Special Issue "CRISPR/Cas in Viral Research"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viral Immunology, Vaccines, and Antivirals".

Deadline for manuscript submissions: closed (31 August 2021).

Special Issue Editors

Dr. Jiri Hejnar
E-Mail Website
Guest Editor
Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
Interests: avian sarcoma/leukosis viruses; epigenetic silencing of retroviruses; receptor for retroviruses; endogenous retroviruses; syncytins; retroviral vectors; retrotransposons; transgenesis in chicken
Special Issues and Collections in MDPI journals
Prof. Dr. Ben Berkhout
E-Mail Website
Guest Editor
Laboratory of Experimental Virology, Department of Medical Microbiology, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
Interests: virology; antiviral approaches; virus evolution; drug resistance
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

The recent breakthroughs in gene-editing methods using clustered regularly interspaced short palindromic repeats (CRISPR) combined with Cas9 nuclease and short guide RNAs (gRNA) have opened a new era in antiviral research. Briefly, just to mention a few relevant applications, both viral genomes and virus transcripts can become targets of CRISPR/Cas9-mediated cleavage and integrated virus copies can be precisely removed using CRISPR/Cas9 tools. Editing the genes of host dependency factors, e.g., receptors for virus entry, can provide invaluable models for virus research and drug screening or even virus-resistant livestock. CRISPR/Cas9 tools may help us to better understand HIV-1 latency and functional elimination of persistent reservoirs in HIV-infected patients. Last but not least, the urgent need for robust and rapid diagnostics could be met with CRISPR-based sensors of viral nucleic acids in the near future.

For this Special Issue, we invite submissions in the form of original research articles, validated methods, resource articles, or reviews that address any aspect of CRISPR-based strategies in basic viral research and innovative applications like diagnostics and antiviral therapies. This Special Issue will cover all kinds of viruses that infect plants, animals, or humans, and we especially welcome manuscripts relevant to the current SARS-CoV-2 outbreak. In summary, our aim is to present an inspiring collection of articles covering the vibrant field of CRISPR/Cas in viral research.

Dr. Jiri Hejnar
Prof. Dr. Ben Berkhout
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 papers will be 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 2200 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

  • gene editing
  • CRISPR/Cas
  • viral genomes
  • viral diagnostics
  • antiviral drug screening

Published Papers (3 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Article
A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gDPass
Viruses 2021, 13(8), 1574; https://doi.org/10.3390/v13081574 - 09 Aug 2021
Viewed by 458
Abstract
Herpesviruses are large DNA viruses, which encode up to 300 different proteins including enzymes enabling efficient replication. Nevertheless, they depend on a multitude of host cell proteins for successful propagation. To uncover cellular host factors important for replication of pseudorabies virus (PrV), an [...] Read more.
Herpesviruses are large DNA viruses, which encode up to 300 different proteins including enzymes enabling efficient replication. Nevertheless, they depend on a multitude of host cell proteins for successful propagation. To uncover cellular host factors important for replication of pseudorabies virus (PrV), an alphaherpesvirus of swine, we performed an unbiased genome-wide CRISPR/Cas9 forward screen. To this end, a porcine CRISPR-knockout sgRNA library (SsCRISPRko.v1) targeting 20,598 genes was generated and used to transduce porcine kidney cells. Cells were then infected with either wildtype PrV (PrV-Ka) or a PrV mutant (PrV-gDPass) lacking the receptor-binding protein gD, which regained infectivity after serial passaging in cell culture. While no cells survived infection with PrV-Ka, resistant cell colonies were observed after infection with PrV-gDPass. In these cells, sphingomyelin synthase 1 (SMS1) was identified as the top hit candidate. Infection efficiency was reduced by up to 90% for PrV-gDPass in rabbit RK13-sgms1KO cells compared to wildtype cells accompanied by lower viral progeny titers. Exogenous expression of SMS1 partly reverted the entry defect of PrV-gDPass. In contrast, infectivity of PrV-Ka was reduced by 50% on the knockout cells, which could not be restored by exogenous expression of SMS1. These data suggest that SMS1 plays a pivotal role for PrV infection, when the gD-mediated entry pathway is blocked. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research)
Show Figures

Figure 1

Article
An MHV-68 Mutator Phenotype Mutant Virus, Confirmed by CRISPR/Cas9-Mediated Gene Editing of the Viral DNA Polymerase Gene, Shows Reduced Viral Fitness
Viruses 2021, 13(6), 985; https://doi.org/10.3390/v13060985 - 26 May 2021
Viewed by 812
Abstract
Drug resistance studies on human γ-herpesviruses are hampered by the absence of an in vitro system that allows efficient lytic viral replication. Therefore, we employed murine γ-herpesvirus-68 (MHV-68) that efficiently replicates in vitro as a model to study the antiviral resistance of γ-herpesviruses. [...] Read more.
Drug resistance studies on human γ-herpesviruses are hampered by the absence of an in vitro system that allows efficient lytic viral replication. Therefore, we employed murine γ-herpesvirus-68 (MHV-68) that efficiently replicates in vitro as a model to study the antiviral resistance of γ-herpesviruses. In this study, we investigated the mechanism of resistance to nucleoside (ganciclovir (GCV)), nucleotide (cidofovir (CDV), HPMP-5azaC, HPMPO-DAPy) and pyrophosphate (foscarnet (PFA)) analogues and the impact of these drug resistance mutations on viral fitness. Viral fitness was determined by dual infection competition assays, where MHV-68 drug-resistant viral clones competed with the wild-type virus in the absence and presence of antivirals. Using next-generation sequencing, the composition of the viral populations was determined at the time of infection and after 5 days of growth. Antiviral drug resistance selection resulted in clones harboring mutations in the viral DNA polymerase (DP), denoted Y383SGCV, Q827RHPMP-5azaC, G302WPFA, K442TPFA, G302W+K442TPFA, C297WHPMPO-DAPy and C981YCDV. Without antiviral pressure, viral clones Q827RHPMP-5azaC, G302WPFA, K442TPFA and G302W+K442TPFA grew equal to the wild-type virus. However, in the presence of antivirals, these mutants had a growth advantage over the wild-type virus that was moderately to very strongly correlated with antiviral resistance. The Y383SGCV mutant was more fit than the wild-type virus with and without antivirals, except in the presence of brivudin. The C297W and C981Y changes were associated with a mutator phenotype and had a severely impaired viral fitness in the absence and presence of antivirals. The mutator phenotype caused by C297W in MHV-68 DP was validated by using a CRISPR/Cas9 genome editing approach. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research)
Show Figures

Figure 1

Article
A Crucial Role of ACBD3 Required for Coxsackievirus Infection in Animal Model Developed by AAV-Mediated CRISPR Genome Editing Technique
Viruses 2021, 13(2), 237; https://doi.org/10.3390/v13020237 - 03 Feb 2021
Cited by 1 | Viewed by 629
Abstract
Genetic screens using CRISPR/Cas9 have been exploited to discover host–virus interactions. These screens have identified viral dependencies on host proteins during their life cycle and potential antiviral strategies. The acyl-CoA binding domain containing 3 (ACBD3) was identified as an essential host factor for [...] Read more.
Genetic screens using CRISPR/Cas9 have been exploited to discover host–virus interactions. These screens have identified viral dependencies on host proteins during their life cycle and potential antiviral strategies. The acyl-CoA binding domain containing 3 (ACBD3) was identified as an essential host factor for the Coxsackievirus B3 (CVB3) infection. Other groups have also investigated the role of ACBD3 as a host factor for diverse enteroviruses in cultured cells. However, it has not been tested if ACBD3 is required in the animal model of CVB3 infection. Owing to embryonic lethality, conventional knockout mice were not available for in vivo study. As an alternative approach, we used adeno-associated virus (AAV)-mediated CRISPR genome editing to generate mice that lacked ACBD3 within the pancreas, the major target organ for CVB3. Delivery of sgRNAs using self-complementary (sc) AAV8 efficiently induced a loss-of-function mutation in the pancreas of the Cas9 knock-in mice. Loss of ACBD3 in the pancreas resulted in a 100-fold reduction in the CVB3 titer within the pancreas and a noticeable reduction in viral protein expression. These results indicate a crucial function of ACBD3 in CVB3 infection in vivo. AAV-mediated CRISPR genome editing may be applicable to many in vivo studies on the virus–host interaction and identify a novel target for antiviral therapeutics. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research)
Show Figures

Figure 1

Back to TopTop