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The Application of Viruses to Biotechnology 2022

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

Deadline for manuscript submissions: closed (26 May 2023) | Viewed by 33370

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Special Issue Editors

Dr. Carla Varanda

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1. ESAS, Instituto Politécnico de Santarém, Quinta do Galinheiro, S. Pedro, 2001-904 Santarém, Portugal
2. CERNAS-Research Centre for Natural Resources, Environment and Society, Coimbra, Portugal
3. MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, 7006-554 Évora, Portugal
Interests: plant pathology; plant virology; molecular diagnosis of plant pathogens; sustainable plant protection; virus-induced gene silencing; gene expression; CRISPR-Cas systems
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Dr. Patrick Materatski

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Guest Editor

Laboratory of Virology, MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Universidade de Évora, Pólo da Mitra, 7006-554 Évora, Portugal
Interests: plant pathology; plant virology; molecular diagnosis of plant pathogens; sustainable plant protection; RNAi; virus-induced gene silencing; siRNAs; gene expression; CRISPR-Cas systems
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to present Volume II as a continuation of the Special Issue (SI) “The Application of Viruses to Biotechnology (https://www.mdpi.com/journal/viruses/special_issues/viruses_biotechnology)” that was closed in April 2021 and which included 15 high-quality articles.

Viruses are simple systems and can be manipulated to be beneficial and used for several purposes in different areas. In medicine, viruses have been used for a long time in vaccines and as vectors to carry materials for the treatment of diseases, such as cancer, taking advantage of their capacity to target specific cells. In agriculture, viruses are being studied to introduce desirable characteristics in plants or render resistance to biotic and abiotic stresses. Viruses have been exploited in nanotechnology for the deposition of specific metals and have been shown to be of great benefit to nanomaterial production. They have also been used for many applications in pharmacology, cosmetics, electronics, and other industries.

With this new SI, we intend to present up-to-date research, showing that viruses can be used to contribute to advances to science that would not be possible without their existence. It is clear that the more they are studied, the more possibilities viruses offer to us.

We invite researchers from all over the world to submit original research and review articles on topics related to the use of viruses as tools, vectors, and/or sources for many biotechnological applications and different fields.

Dr. Carla Varanda
Dr. Patrick Materatski
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.

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Related Special Issues

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The Application of Viruses to Biotechnology in Viruses (16 articles)

Published Papers (9 papers)

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Editorial

Jump to: Research, Review, Other

4 pages, 201 KiB

Open AccessEditorial

New Insights into the Applications of Viruses to Biotechnology

by Patrick Materatski and Carla Varanda

Viruses 2023, 15(12), 2322; https://doi.org/10.3390/v15122322 - 26 Nov 2023

Viewed by 2535

Abstract

Viruses are responsible for many devastating human and animal diseases, such as Ebola, rabies, HIV, smallpox, influenza, dengue, and SARS-CoV-2 [...] Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

Research

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22 pages, 6028 KiB

Open AccessArticle

Targeting FOXP3 Tumor-Intrinsic Effects Using Adenoviral Vectors in Experimental Breast Cancer

by Alejandro J. Nicola Candia, Matías Garcia Fallit, Jorge A. Peña Agudelo, Melanie Pérez Küper, Nazareno Gonzalez, Mariela A. Moreno Ayala, Emilio De Simone, Carla Giampaoli, Noelia Casares, Adriana Seilicovich, Juan José Lasarte, Flavia A. Zanetti and Marianela Candolfi

Viruses 2023, 15(9), 1813; https://doi.org/10.3390/v15091813 - 25 Aug 2023

Cited by 3 | Viewed by 2336

Abstract

The regulatory T cell master transcription factor, Forkhead box P3 (Foxp3), has been detected in cancer cells; however, its role in breast tumor pathogenesis remains controversial. Here we assessed Foxp3 tumor intrinsic effects in experimental breast cancer using a Foxp3 binder peptide (P60) that impairs Foxp3 nuclear translocation. Cisplatin upregulated Foxp3 expression in HER2+ and triple-negative breast cancer (TNBC) cells. Foxp3 inhibition with P60 enhanced chemosensitivity and reduced cell survival and migration in human and murine breast tumor cells. We also developed an adenoviral vector encoding P60 (Ad.P60) that efficiently transduced breast tumor cells, reduced cell viability and migration, and improved the cytotoxic response to cisplatin. Conditioned medium from transduced breast tumor cells contained lower levels of IL-10 and improved the activation of splenic lymphocytes. Intratumoral administration of Ad.P60 in breast-tumor-bearing mice significantly reduced tumor infiltration of Tregs, delayed tumor growth, and inhibited the development of spontaneous lung metastases. Our results suggest that Foxp3 exerts protumoral intrinsic effects in breast cancer cells and that gene-therapy-mediated blockade of Foxp3 could constitute a therapeutic strategy to improve the response of these tumors to standard treatment. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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17 pages, 3010 KiB

Open AccessArticle

LSDV-Vectored SARS-CoV-2 S and N Vaccine Protects against Severe Clinical Disease in Hamsters

by Warren R. J. de Moor, Anna-Lise Williamson, Georgia Schäfer, Nicola Douglass, Sophette Gers, Andrew D. Sutherland, Melissa J. Blumenthal, Emmanuel Margolin, Megan L. Shaw, Wolfgang Preiser and Rosamund Chapman

Viruses 2023, 15(7), 1409; https://doi.org/10.3390/v15071409 - 21 Jun 2023

Cited by 1 | Viewed by 2124

Abstract

The SARS-CoV-2 pandemic demonstrated the need for potent and broad-spectrum vaccines. This study reports the development and testing of a lumpy skin disease virus (LSDV)-vectored vaccine against SARS-CoV-2, utilizing stabilized spike and conserved nucleocapsid proteins as antigens to develop robust immunogenicity. Construction of the vaccine (LSDV-SARS2-S,N) was confirmed by polymerase chain reaction (PCR) amplification and sequencing. In vitro characterization confirmed that cells infected with LSDV-SARS2-S,N expressed SARS-CoV-2 spike and nucleocapsid protein. In BALB/c mice, the vaccine elicited high magnitude IFN-γ ELISpot responses (spike: 2808 SFU/10⁶ splenocytes) and neutralizing antibodies (ID₅₀ = 6552). Testing in hamsters, which emulate human COVID-19 disease progression, showed the development of high titers of neutralizing antibodies against the Wuhan and Delta SARS-CoV-2 variants (Wuhan ID₅₀ = 2905; Delta ID₅₀ = 4648). Additionally, hamsters vaccinated with LSDV-SARS2-S,N displayed significantly less weight loss, lung damage, and reduced viral RNA copies following SARS-CoV-2 infection with the Delta variant as compared to controls, demonstrating protection against disease. These data demonstrate that LSDV-vectored vaccines display promise as an effective SARS-CoV-2 vaccine and as a potential vaccine platform for communicable diseases in humans and animals. Further efficacy testing and immune response analysis, particularly in non-human primates, are warranted. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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12 pages, 14439 KiB

Open AccessArticle

Querying Recombination Junctions of Replication-Competent Adeno-Associated Viruses in Gene Therapy Vector Preparations with Single Molecule, Real-Time Sequencing

by Mitchell Yip, Jing Chen, Yan Zhi, Ngoc Tam Tran, Suk Namkung, Eric Pastor, Guangping Gao and Phillip W. L. Tai

Viruses 2023, 15(6), 1228; https://doi.org/10.3390/v15061228 - 24 May 2023

Viewed by 3040

Abstract

Clinical-grade preparations of adeno-associated virus (AAV) vectors used for gene therapy typically undergo a series of diagnostics to determine titer, purity, homogeneity, and the presence of DNA contaminants. One type of contaminant that remains poorly investigated is replication-competent (rc)AAVs. rcAAVs form through recombination of DNA originating from production materials, yielding intact, replicative, and potentially infectious virus-like virions. They can be detected through the serial passaging of lysates from cells transduced by AAV vectors in the presence of wildtype adenovirus. Cellular lysates from the last passage are subjected to qPCR to detect the presence of the rep gene. Unfortunately, the method cannot be used to query the diversity of recombination events, nor can qPCR provide insights into how rcAAVs arise. Thus, the formation of rcAAVs through errant recombination events between ITR-flanked gene of interest (GOI) constructs and expression constructs carrying the rep-cap genes is poorly described. We have used single molecule, real-time sequencing (SMRT) to analyze virus-like genomes expanded from rcAAV-positive vector preparations. We present evidence that sequence-independent and non-homologous recombination between the ITR-bearing transgene and the rep/cap plasmid occurs under several events and rcAAVs spawn from diverse clones. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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21 pages, 29740 KiB

Open AccessArticle

Evaluation of Baculoviruses as Gene Therapy Vectors for Brain Cancer

by Matías Garcia Fallit, Matías L. Pidre, Antonela S. Asad, Jorge A. Peña Agudelo, Mariana B. Vera, Alejandro J. Nicola Candia, Sofia B. Sagripanti, Melanie Pérez Kuper, Leslie C. Amorós Morales, Abril Marchesini, Nazareno Gonzalez, Carla M. Caruso, Víctor Romanowski, Adriana Seilicovich, Guillermo A. Videla-Richardson, Flavia A. Zanetti and Marianela Candolfi

Viruses 2023, 15(3), 608; https://doi.org/10.3390/v15030608 - 22 Feb 2023

Cited by 7 | Viewed by 3293

Abstract

We aimed to assess the potential of baculoviral vectors (BV) for brain cancer gene therapy. We compared them with adenoviral vectors (AdV), which are used in neuro-oncology, but for which there is pre-existing immunity. We constructed BVs and AdVs encoding fluorescent reporter proteins and evaluated their transduction efficiency in glioma cells and astrocytes. Naïve and glioma-bearing mice were intracranially injected with BVs to assess transduction and neuropathology. Transgene expression was also assessed in the brain of BV-preimmunized mice. While the expression of BVs was weaker than AdVs in murine and human glioma cell lines, BV-mediated transgene expression in patient-derived glioma cells was similar to AdV-mediated transduction and showed strong correlation with clathrin expression, a protein that interacts with the baculovirus glycoprotein GP64, mediating BV endocytosis. BVs efficiently transduced normal and neoplastic astrocytes in vivo, without apparent neurotoxicity. BV-mediated transgene expression was stable for at least 21 days in the brain of naïve mice, but it was significantly reduced after 7 days in mice systemically preimmunized with BVs. Our findings indicate that BVs efficiently transduce glioma cells and astrocytes without apparent neurotoxicity. Since humans do not present pre-existing immunity against BVs, these vectors may constitute a valuable tool for the delivery of therapeutic genes into the brain. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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10 pages, 2407 KiB

Open AccessCommunication

Production and Evaluation of Chicken Egg Yolk Immunoglobulin (IgY) against Human and Simian Rotaviruses

by Gentil Arthur Bentes, Natália Maria Lanzarini, Juliana Rodrigues Guimarães, Marcos Bryan Heinemann, Eduardo de Mello Volotão, Alexandre dos Santos da Silva, Luiz Guilherme Dias Heneine, Jaqueline Mendes de Oliveira and Marcelo Alves Pinto

Viruses 2022, 14(9), 1995; https://doi.org/10.3390/v14091995 - 9 Sep 2022

Cited by 5 | Viewed by 2652

Abstract

Producing specific antibodies in chickens is an attractive approach for diagnosis or therapeutic applications. Besides the high immunoglobulin Y (IgY) yield transferred to the egg yolk and its suitability for large-scale production, such an approach is more bioethical for animal maintenance. The IgY technology offers new possibilities for application in human and veterinary diagnostics and therapeutics, including strategies for treating severe intestinal diseases in children, particularly in emerging countries. Herein, we describe the production and purification of polyclonal antibodies against rotavirus group A (RVA) in immunised hens aiming at its application in prophylaxis and treatment of rotavirus-induced diarrhoea. For this purpose, we inoculated Rhodia laying chickens (Gallus gallus domesticus) with two or three doses of RVA combined with adjuvants or only adjuvants (control group). As the egg-laying period began, the yolk protein purification processes yielded a high concentration of specific IgY, the highest titre resulting from the group of hens that received three doses of the immunogen. The purified IgY blocked the functional activity of RVA in MA-104 cells, thus confirming the neutralisation ability. Therefore, anti-RVA IgY could be a promising candidate for pre- and post-exposure prevention or treatment of rotavirus-induced diarrhoea. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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18 pages, 1584 KiB

Open AccessArticle

An Adenoviral Vector as a Versatile Tool for Delivery and Expression of miRNAs

by Jonas Scholz, Patrick Philipp Weil, Daniel Pembaur, Georgia Koukou, Malik Aydin, Dorota Hauert, Jan Postberg, Florian Kreppel and Claudia Hagedorn

Viruses 2022, 14(9), 1952; https://doi.org/10.3390/v14091952 - 2 Sep 2022

Cited by 5 | Viewed by 2064

Abstract

Only two decades after discovering miRNAs, our understanding of the functional effects of deregulated miRNAs in the development of diseases, particularly cancer, has been rapidly evolving. These observations and functional studies provide the basis for developing miRNA-based diagnostic markers or new therapeutic strategies. Adenoviral (Ad) vectors belong to the most frequently used vector types in gene therapy and are suitable for strong short-term transgene expression in a variety of cells. Here, we report the set-up and functionality of an Ad-based miRNA vector platform that can be employed to deliver and express a high level of miRNAs efficiently. This vector platform allows fast and efficient vector production to high titers and the expression of pri-miRNA precursors under the control of a polymerase II promoter. In contrast to non-viral miRNA delivery systems, this Ad-based miRNA vector platform allows accurate dosing of the delivered miRNAs. Using a two-vector model, we showed that Ad-driven miRNA expression was sufficient in down-regulating the expression of an overexpressed and highly stable protein. Additional data corroborated the downregulation of multiple endogenous target RNAs using the system presented here. Additionally, we report some unanticipated synergistic effects on the transduction efficiencies in vitro when cells were consecutively transduced with two different Ad-vectors. This effect might be taken into consideration for protocols using two or more different Ad vectors simultaneously. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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Review

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21 pages, 1862 KiB

Open AccessReview

Gene Therapy for β-Hemoglobinopathies: From Discovery to Clinical Trials

by Eva Eugenie Rose Segura, Paul George Ayoub, Kevyn Lopez Hart and Donald Barry Kohn

Viruses 2023, 15(3), 713; https://doi.org/10.3390/v15030713 - 9 Mar 2023

Cited by 6 | Viewed by 6803

Abstract

Investigations to understand the function and control of the globin genes have led to some of the most exciting molecular discoveries and biomedical breakthroughs of the 20th and 21st centuries. Extensive characterization of the globin gene locus, accompanied by pioneering work on the utilization of viruses as human gene delivery tools in human hematopoietic stem and progenitor cells (HPSCs), has led to transformative and successful therapies via autologous hematopoietic stem-cell transplant with gene therapy (HSCT-GT). Due to the advanced understanding of the β-globin gene cluster, the first diseases considered for autologous HSCT-GT were two prevalent β-hemoglobinopathies: sickle cell disease and β-thalassemia, both affecting functional β-globin chains and leading to substantial morbidity. Both conditions are suitable for allogeneic HSCT; however, this therapy comes with serious risks and is most effective using an HLA-matched family donor (which is not available for most patients) to obtain optimal therapeutic and safe benefits. Transplants from unrelated or haplo-identical donors carry higher risks, although they are progressively improving. Conversely, HSCT-GT utilizes the patient’s own HSPCs, broadening access to more patients. Several gene therapy clinical trials have been reported to have achieved significant disease improvement, and more are underway. Based on the safety and the therapeutic success of autologous HSCT-GT, the U.S. Food and Drug Administration (FDA) in 2022 approved an HSCT-GT for β-thalassemia (Zynteglo™). This review illuminates the β-globin gene research journey, adversities faced, and achievements reached; it highlights important molecular and genetic findings of the β-globin locus, describes the predominant globin vectors, and concludes by describing promising results from clinical trials for both sickle cell disease and β-thalassemia. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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Other

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10 pages, 466 KiB

Open AccessCase Report

Clearance of Persistent SARS-CoV-2 RNA Detection in a NFκB-Deficient Patient in Association with the Ingestion of Human Breast Milk: A Case Report

by Janine S. Sabino, Mariene R. Amorim, William M. de Souza, Lia F. Marega, Luciana S. Mofatto, Daniel A. Toledo-Teixeira, Julia Forato, Rodrigo G. Stabeli, Maria Laura Costa, Fernando R. Spilki, Ester C. Sabino, Nuno R. Faria, Bruno D. Benites, Marcelo Addas-Carvalho, Raquel S. B. Stucchi, Dewton M. Vasconcelos, Scott C. Weaver, Fabiana Granja, José Luiz Proenca-Modena and Maria Marluce dos S. Vilela

Viruses 2022, 14(5), 1042; https://doi.org/10.3390/v14051042 - 13 May 2022

Cited by 1 | Viewed by 7162

Abstract

Currently, there are no evidence-based treatment options for long COVID-19, and it is known that SARS-CoV-2 can persist in part of the infected patients, especially those with immunosuppression. Since there is a robust secretion of SARS-CoV-2-specific highly-neutralizing IgA antibodies in breast milk, and because this immunoglobulin plays an essential role against respiratory virus infection in mucosa cells, being, in addition, more potent in neutralizing SARS-CoV-2 than IgG, here we report the clinical course of an NFκB-deficient patient chronically infected with the SARS-CoV-2 Gamma variant, who, after a non-full effective treatment with plasma infusion, received breast milk from a vaccinated mother by oral route as treatment for COVID-19. After such treatment, the symptoms improved, and the patient was systematically tested negative for SARS-CoV-2. Thus, we hypothesize that IgA and IgG secreted antibodies present in breast milk could be useful to treat persistent SARS-CoV-2 infection in immunodeficient patients. Full article

(This article belongs to the Special Issue The Application of Viruses to Biotechnology 2022)

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