaction of this pandemic virus with its host cell. Full article
(This article belongs to the Special Issue Innovative Imaging in Viral Research)
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12 pages, 2138 KiB  
Article
Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells
by Jian-Hua Chen, Bieke Vanslembrouck, Axel Ekman, Vesa Aho, Carolyn A. Larabell, Mark A. Le Gros, Maija Vihinen-Ranta and Venera Weinhardt
Viruses 2022, 14(12), 2651; https://doi.org/10.3390/v14122651 - 27 Nov 2022
Cited by 5 | Viewed by 3076
Abstract
Upon infection, viruses hijack the cell machinery and remodel host cell structures to utilize them for viral proliferation. Since viruses are about a thousand times smaller than their host cells, imaging virus-host interactions at high spatial resolution is like looking for a needle [...] Read more.
Upon infection, viruses hijack the cell machinery and remodel host cell structures to utilize them for viral proliferation. Since viruses are about a thousand times smaller than their host cells, imaging virus-host interactions at high spatial resolution is like looking for a needle in a haystack. Scouting gross cellular changes with fluorescent microscopy is only possible for well-established viruses, where fluorescent tagging is developed. Soft X-ray tomography (SXT) offers 3D imaging of entire cells without the need for chemical fixation or labeling. Here, we use full-rotation SXT to visualize entire human B cells infected by the herpes simplex virus 1 (HSV-1). We have mapped the temporospatial remodeling of cells during the infection and observed changes in cellular structures, such as the presence of cytoplasmic stress granules and multivesicular structures, formation of nuclear virus-induced dense bodies, and aggregates of capsids. Our results demonstrate the power of SXT imaging for scouting virus-induced changes in infected cells and understanding the orchestration of virus-host remodeling quantitatively. Full article
(This article belongs to the Special Issue Innovative Imaging in Viral Research)
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13 pages, 3779 KiB  
Article
Concentration of SARS-CoV-2-Infected Cell Culture Supernatants for Detection of Virus-like Particles by Scanning Electron Microscopy
by Marion Le Bideau, Lea Robresco, Jean-Pierre Baudoin and Bernard La Scola
Viruses 2022, 14(11), 2388; https://doi.org/10.3390/v14112388 - 28 Oct 2022
Cited by 4 | Viewed by 2854
Abstract
There is currently a need for new rapid viral diagnostic electron microscopy methods. Although the gold standard remains the transmission electron microscopy (TEM) negative staining method for electron microscopic examination of samples containing a virus, difficulties can arise when the virus particle content [...] Read more.
There is currently a need for new rapid viral diagnostic electron microscopy methods. Although the gold standard remains the transmission electron microscopy (TEM) negative staining method for electron microscopic examination of samples containing a virus, difficulties can arise when the virus particle content of the sample that has to be examined is poor. Such samples include supernatants of virus-infected cells that can be difficult to examine, as sometimes only a few virus particles are released in the culture medium upon infection. In addition to TEM, scanning electron microscopy (SEM) can also be used for visualizing virus particles. One advantage of SEM over TEM is its ability to rapidly screen several large specimens, such as microscopy slides. In this study, we investigated this possibility and tested different coating molecules as well as the effect of centrifugation for analyzing SARS-CoV-2-virus-infected cell culture supernatants deposited on microscopy glass slides by SEM. We found that centrifugation of 25XConcanavalinA-coated microscopy glass slides in shell vials provided an improved method for concentrating SARS-CoV-2-virus-infected cell supernatants for virus-like particle detection by SEM. Full article
(This article belongs to the Special Issue Innovative Imaging in Viral Research)
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Other

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9 pages, 1661 KiB  
Opinion
Spying on SARS-CoV-2 with Fluorescent Tags and Protease Reporters
by Tsz-Leung To, Xiaoquan Li and Xiaokun Shu
Viruses 2023, 15(10), 2005; https://doi.org/10.3390/v15102005 - 27 Sep 2023
Cited by 1 | Viewed by 2144
Abstract
The SARS-CoV-2 coronavirus has caused worldwide disruption through the COVID-19 pandemic, providing a sobering reminder of the profound impact viruses can have on human well-being. Understanding virus life cycles and interactions with host cells lays the groundwork for exploring therapeutic strategies against virus-related [...] Read more.
The SARS-CoV-2 coronavirus has caused worldwide disruption through the COVID-19 pandemic, providing a sobering reminder of the profound impact viruses can have on human well-being. Understanding virus life cycles and interactions with host cells lays the groundwork for exploring therapeutic strategies against virus-related diseases. Fluorescence microscopy plays a vital role in virus imaging, offering high spatiotemporal resolution, sensitivity, and spectroscopic versatility. In this opinion piece, we first highlight two recent techniques, SunTag and StayGold, for the in situ imaging of viral RNA translation and viral assembly. Next, we discuss a new class of genetically encoded fluorogenic protease reporters, such as FlipGFP, which can be customized to monitor SARS-CoV-2’s main (Mpro) or papain-like (PLpro) protease activity. These assays have proven effective in identifying potential antivirals through high-throughput screening, making fluorogenic viral protease reporters a promising platform for viral disease diagnostics and therapeutics. Full article
(This article belongs to the Special Issue Innovative Imaging in Viral Research)
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9 pages, 1903 KiB  
Technical Note
Intramuscular [18F]F-FDG Administration for Successful PET Imaging of Golden Hamsters in a Maximum Containment Laboratory Setting
by Hui Wang, Jurgen Seidel, Christopher Bartos, Russell Byrum, Philip J. Sayre, Kurt Cooper, Yu Cong, Dong-Yun Kim, Claudia Calcagno, Jens H. Kuhn, Anya Crane, Jiro Wada, Reed F. Johnson, Dima A. Hammoud and Ji Hyun Lee
Viruses 2022, 14(11), 2492; https://doi.org/10.3390/v14112492 - 11 Nov 2022
Viewed by 2283
Abstract
Positron emission tomography (PET) is becoming an important tool for the investigation of emerging infectious diseases in animal models. Usually, PET imaging is performed after intravenous (IV) radiotracer administration. However, IV injections are difficult to perform in some small animals, such as golden [...] Read more.
Positron emission tomography (PET) is becoming an important tool for the investigation of emerging infectious diseases in animal models. Usually, PET imaging is performed after intravenous (IV) radiotracer administration. However, IV injections are difficult to perform in some small animals, such as golden hamsters. This challenge is particularly evident in longitudinal imaging studies, and even more so in maximum containment settings used to study high-consequence pathogens. We propose the use of intramuscular (IM) administration of 2-deoxy-2[18F]fluoro-D-glucose ([18F]F-FDG) for PET imaging of hamsters in a biosafety level 4 (BSL-4) laboratory setting. After [18F]F-FDG administration via IM or IV (through surgically implanted vascular access ports), eight hamsters underwent static or dynamic PET scans. Time–activity curves (TACs) and standardized uptake values (SUVs) in major regions of interest (ROIs) were used to compare the two injection routes. Immediately after injection, TACs differed between the two routes. At 60 min post-injection, [18F]F-FDG activity for both routes reached a plateau in most ROIs except the brain, with higher accumulation in the liver, lungs, brain, and nasal cavities observed in the IM group. IM delivery of [18F]F-FDG is an easy, safe, and reliable alternative for longitudinal PET imaging of hamsters in a BSL-4 laboratory setting. Full article
(This article belongs to the Special Issue Innovative Imaging in Viral Research)
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