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Viruses
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Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses
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Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 15693

Special Issue Editors

Dr. Yohei Kurosaki

E-Mail Website
Guest Editor
National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
Interests: virus heamorrhagic fever; emerging viruses; filovirus; vector-borne viruses; molecular diagnostics; epidemiology; virus genomics; next-generation sequencing
Dr. Danyelly Bruneska Gondim Martins

E-Mail Website1 Website2
Guest Editor
Universidade Federal de Pernambuco (Federal University of Pernambuco), Recife 50670-901, Brazil
Interests: cancer; biomarkers; infeccious diseases; point-of-care
Dr. José Luiz Lima Filho

E-Mail Website
Guest Editor
Universidade Federal de Pernambuco (Federal University of Pernambuco), Recife 50670-901, Brazil
Interests: biosensor; molecular biology; point of care; instrumentation; microbiology; epidemiology

Special Issue Information

Dear Colleagues,

In the last decade, there has been massive and borderless viral disease outbreaks caused by Ebola virus, Zika virus, and SARS-CoV-2. It is highly likely that this trend will continue, and it is undeniable that a new global epidemic will occur in the near future. In the situation of COVID-19, a very large number of people have been tested to confirm virus infection, and genetic variants that could enhance the transmission of the virus have emerged. In order to overcome this situation, cost-effective, labor-saving, high-throughput molecular diagnostic technologies for detecting viruses and their genetic mutations need to be continuously developed. Furthermore, surveillance of zoonotic viruses is also necessary in the preparedness for the next spillover of known or unknown pathogenic viruses from nature to human communities. In this Special Issue, we focus on novel and effective technologies for detecting viruses or biomarkers that indicate virus infection using nucleic acid amplification, antigen detection, and next-generation sequencing, as well as other germinating techniques that can be applied to the detection of emerging viruses.

Dr. Yohei Kurosaki
Dr. Danyelly Bruneska Gondim Martins
Dr. José Luiz Lima Filho
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 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

  • emerging virus
  • molecular diagnostics
  • biomarkers
  • nucleic acid amplification
  • antigen detection
  • next-generation sequencing
  • variant detection
  • outbreak preparedness

Published Papers (6 papers)

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Research

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18 pages, 2923 KiB  
Article
A Cellular Assay for Spike/ACE2 Fusion: Quantification of Fusion-Inhibitory Antibodies after COVID-19 and Vaccination
by Fabien Abdul, Pascale Ribaux, Aurélie Caillon, Astrid Malézieux-Picard, Virginie Prendki, Nathalie Vernaz, Nikolay Zhukovsky, Flavien Delhaes, Karl-Heinz Krause and Olivier Preynat-Seauve
Viruses 2022, 14(10), 2118; https://doi.org/10.3390/v14102118 - 25 Sep 2022
Cited by 1 | Viewed by 1729
Abstract
Not all antibodies against SARS-CoV-2 inhibit viral entry, and hence, infection. Neutralizing antibodies are more likely to reflect real immunity; however, certain tests investigate protein/protein interaction rather than the fusion event. Viral and pseudoviral entry assays detect functionally active antibodies but are limited [...] Read more.
Not all antibodies against SARS-CoV-2 inhibit viral entry, and hence, infection. Neutralizing antibodies are more likely to reflect real immunity; however, certain tests investigate protein/protein interaction rather than the fusion event. Viral and pseudoviral entry assays detect functionally active antibodies but are limited by biosafety and standardization issues. We have developed a Spike/ACE2-dependent fusion assay, based on a split luciferase. Hela cells stably transduced with Spike and a large fragment of luciferase were co-cultured with Hela cells transduced with ACE2 and the complementary small fragment of luciferase. Cell fusion occurred rapidly allowing the measurement of luminescence. Light emission was abolished in the absence of Spike and reduced in the presence of proteases. Sera from COVID-19-negative, non-vaccinated individuals or from patients at the moment of first symptoms did not lead to a significant reduction of fusion. Sera from COVID-19-positive patients as well as from vaccinated individuals reduced the fusion. This assay was more correlated to pseudotyped-based entry assay rather than serology or competitive ELISA. In conclusion, we report a new method measuring fusion-inhibitory antibodies in serum, combining the advantage of a complete Spike/ACE2 interaction active on entry with a high degree of standardization, easily allowing automation in a standard bio-safety environment. Full article
(This article belongs to the Special Issue Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses)
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16 pages, 2551 KiB  
Article
Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches
by Nathalie Mugnier, Aurélien Griffon, Bruno Simon, Maxence Rambaud, Hadrien Regue, Antonin Bal, Gregory Destras, Maud Tournoud, Magali Jaillard, Abel Betraoui, Emmanuelle Santiago, Valérie Cheynet, Alexandre Vignola, Véronique Ligeon, Laurence Josset and Karen Brengel-Pesce
Viruses 2022, 14(8), 1674; https://0-doi-org.brum.beds.ac.uk/10.3390/v14081674 - 29 Jul 2022
Cited by 2 | Viewed by 1459
Abstract
Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) [...] Read more.
Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) to analyse SARS-CoV-2 NGS data generated on common sequencing platforms using a variety of commercially available reagents. This application performs in one click a quality check, a reference-based genome assembly, and the analysis of the generated consensus sequence as to coverage of the reference genome, mutation screening and variant identification according to the up-to-date Nextstrain clade and Pango lineage. In this study, we validated the EPISEQ SARS-CoV-2 pipeline against a reference pipeline and compared the performance of NGS data generated by different sequencing protocols using EPISEQ SARS-CoV-2. We showed a strong agreement in SARS-CoV-2 clade and lineage identification (>99%) and in spike mutation detection (>99%) between EPISEQ SARS-CoV-2 and the reference pipeline. The comparison of several sequencing approaches using EPISEQ SARS-CoV-2 revealed 100% concordance in clade and lineage classification. It also uncovered reagent-related sequencing issues with a potential impact on SARS-CoV-2 mutation reporting. Altogether, EPISEQ SARS-CoV-2 allows an easy, rapid and reliable analysis of raw NGS data to support the sequencing efforts of laboratories with limited bioinformatics capacity and those willing to accelerate genomic surveillance of SARS-CoV-2. Full article
(This article belongs to the Special Issue Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses)
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16 pages, 2660 KiB  
Article
B-Cell-Epitope-Based Fluorescent Quantum Dot Biosensors for SARS-CoV-2 Enable Highly Sensitive COVID-19 Antibody Detection
by Yucheng Zheng, Kun Song, Kun Cai, Linlin Liu, Dixiao Tang, Wenbo Long, Bohui Zhai, Jianjun Chen, Yanbing Tao, Yunong Zhao, Simeng Liang, Qing Huang, Qianyun Liu, Qi Zhang, Yu Chen, Yingle Liu, Huayao Li, Ping Wang, Ke Lan, Huan Liu and Ke Xuadd Show full author list remove Hide full author list
Viruses 2022, 14(5), 1031; https://0-doi-org.brum.beds.ac.uk/10.3390/v14051031 - 12 May 2022
Cited by 7 | Viewed by 3364
Abstract
A new antibody diagnostic assay with more rapid and robust properties is demanded to quantitatively evaluate anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity in a large population. Here, we developed a nanometer-scale fluorescent biosensor system consisting of CdSe-ZnS quantum dots (QDs) coupled [...] Read more.
A new antibody diagnostic assay with more rapid and robust properties is demanded to quantitatively evaluate anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity in a large population. Here, we developed a nanometer-scale fluorescent biosensor system consisting of CdSe-ZnS quantum dots (QDs) coupled with the highly sensitive B-cell epitopes of SARS-CoV-2 that could remarkably identify the corresponding antibody with a detection limit of 100 pM. Intriguingly, we found that fluorescence quenching of QDs was stimulated more obviously when coupled with peptides than the corresponding proteins, indicating that the energy transfer between QDs and peptides was more effective. Compared to the traditional enzyme-linked immunosorbent assay (ELISA), the B-cell-epitope-based QD-biosensor could robustly distinguish coronavirus disease 2019 (COVID-19) antibody-positive patients from uninfected individuals with a higher sensitivity (92.3–98.1% positive rates by QD-biosensor vs. 78.3–83.1% positive rates by ELISAs in 207 COVID-19 patients’ sera) in a more rapid (5 min) and labor-saving manner. Taken together, the ‘QD-peptides’ biosensor provided a novel real-time, quantitative, and high-throughput method for clinical diagnosis and home-use tests. Full article
(This article belongs to the Special Issue Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses)
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17 pages, 3732 KiB  
Article
Comprehensive Comparison of Novel Bovine Leukemia Virus (BLV) Integration Sites between B-Cell Lymphoma Lines BLSC-KU1 and BLSC-KU17 Using the Viral DNA Capture High-Throughput Sequencing Method
by Meripet Polat Yamanaka, Susumu Saito, Kazuyoshi Hosomichi and Yoko Aida
Viruses 2022, 14(5), 995; https://0-doi-org.brum.beds.ac.uk/10.3390/v14050995 - 07 May 2022
Cited by 4 | Viewed by 2563
Abstract
Bovine leukemia virus (BLV) infects cattle and integrates into host DNA, causing enzootic bovine leukosis (EBL), an aggressive B-cell lymphoma. Here, we developed a novel proviral DNA-capture sequencing (proviral DNA-capture-seq) method investigating BLV proviral integration in two B-cell lymphoma lines, BLSC-KU1 and BLSC-KU17, [...] Read more.
Bovine leukemia virus (BLV) infects cattle and integrates into host DNA, causing enzootic bovine leukosis (EBL), an aggressive B-cell lymphoma. Here, we developed a novel proviral DNA-capture sequencing (proviral DNA-capture-seq) method investigating BLV proviral integration in two B-cell lymphoma lines, BLSC-KU1 and BLSC-KU17, derived from BLV-infected cattle with EBL. We designed BLV-specific biotinylated probes to capture the provirus genome and enrich libraries for next-generation sequencing. Validation showed high specificity and efficient enrichment of target sequence reads as well as identification of three BLV proviral integration sites on BLV persistently infected FLK-BLV cells as a positive control. We successfully detected a single BLV proviral integration site on chromosome 19 of BLSC-KU1 and chromosome 9 of BLSC-KU17, which were confirmed by standard PCR and Sanger sequencing. Further, a defective provirus in BLSC-KU1 and complete BLV proviral sequence in BLSC-KU17 were confirmed using long PCR and sequencing. This is the first study to provide comprehensive information on BLV proviral structure and viral integration in BLSC-KU1 and BLSC-KU17. Moreover, the proposed method can facilitate understanding of the detailed mechanisms underlying BLV-induced leukemogenesis and may be used as an innovative tool to screen BLV-infected cattle at risk at an earlier stage than those that have already developed lymphoma. Full article
(This article belongs to the Special Issue Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses)
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Review

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15 pages, 1221 KiB  
Review
Pivoting Novel Exosome-Based Technologies for the Detection of SARS-CoV-2
by Christine Happel, Chariz Peñalber-Johnstone and Danilo A. Tagle
Viruses 2022, 14(5), 1083; https://0-doi-org.brum.beds.ac.uk/10.3390/v14051083 - 18 May 2022
Cited by 3 | Viewed by 3075
Abstract
The National Institutes of Health (NIH) launched the Rapid Acceleration of Diagnostics (RADx) initiative to meet the needs for COVID-19 diagnostic and surveillance testing, and to speed its innovation in the development, commercialization, and implementation of new technologies and approaches. The RADx Radical [...] Read more.
The National Institutes of Health (NIH) launched the Rapid Acceleration of Diagnostics (RADx) initiative to meet the needs for COVID-19 diagnostic and surveillance testing, and to speed its innovation in the development, commercialization, and implementation of new technologies and approaches. The RADx Radical (RADx-Rad) initiative is one component of the NIH RADx program which focuses on the development of new or non-traditional applications of existing approaches, to enhance their usability, accessibility, and/or accuracy for the detection of SARS-CoV-2. Exosomes are a subpopulation of extracellular vesicles (EVs) 30–140 nm in size, that are critical in cell-to-cell communication. The SARS-CoV-2 virus has similar physical and molecular properties as exosomes. Therefore, the novel tools and technologies that are currently in development for the isolation and detection of exosomes, may prove to be invaluable in screening for SARS-CoV-2 viral infection. Here, we describe how novel exosome-based technologies are being pivoted for the detection of SARS-CoV-2 and/or the diagnosis of COVID-19. Considerations for these technologies as they move toward clinical validation and commercially viable diagnostics is discussed along with their future potential. Ultimately, the technologies in development under the NIH RADx-Rad exosome-based non-traditional technologies toward multi-parametric and integrated approaches for SARS-CoV-2 program represent a significant advancement in diagnostic technology, and, due to a broad focus on the biophysical and biochemical properties of nanoparticles, the technologies have the potential to be further pivoted as tools for future infectious agents. Full article
(This article belongs to the Special Issue Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses)
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12 pages, 835 KiB  
Review
Mass Spectrometry Approaches for SARS-CoV-2 Detection: Harnessing for Application in Food and Environmental Samples
by Esaú Bojórquez-Velázquez, Miriam Livier Llamas-García, José M. Elizalde-Contreras, Jesús Alejandro Zamora-Briseño and Eliel Ruiz-May
Viruses 2022, 14(5), 872; https://0-doi-org.brum.beds.ac.uk/10.3390/v14050872 - 22 Apr 2022
Cited by 2 | Viewed by 2142
Abstract
The public health crisis caused by the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 has drastically changed our lifestyle in virtually all contexts around the world. SARS-CoV-2 is mainly airborne, transmitted by the salivary droplets produced when infected [...] Read more.
The public health crisis caused by the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 has drastically changed our lifestyle in virtually all contexts around the world. SARS-CoV-2 is mainly airborne, transmitted by the salivary droplets produced when infected people cough or sneeze. In addition, diarrhea symptoms and the detection of SARS-CoV-2 in feces suggest a fecal–oral route of contagion. Currently, the high demand for SARS-CoV-2 diagnosis has surpassed the availability of PCR and immunodetection probes and has prompted the development of other diagnostic alternatives. In this context, mass spectrometry (MS) represents a mature, robust alternative platform for detection of SARS-CoV-2 and other human viruses. This possibility has raised great interest worldwide. Therefore, it is time for the global application of MS as a feasible option for detecting SARS-CoV-2, not only in human fluids, but also in other matrices such as foods and wastewater. This review covers the most relevant established methods for MS-based SARS-CoV-2 detection and discusses the future application of these tools in different matrices. Significance: The Coronavirus Disease 2019 (COVID-19) pandemic highlighted the pros and cons of currently available PCR and immunodetection tools. The great concern over the infective potential of SARS-CoV-2 viral particles that can persist for several hours on different surfaces under various conditions further evidenced the need for reliable alternatives and high-throughput methods to meet the needs for mass detection of SARS-CoV-2. In this context, MS-based proteomics emerging from fundamental studies in life science can offer a robust option for SARS-CoV-2 detection in human fluids and other matrices. In addition, the substantial efforts towards detecting SARS-CoV-2 in clinal samples, position MS to support the detection of this virus in different matrices such as the surfaces of the packing food process, frozen foods, and wastewaters. Proteomics and mass spectrometry are, therefore, well positioned to play a role in the epidemiological control of COVID-19 and other future diseases. We are currently witnessing the opportunity to generate technologies to overcome prolonged pandemics for the first time in human history. Full article
(This article belongs to the Special Issue Novel Diagnostic Technologies for SARS-CoV-2 and Other Emerging Viruses)
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