FELUDA: India’s first CRISPR Covid-19 test

Context: The Tata CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) test, powered by CSIR-IGIB (Institute of Genomics and Integrative Biology), FELUDA, received regulatory approvals from the Drug Controller General of India (DCGI) for commercial launch.

Analysis

  • The indigenous test has high quality benchmarks with very high sensitivity and specificity for detecting the novel coronavirus.
  • This test uses an indigenously developed, cutting-edge CRISPR technology for detection of the genomic sequence of SARS-CoV-2 virus.
  • CRISPR is a genome editing technology to diagnosing diseases.
  • The Tata CRISPR test is the world’s first diagnostic test to deploy a specially adapted Cas9 protein to successfully detect the virus causing Covid-19.

CRISPR/Cas9

  • CRISPR/Cas9 is a simple but powerful gene-editing technology that can be harnessed to modify, delete or correct disease-causing abnormalities at their genetic sources.
  • CRISPR refers to Clustered Regularly Interspaced Short Palindromic Repeats of genetic information, which some bacterial species use as an antiviral mechanism in combination with the Cas9 enzyme.
  • Cas9 – a CRISPR-Associated endonuclease – acts as “molecular scissors” to cut DNA at a specific location and inserts a foreign piece of DNA to correct the mutation that causes the disease.
  • However, in addition to binding to the intended target on the DNA, the commonly used Cas9 protein from Strepotococcus pyogenes bacteria (SpCas9) and its engineered derivative tend to potentially bind to DNA at multiple unintended sites thereby leading to unnecessary alterations in the DNA.
  • The Cas9 protein is supposed to bind to the DNA only when there is a perfect match between the DNA and the protein, thus reducing the chances of the protein binding at non-target sites on the DNA.
  • But even when three mismatches exist between the protein and the DNA, the currently used SpCas9 protein binds and cleaves the DNA.
  • In contrast, the new FnCas9 protein, derived from a bacterium — Francisella novicida, showed negligible binding when there exists more than one mismatch in the target DNA.
  • The high specificity of the new FnCas9 protein arises due to reduced affinity to bind to DNA when there is even a single mismatch.

Sensitivity Vs Specificity

  • Sensitivity measures how often a test correctly generates a positive result for people who have the condition that’s being tested for (also known as the “true positive” rate).
  • A test that’s highly sensitive will flag almost everyone who has the disease and not generate many false-negative results.
  • Example: a test with 90% sensitivity will correctly return a positive result for 90% of people who have the disease, but will return a negative result — a false-negative — for 10% of the people who have the disease and should have tested positive.
  • Specificity measures a test’s ability to correctly generate a negative result for people who don’t have the condition that’s being tested for (also known as the “true negative” rate).
  • A high-specificity test will correctly rule out almost everyone who doesn’t have the disease and won’t generate many false-positive results.
  • Example: a test with 90% specificity will correctly return a negative result for 90% of people who don’t have the disease, but will return a positive result — a false-positive — for 10% of the people who don’t have the disease and should have tested negative.

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