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Next-Generation Rapid Advanced Molecular Diagnostics of COVID-19 by CRISPR-Cas

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Diagnostic Strategies for COVID-19 and other Coronaviruses

Part of the book series: Medical Virology: From Pathogenesis to Disease Control ((MVPDC))

Abstract

The world is looking towards the development of early diagnosis, treatment, and prevention of Coronavirus disease (COVID-19) caused by SARS-CoV-2 in order to restrict its rapid transmission and mortality among the human population. Globally, more than 5 million cases have been reported with 0.3 million deaths by the end of May 2020. Currently, the World Health Organization (WHO) adopted the screening and diagnosis of SARS-CoV-2 infection with quantitative RT-PCR (qRT-PCR)-based kits; however, the suitability of such kits is restricted due to the requirement of specialized instruments, well-trained personnel, and unavailability in resource-limited areas. The CRISPR-Cas system has recently emerged as a versatile tool for medical research for gene editing, epigenetic control, and disease diagnosis. The use of CRISPR-Cas-based detection of SARS-CoV-2 infection may results in the development of rapid, affordable, and multiplexed point-of-care diagnostic system with high specificity and sensitivity. In this article, we have covered the CRISPR-Cas-based efficient techniques developed for the diagnosis of the SARS-CoV-2 and their suitability for COVID-19 surveillance.

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Abbreviations

CARMEN:

Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids

Cas:

CRISPR-associated proteins

CASLFA:

Clustered Regularly Interspaced Short Palindromic Repeats/Cas9-Mediated Lateral Flow Nucleic Acid Assay

COVID-19:

Coronavirus disease

CRISPR:

Clustered regularly interspaced short palindromic repeats

dCas9:

Nuclease-deactivated Cas9

FELUDA:

FnCas9 Editor-Linked Uniform Detection Assay

FnCas9:

Francisella novicida Cas9

HEPN:

Higher eukaryotes and prokaryotes nucleotide-binding domain

HOLMES:

One-hour low-cost multipurpose highly efficient system

HUDSON:

Heating unextracted diagnostic samples to obliterate nucleases

LAMP:

Loop-mediated isothermal amplification

NASBACC:

Nucleic acid sequence-based amplification-CRISPR cleavage

NHEJ:

Non-homologous end joining

Nsp:

Non-structural proteins

PAM:

Protospacer adjacent motif

PC:

Paired dCas9

RCA:

Rolling circle amplification

RCH:

RCA-CRISPR-split-HRP

RPA:

Recombinase polymerase amplification

RT-qPCR:

Quantitative polymerase chain reaction

SARS-CoV-2:

Severe Acute Respiratory Syndrome Coronavirus 2

sgRNA:

Single guide RNA

SHERLOCK:

Specific high sensitivity enzymatic reporter unlocking

SpCas9:

Streptococcus pyogenes Cas9

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Authors and Affiliations

  1. Amity Institute of Virology & Immunology, Amity University Uttar Pradesh, Noida, India

    Ashish Srivastava & Taruna Gupta

  2. Centre for Advanced Research (CFAR), Faculty of Medicine, King George’s Medical University (KGMU), Lucknow, India

    Swatantra Kumar & Shailendra K. Saxena

Authors
  1. Ashish Srivastava
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  2. Taruna Gupta
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  3. Swatantra Kumar
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  4. Shailendra K. Saxena
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Corresponding author

Correspondence to Shailendra K. Saxena .

Editor information

Editors and Affiliations

  1. School of Biochemical Engineering, Indian Institute of Technology, Varanasi, India

    Pranjal Chandra

  2. Division of Oncology, Stanford Medicine, California, CA, USA

    Sharmili Roy

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Srivastava, A., Gupta, T., Kumar, S., Saxena, S.K. (2020). Next-Generation Rapid Advanced Molecular Diagnostics of COVID-19 by CRISPR-Cas. In: Chandra, P., Roy, S. (eds) Diagnostic Strategies for COVID-19 and other Coronaviruses. Medical Virology: From Pathogenesis to Disease Control. Springer, Singapore. https://doi.org/10.1007/978-981-15-6006-4_9

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