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A special issue of Viruses (ISSN 1999-4915).

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 68832

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Dr. Eric O. Freed

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Director, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
Interests: HIV dynamics and replication
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Albert Bosch

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Enteric Virus Laboratory, Section Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, Avda. Diagonal 643, 08028 Barcelona, Spain
Interests: hepatitis A virus, astrovirus, norovirus, rotavirus, gastroenteritis agents, enteric hepatitis agents
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Special Issue Information

Dear Colleagues,

This Special Issue is related to the conference “Viruses 2020: Novel Concepts in Virology” which will be held in Barcelona, Spain, 5–7 February 2020.

Because of their global impact on human, animal, and plant health and their utility as tractable model systems, viruses continue to play a central role in all aspects of biomedical research, ranging from molecular and cell biology, structural biology, and immunology to evolution, epidemiology, and bioinformatics.

Symposium participants, as well as all researchers working in the field, are cordially invited to contribute original research papers or reviews to this Special Issue of Viruses.

Dr. Eric O. Freed
Dr. Albert Bosch
Guest Editors

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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.

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Published Papers (10 papers)

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Research

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12 pages, 968 KiB

Open AccessArticle

Nationwide Screening for Bee Viruses and Parasites in Belgian Honey Bees

by Severine Matthijs, Valérie De Waele, Valerie Vandenberge, Bénédicte Verhoeven, Jacqueline Evers, Marleen Brunain, Claude Saegerman, Paul J. J. De Winter, Stefan Roels, Dirk C. de Graaf and Nick De Regge

Viruses 2020, 12(8), 890; https://doi.org/10.3390/v12080890 - 14 Aug 2020

Cited by 14 | Viewed by 4763

Abstract

The health of honey bees is threatened by multiple factors, including viruses and parasites. We screened 557 honey bee (Apis mellifera) colonies from 155 beekeepers distributed all over Belgium to determine the prevalence of seven widespread viruses and two parasites (Varroa sp. and Nosema sp.). Deformed wing virus B (DWV-B), black queen cell virus (BQCV), and sacbrood virus (SBV) were highly prevalent and detected by real-time RT-PCR in more than 95% of the colonies. Acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV) and deformed wing virus A (DWV-A) were prevalent to a lower extent (between 18 and 29%). Most viruses were only present at low or moderate viral loads. Nevertheless, about 50% of the colonies harbored at least one virus at high viral load (>10⁷ genome copies/bee). Varroa mites and Nosema sp. were found in 81.5% and 59.7% of the honey bee colonies, respectively, and all Nosema were identified as Nosema ceranae by real time PCR. Interestingly, we found a significant correlation between the number of Varroa mites and DWV-B viral load. To determine the combined effect of these and other factors on honey bee health in Belgium, a follow up of colonies over multiple years is necessary. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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13 pages, 1929 KiB

Open AccessArticle

BKTyper: Free Online Tool for Polyoma BK Virus VP1 and NCCR Typing

by Joan Martí-Carreras, Olga Mineeva-Sangwo, Dimitrios Topalis, Robert Snoeck, Graciela Andrei and Piet Maes

Viruses 2020, 12(8), 837; https://doi.org/10.3390/v12080837 - 31 Jul 2020

Cited by 7 | Viewed by 4655

Abstract

Human BK polyomavirus (BKPyV) prevalence has been increasing due to the introduction of more potent immunosuppressive agents in transplant recipients, and its clinical interest. BKPyV has been linked mostly to polyomavirus-associated hemorrhagic cystitis, in allogenic hematopoietic stem cell transplant, and polyomavirus-associated nephropathy in kidney transplant patients. BKPyV is a circular double-stranded DNA virus that encodes for seven proteins, of which Viral Protein 1 (VP1), the major structural protein, has been extensively used for genotyping. BKPyV also contains the noncoding control region (NCCR), configured by five repeat blocks (OPQRS) known to be highly repetitive and diverse, and linked to viral infectivity and replication. BKPyV genetic diversity has been mainly studied based on the NCCR and VP1, due to the high occurrence of BKPyV-associated diseases in transplant patients and their clinical implications. Here BKTyper is presented, a free online genotyper for BKPyV, based on a VP1 genotyping and a novel algorithm for NCCR block identification. VP1 genotyping is based on a modified implementation of the BK typing and grouping regions (BKTGR) algorithm, providing a maximum-likelihood phylogenetic tree using a custom internal BKPyV database. Novel NCCR block identification relies on a minimum of 12-bp motif recognition and a novel sorting algorithm. A graphical representation of the OPQRS block organization is provided. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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19 pages, 3825 KiB

Open AccessArticle

Divergent Traits and Ligand-Binding Properties of the Cytomegalovirus CD48 Gene Family

by Pablo Martínez-Vicente, Domènec Farré, Pablo Engel and Ana Angulo

Viruses 2020, 12(8), 813; https://doi.org/10.3390/v12080813 - 28 Jul 2020

Cited by 2 | Viewed by 2718

Abstract

The genesis of gene families by the capture of host genes and their subsequent duplication is a crucial process in the evolution of large DNA viruses. CD48 is a cell surface molecule that interacts via its N-terminal immunoglobulin (Ig) domain with the cell surface receptor 2B4 (CD244), regulating leukocyte cytotoxicity. We previously reported the presence of five CD48 homologs (vCD48s) in two related cytomegaloviruses, and demonstrated that one of them, A43, binds 2B4 and acts as a soluble CD48 decoy receptor impairing NK cell function. Here, we have characterized the rest of these vCD48s. We show that they are highly glycosylated proteins that display remarkably distinct features: divergent biochemical properties, cellular locations, and temporal expression kinetics. In contrast to A43, none of them interacts with 2B4. Consistent with this, molecular modeling of the N-terminal Ig domains of these vCD48s evidences notable changes as compared to CD48, suggesting that they interact with alternative targets. Accordingly, we demonstrate that one of them, S30, tightly binds CD2, a crucial T- and NK-cell adhesion and costimulatory molecule. Thus, our findings show how a key host immune receptor gene captured by a virus can be subsequently remodeled to evolve new immunoevasins with altered binding properties. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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9 pages, 1496 KiB

Open AccessArticle

Transport of Phage in Melon Plants and Inhibition of Progression of Bacterial Fruit Blotch

by Aryan Rahimi-Midani and Tae-Jin Choi

Viruses 2020, 12(4), 477; https://doi.org/10.3390/v12040477 - 23 Apr 2020

Cited by 14 | Viewed by 4583

Abstract

Bacterial fruit blotch (BFB) is an economically important disease in melons and watermelons for which no effective control method is available. Application of phytobacterium-infecting phage has been evaluated as an alternative means of preventing bacterial diseases in plants. Coating of seeds with bacteriophages infecting Acidovorax citrulli, the causal agent of BFB, is effective for controlling the disease, as shown in our previous study. We evaluated the transport of bacteriophage ACPWH from soil to the leaves of melon plants, and we also evaluated its effect on BFB. Leaves of melon plants were spray-inoculated with A. citrulli, and bacteriophage ACPWH was added to soil after symptoms had developed. ACPWH was detected by PCR in foliar tissue 8 h after addition to soil. DAPI-stained ACPWH accumulated at the leaf tip after 24 h. Melon treated with ACPWH showed 27% disease severity, compared to 80% for the non-treated control, indicating that ACPWH can be used to control BFB. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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13 pages, 963 KiB

Open AccessArticle

Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology

by Laurence Thirion, Audrey Dubot-Peres, Laura Pezzi, Iban Corcostegui, Mhammed Touinssi, Xavier de Lamballerie and Remi N. Charrel

Viruses 2020, 12(2), 159; https://doi.org/10.3390/v12020159 - 30 Jan 2020

Cited by 16 | Viewed by 5263

Abstract

Real-time molecular techniques have become the reference methods for direct diagnosis of pathogens. The reduction of steps is a key factor in order to decrease the risk of human errors resulting in invalid series and delayed results. We describe here a process of preparation of oligonucleotide primers and hydrolysis probe in a single tube at predefined optimized concentrations that are stabilized via lyophilization (Lyoph-P&P). Lyoph-P&P was compared versus the classic protocol using extemporaneously prepared liquid reagents using (i) sensitivity study, (ii) long-term stability at 4 °C, and (iii) long-term stability at 37 °C mimicking transportation without cold chain. Two previously published molecular assays were selected for this study. They target two emerging viruses that are listed on the blueprint of the WHO as to be considered for preparedness and response actions: chikungunya virus (CHIKV) and Rift Valley fever phlebovirus (RVFV). Results of our study demonstrate that (i) Lyoph-P&P is stable for at least 4 days at 37 °C supporting shipping without the need of cold chain, (ii) Lyoph-P&P rehydrated solution is stable at +4 °C for at least two weeks, (iii) sensitivity observed with Lyoph-P&P is at least equal to, often better than, that observed with liquid formulation, (iv) validation of results observed with low-copy specimens is rendered easier by higher fluorescence level. In conclusion, Lyoph-P&P holds several advantages over extemporaneously preparer liquid formulation that merit to be considered when a novel real-time molecular assay is implemented in a laboratory in charge of routine diagnostic activity. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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15 pages, 3493 KiB

Open AccessArticle

Ts2631 Endolysin from the Extremophilic Thermus scotoductus Bacteriophage vB_Tsc2631 as an Antimicrobial Agent against Gram-Negative Multidrug-Resistant Bacteria

by Magdalena Plotka, Malgorzata Kapusta, Sebastian Dorawa, Anna-Karina Kaczorowska and Tadeusz Kaczorowski

Viruses 2019, 11(7), 657; https://doi.org/10.3390/v11070657 - 18 Jul 2019

Cited by 53 | Viewed by 5743

Abstract

Bacteria that thrive in extreme conditions and the bacteriophages that infect them are sources of valuable enzymes resistant to denaturation at high temperatures. Many of these heat-stable proteins are useful for biotechnological applications; nevertheless, none have been utilized as antibacterial agents. Here, we demonstrate the bactericidal potential of Ts2631 endolysin from the extremophilic bacteriophage vB_Tsc2631, which infects Thermus scotoductus, against the alarming multidrug-resistant clinical strains of Acinetobacter baumannii, Pseudomonas aeruginosa and pathogens from the Enterobacteriaceae family. A 2–3.7 log reduction in the bacterial load was observed in antibacterial tests against A. baumannii and P. aeruginosa after 1.5 h. The Ts2631 activity was further enhanced by ethylenediaminetetraacetic acid (EDTA), a metal ion chelator (4.2 log reduction in carbapenem-resistant A. baumannii) and, to a lesser extent, by malic acid and citric acid (2.9 and 3.3 log reductions, respectively). The EDTA/Ts2631 combination reduced all pathogens of the Enterobacteriaceae family, particularly multidrug-resistant Citrobacter braakii, to levels below the detection limit (>6 log); these results indicate that Ts2631 endolysin could be useful to combat Gram-negative pathogens. The investigation of A. baumannii cells treated with Ts2631 endolysin variants under transmission electron and fluorescence microscopy demonstrates that the intrinsic antibacterial activity of Ts2631 endolysin is dependent on the presence of its N-terminal tail. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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Review

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37 pages, 2367 KiB

Open AccessReview

The Multiple Roles of Hepatitis B Virus X Protein (HBx) Dysregulated MicroRNA in Hepatitis B Virus-Associated Hepatocellular Carcinoma (HBV-HCC) and Immune Pathways

by Kurt Sartorius, Leo Swadling, Ping An, Julia Makarova, Cheryl Winkler, Anil Chuturgoon and Anna Kramvis

Viruses 2020, 12(7), 746; https://doi.org/10.3390/v12070746 - 10 Jul 2020

Cited by 32 | Viewed by 5555

Abstract

Currently, the treatment of hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC) [HBV-HCC] relies on blunt tools that are unable to offer effective therapy for later stage pathogenesis. The potential of miRNA to treat HBV-HCC offer a more targeted approach to managing this lethal carcinoma; however, the complexity of miRNA as an ancillary regulator of the immune system remains poorly understood. This review examines the overlapping roles of HBx-dysregulated miRNA in HBV-HCC and immune pathways and seeks to demonstrate that specific miRNA response in immune cells is not independent of their expression in hepatocytes. This interplay between the two pathways may provide us with the possibility of using candidate miRNA to manipulate this interaction as a potential therapeutic option. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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44 pages, 1185 KiB

Open AccessReview

Challenges in Laboratory Diagnosis of the Novel Coronavirus SARS-CoV-2

by Nadin Younes, Duaa W. Al-Sadeq, Hadeel AL-Jighefee, Salma Younes, Ola Al-Jamal, Hanin I. Daas, Hadi. M. Yassine and Gheyath K. Nasrallah

Viruses 2020, 12(6), 582; https://doi.org/10.3390/v12060582 - 26 May 2020

Cited by 285 | Viewed by 24913

Abstract

The recent outbreak of the Coronavirus disease 2019 (COVID-19) has quickly spread worldwide since its discovery in Wuhan city, China in December 2019. A comprehensive strategy, including surveillance, diagnostics, research, clinical treatment, and development of vaccines, is urgently needed to win the battle against COVID-19. The past three unprecedented outbreaks of emerging human coronavirus infections at the beginning of the 21st century have highlighted the importance of readily available, accurate, and rapid diagnostic technologies to contain emerging and re-emerging pandemics. Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) based assays performed on respiratory specimens remain the gold standard for COVID-19 diagnostics. However, point-of-care technologies and serologic immunoassays are rapidly emerging with high sensitivity and specificity as well. Even though excellent techniques are available for the diagnosis of symptomatic patients with COVID-19 in well-equipped laboratories; critical gaps still remain in screening asymptomatic people who are in the incubation phase of the virus, as well as in the accurate determination of live viral shedding during convalescence to inform decisions for ending isolation. This review article aims to discuss the currently available laboratory methods and surveillance technologies available for the detection of COVID-19, their performance characteristics and highlight the gaps in current diagnostic capacity, and finally, propose potential solutions. We also summarize the specifications of the majority of the available commercial kits (PCR, EIA, and POC) for laboratory diagnosis of COVID-19. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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23 pages, 2834 KiB

Open AccessReview

The Interplay between HIV-1 Gag Binding to the Plasma Membrane and Env Incorporation

by R. Elliot Murphy and Jamil S. Saad

Viruses 2020, 12(5), 548; https://doi.org/10.3390/v12050548 - 16 May 2020

Cited by 20 | Viewed by 5575

Abstract

Advancement in drug therapies and patient care have drastically improved the mortality rates of HIV-1 infected individuals. Many of these therapies were developed or improved upon by using structure-based techniques, which underscore the importance of understanding essential mechanisms in the replication cycle of HIV-1 at the structural level. One such process which remains poorly understood is the incorporation of the envelope glycoprotein (Env) into budding virus particles. Assembly of HIV particles is initiated by targeting of the Gag polyproteins to the inner leaflet of the plasma membrane (PM), a process mediated by the N-terminally myristoylated matrix (MA) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂). There is strong evidence that formation of the Gag lattice on the PM is a prerequisite for the incorporation of Env into budding particles. It is also suggested that Env incorporation is mediated by an interaction between its cytoplasmic tail (gp41CT) and the MA domain of Gag. In this review, we highlight the latest developments and current efforts to understand the interplay between gp41CT, MA, and the membrane during assembly. Elucidation of the molecular determinants of Gag–Env–membrane interactions may help in the development of new antiviral therapeutic agents that inhibit particle assembly, Env incorporation and ultimately virus production. Full article

(This article belongs to the Special Issue Novel Concepts in Virology)

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Other

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7 pages, 194 KiB

Open AccessCommentary

Phages Needed against Resistant Bacteria

by Karin Moelling

Viruses 2020, 12(7), 743; https://doi.org/10.3390/v12070743 - 10 Jul 2020

Cited by 2 | Viewed by 2712

Abstract

Phages have been known for more than 100 years. They have been applied to numerous infectious diseases and have proved to be effective in many cases. However, they have been neglected due to the era of antibiotics. With the increase of antibiotic-resistant microorganisms, we need additional therapies. Whether or not phages can fulfill this expectation needs to be verified and tested according to the state-of-the-art of international regulations. These regulations fail, however, with respect to GMP production of phages. Phages are biologicals, not chemical compounds, which cannot be produced under GMP regulations. This needs to be urgently changed to allow progress to determine how phages can enter routine clinical settings. Full article

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