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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats is a adaptive immune system found in bacteria and archaea that protects against viral infections. This system enables prokaryotic cells to identify, remember, and neutralize foreign genetic elements, primarily bacteriophages, by storing fragments of the invader’s DNA as a genetic memory.The CRISPR immune response begins during an initial infection. Cas (CRISPR-associated) proteins play a central role in this...
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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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Updated: Oct 18, 2025

DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning
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DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning

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Virus detection via programmable Type III-A CRISPR-Cas systems.

Sagar Sridhara1,2, Hemant N Goswami1, Charlisa Whyms3

  • 1Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.

Nature Communications
|September 28, 2021
PubMed
Summary
This summary is machine-generated.

A novel virus detection method utilizes the Type III-A CRISPR-Cas system for rapid, sensitive diagnostics. This system offers high accuracy for detecting SARS-CoV-2 without complex equipment.

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Virology

Background:

  • CRISPR-Cas systems offer rapid, sensitive virus detection without thermocyclers.
  • Type III-A CRISPR-Cas, an RNA-activated immune effector, has not been widely used for disease detection due to complex reconstitution.
  • Existing assays require thermocyclers, limiting point-of-care applications.

Purpose of the Study:

  • To develop and apply a novel virus detection method using an in vivo-reconstituted Type III-A CRISPR-Cas system.
  • To leverage the dual nucleic acid cleavage and signal amplification capabilities of Type III-A CRISPR-Cas for enhanced sensitivity.
  • To demonstrate the system's efficacy in detecting SARS-CoV-2.

Main Methods:

  • Construction of an in vivo-reconstituted Type III-A CRISPR-Cas system.
  • Harnessing RNA- and transcription-activated dual nucleic acid cleavage activities.
  • Utilizing internal signal amplification for enhanced detection.

Main Results:

  • The Type III-A system achieved 2000 copies/μl sensitivity in amplification-free detection of SARS-CoV-2.
  • Sensitivity reached 60 copies/μl with isothermal amplification within 30 minutes.
  • The method successfully diagnosed SARS-CoV-2-infected patients in both settings.

Conclusions:

  • The in vivo-reconstituted Type III-A CRISPR-Cas system provides a highly sensitive and rapid nucleic acid detection method.
  • Its flexible reaction conditions and amplification strategy offer broad applicability for various diagnostic settings.
  • This system presents a promising alternative to existing virus detection assays, potentially enabling point-of-care diagnostics.