The Use of CRISPR-Cas Systems for Viral Detection: A Bibliometric Analysis and Systematic Review

Abstract

Viral infections impose a significant burden on global public health and the economy. This study examines the current state of CRISPR-Cas system research, focusing on their applications in viral detection and their evolution over recent years. A bibliometric analysis and systematic review were conducted using articles published between 2019 and 2024, retrieved from Web of Science, Scopus, and PubMed databases. Out of 2713 identified articles, 194 were included in the analysis. The findings reveal substantial growth in scientific output related to CRISPR-Cas systems, with the United States leading in research and development in this field. The rapid increase in CRISPR-Cas research during this period underscores its immense potential to transform viral diagnostics. With advantages such as speed, precision, and suitability for deployment in resource-limited settings, CRISPR-Cas systems outperform many traditional diagnostic methods. The concerted efforts of scientists worldwide further highlight the promising future of this technology. CRISPR-Cas systems are emerging as a powerful alternative, offering the possibility of expedited and accessible point-of-care testing and paving the way for more equitable and effective diagnostics on a global scale.

Keywords: CRISPR-Cas systems; bibliometric analysis; isothermal amplification; viral diagnostic assay.

Figure 1

PRISMA flow diagram.

Figure 2

The number of publications of the related documents from 2019 to 2024.

Figure 3

List of the most common viruses for which CRISPR-Cas-based diagnostic tests have been developed.

Figure 4

Top 10 productive journals on CRISPR-Cas systems for viral infection detection from 2019 to 2024.

Figure 5

Top 10 authors who published on CRISPR-Cas systems for viral infection detection from 2019 to 2024.

Figure 6

Global scientific production on CRISPR-Cas systems for viral infection detection from 2019 to 2024.

Figure 7

Top 10 productive institutions on CRISPR-Cas systems for viral infection detection from 2019 to 2024.

Figure 8

Keywords co-occurrence (n ≥ 5) clusters of CRISPR-Cas systems from 2019 to 2024 for viral infection detection, visualized by VOSviewer.

Figure 9

Authors’ collaboration network.

Figure 10

Citation counts of the top 10 most cited articles in the field of CRISPR-based viral detection [47,48,49,50,51,52,53,54,55,56].

Figure 11

Schematic illustration of the molecular mechanisms of CRISPR/Cas12 and CRISPR/Cas13 systems, highlighting their crRNA structure, target interaction, and cleavage behavior. Cas12 proteins bind to double-stranded DNA near a thymine-rich PAM sequence (e.g., TTN or TTTN), initiating an R-loop formation via crRNA–DNA hybridization. Once bound, Cas12 employs its RuvC domain to cleave both DNA strands, producing staggered cuts. In contrast, Cas13 targets single-stranded RNA sequences in a PAM-independent manner, requiring instead a protospacer flanking site (PFS), typically a non-G nucleotide. Upon target recognition, Cas13 becomes activated and initiates both the specific cleavage of the target RNA and non-specific collateral cleavage of surrounding ssRNA molecules. The crRNAs guiding Cas12 and Cas13 differ in size and structural organization, with Cas12 utilizing a mature crRNA of 42–44 nt (including a 21 nt direct repeat), while Cas13 uses a longer crRNA of 64–66 nt with a 28–30 nt direct repeat. The seed region in Cas12 is well defined (6–8 nt), while Cas13 lacks a strictly conserved seed sequence.

Figure 12

Simplified illustration of CRISPR-Cas12 and Cas13 detection workflows and signal readout strategies for nucleic acid diagnostics. (A) Amplification-dependent detection using CRISPR-Cas13 systems. DNA or RNA targets are first amplified (via RPA, LAMP, or PCR), then transcribed (for dsDNA) into ssRNA before Cas13-mediated detection. Cas13 exhibits trans collateral cleavage activity upon target recognition. (B) Amplification-dependent detection using CRISPR-Cas12 systems. DNA or cDNA is amplified and detected through Cas12-mediated cleavage activity. Cas12 recognizes target DNA via a specific PAM sequence and exhibits staggered cleavage. (C) Amplification-free strategies to enhance sensitivity. These include direct detection of viral nucleic acids by Cas12 or Cas13 without prior amplification, the use of multiple crRNAs (RNP multiplexing), ultrasensitive platforms (e.g., Digital CRISPR), signal amplification cascades, and post-signal enhancement techniques such as SERS biosensors. (D) CRISPR-based signal readout methods. The figure illustrates four commonly used detection strategies in CRISPR diagnostics: Fluorescence readout target recognition induces collateral cleavage and fluorescence signal; the green and grey curves represent the presence and absence of target, respectively. Lateral flow assays a visible band at the test line (T) indicates a positive result. Colorimetric detection AuNP aggregation produces a visible color change from yellow to red. Electrochemical biosensor signal detection is based on voltage/current changes in response to target recognition.