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Viruses
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CRISPR/Cas in Viral Research 2024
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CRISPR/Cas in Viral Research 2024

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 (30 September 2024) | Viewed by 9878

Special Issue Editor

Dr. Shuliang Chen

E-Mail Website
Guest Editor
State Key Laboratory of Virology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
Interests: gene targeting; CRISPR-Cas; host genes; virus; antiviral strategy; hiv; crispr; SARS-CoV-2; HIV; Cas9; Cas12a; transient; RNP; HIV-host interaction; lentiviral vectors; TRIM5α; human immunodeficiency virus type 1 (HIV-1); C-peptide; miRNA

Special Issue Information

Dear Colleagues,

A decade ago, clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated proteins (Cas) were discovered and used for gene editing in mammalian cells. This revolutionary system has since found various applications in understanding, combating, and even engineering viruses. After that, many iterative gene targeting tools that reformed based on CRISPR/Cas have been widely developed, including base editor, prime editing, SHERLOCK, DETECTR, PAC-MAN, ABACAS, pfAGO, IscB proteins, OMEGA, and Fanzor et al. However, only a few of them have been used in viral research. In fact, these gene targeting tools would have played pivotal roles in several viral areas, such as viral genome editing, antiviral defense, viral pathogenesis, vaccine development, viral detection/diagnostics, viral evolution, and viral resistance. Overall, CRISPR/Cas has the potential to transform viral research by enabling precise genetic modifications, offering new insights into viral pathogenesis, and enhancing our ability to combat viral threats. As technology advances, CRISPR/Cas is expected to remain a key player in antiviral research, promising progress in the fight against infectious diseases. This Special Issue seeks to gather comprehensive research findings on CRISPR/Cas and related technologies in viral studies, encompassing all virus species. We welcome original research studies, methodologies, bioinformatics, and reviews related to the use of CRISPR/Cas in viral research.

Dr. Shuliang Chen
Guest Editor

Manuscript Submission Information

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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.

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

  • CRISPR/Cas
  • gene targeting and antiviral defense
  • viral genome editing
  • viral detection and diagnostic
  • viral pathogenesis
  • vaccine development and antiviral drug discovery
  • viral evolution

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Related Special Issues

Published Papers (4 papers)

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Research

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23 pages, 1995 KiB  
Article
Adapting Next-Generation Sequencing to in Process CRISPR-Cas9 Genome Editing of Recombinant AcMNPV Vectors: From Shotgun to Tiled-Amplicon Sequencing
by Madhuja Chakraborty, Lisa Nielsen, Delaney Nash, Jozef I. Nissimov, Trevor C. Charles and Marc G. Aucoin
Viruses 2025, 17(3), 437; https://doi.org/10.3390/v17030437 - 18 Mar 2025
Viewed by 369
Abstract
The alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most commonly used virus in the Baculovirus Expression Vector System (BEVS) and has been utilized for the production of many human and veterinary biologics. AcMNPV has a large dsDNA genome that [...] Read more.
The alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most commonly used virus in the Baculovirus Expression Vector System (BEVS) and has been utilized for the production of many human and veterinary biologics. AcMNPV has a large dsDNA genome that remains understudied, and relatively unmodified from the wild-type, especially considering how extensively utilized it is as an expression vector. Previously, our group utilized CRISPR-Cas9 genome engineering that revealed phenotypic changes when baculovirus genes are targeted using either co-expressed sgRNA or transfected sgRNA into a stable insect cell line that produced the Cas9 protein. Here, we describe a pipeline to sequence the recombinant AcMNPV expression vectors using shotgun sequencing, provide a set of primers for tiled-amplicon sequencing, show that untargeted baculovirus vector genomes remain relatively unchanged when amplified in Sf9-Cas9 cells, and confirm that AcMNPV gp64 gene disruption can minimize baculovirus contamination in cell cultures. Our findings provide a robust baseline for analyzing in process genome editing of baculoviruses. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research 2024)
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12 pages, 5227 KiB  
Article
On-Site and Visual Detection of the H5 Subtype Avian Influenza Virus Based on RT-RPA and CRISPR/Cas12a
by Xu Zhou, Siwen Wang, Yue Ma, Yongping Jiang, Yanbing Li, Jianzhong Shi, Guohua Deng, Guobin Tian, Huihui Kong and Xiurong Wang
Viruses 2024, 16(5), 753; https://doi.org/10.3390/v16050753 - 10 May 2024
Cited by 7 | Viewed by 2998
Abstract
Avian influenza viruses (AIVs) of the H5 subtype rank among the most serious pathogens, leading to significant economic losses in the global poultry industry and posing risks to human health. Therefore, rapid and accurate virus detection is crucial for the prevention and control [...] Read more.
Avian influenza viruses (AIVs) of the H5 subtype rank among the most serious pathogens, leading to significant economic losses in the global poultry industry and posing risks to human health. Therefore, rapid and accurate virus detection is crucial for the prevention and control of H5 AIVs. In this study, we established a novel detection method for H5 viruses by utilizing the precision of CRISPR/Cas12a and the efficiency of RT-RPA technologies. This assay facilitates the direct visualization of detection results through blue light and lateral flow strips, accurately identifying H5 viruses with high specificity and without cross-reactivity against other AIV subtypes, NDV, IBV, and IBDV. With detection thresholds of 1.9 copies/μL (blue light) and 1.9 × 103 copies/μL (lateral flow strips), our method not only competes with but also slightly surpasses RT-qPCR, demonstrating an 80.70% positive detection rate across 81 clinical samples. The RT-RPA/CRISPR-based detection method is characterized by high sensitivity, specificity, and independence from specialized equipment. The immediate field applicability of the RT-RPA/CRISPR approach underscores its importance as an effective tool for the early detection and management of outbreaks caused by the H5 subtype of AIVs. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research 2024)
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Review

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25 pages, 1700 KiB  
Review
Applications of CRISPR/Cas as a Toolbox for Hepatitis B Virus Detection and Therapeutics
by Anuj Kumar, Emmanuel Combe, Léa Mougené, Fabien Zoulim and Barbara Testoni
Viruses 2024, 16(10), 1565; https://doi.org/10.3390/v16101565 - 2 Oct 2024
Viewed by 3126
Abstract
Hepatitis B virus (HBV) infection remains a significant global health challenge, leading to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Covalently closed circular DNA (cccDNA) and integrated HBV DNA are pivotal in maintaining viral persistence. Recent advances in CRISPR/Cas technology offer innovative [...] Read more.
Hepatitis B virus (HBV) infection remains a significant global health challenge, leading to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Covalently closed circular DNA (cccDNA) and integrated HBV DNA are pivotal in maintaining viral persistence. Recent advances in CRISPR/Cas technology offer innovative strategies to inhibit HBV by directly targeting both cccDNA and integrated HBV DNA or indirectly by degrading HBV RNAs or targeting host proteins. This review provides a comprehensive overview of the latest advancements in using CRISPR/Cas to inhibit HBV, with a special highlight on newer non-double-strand (non-DSB) break approaches. Beyond the canonical use of CRISPR/Cas for target inhibition, we discuss additional applications, including HBV diagnosis and developing models to understand cccDNA biology, highlighting the diverse use of this technology in the HBV field. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research 2024)
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Other

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9 pages, 1226 KiB  
Brief Report
PfAgo-Based Zika Virus Detection
by Yuhao Chen, Xianyi Zhang, Xuan Yang, Lifang Su, Weiran Chen, Jixiang Zhao, Yunhong Hu, Yuan Wang, Ying Wu and Yanming Dong
Viruses 2024, 16(4), 539; https://doi.org/10.3390/v16040539 - 30 Mar 2024
Cited by 4 | Viewed by 2349
Abstract
As a mosquito-borne flavivirus, Zika virus (ZIKV) has been identified as a global health threat. The virus has been linked to severe congenital disabilities, including microcephaly and other congenital malformations, resulting in fatal intrauterine death. Therefore, developing sensitive and specific methods for the [...] Read more.
As a mosquito-borne flavivirus, Zika virus (ZIKV) has been identified as a global health threat. The virus has been linked to severe congenital disabilities, including microcephaly and other congenital malformations, resulting in fatal intrauterine death. Therefore, developing sensitive and specific methods for the early detection and accurate diagnosis of the ZIKV is essential for controlling its spread and mitigating its impact on public health. Herein, we set up a novel nucleic acid detection system based on Pyrococcus furiosus Argonaute (PfAgo)-mediated nucleic acid detection, targeting the non-structural protein 5 (NS5) region of the ZIKV genome (abbreviated ZIKV-PAND). Without preamplification with the polymerase chain reaction (PCR), the minimum detection concentration (MDC) of ZIKV-PAND was about 10 nM. When introducing an amplification step, the MDC can be dramatically decreased to the aM level (8.3 aM), which is comparable to qRT-PCR assay (1.6 aM). In addition, the diagnostic findings from the analysis of simulated clinical samples or Zika virus samples using ZIKV-PAND show a complete agreement of 100% with qRT-PCR assays. This correlation can aid in the implementation of molecular testing for clinical diagnoses and the investigation of ZIKV infection on an epidemiological scale. Full article
(This article belongs to the Special Issue CRISPR/Cas in Viral Research 2024)
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