Researchers at the University of California San Diego have combined experts from molecular genetics, chemistry and health sciences to develop rapid diagnostic technology that detects SARS-CoV-2, the coronavirus that causes COVID-19.
The new SENSR (Sensitive Enzymatic Nucleic Acid Sequence Reporter), which is described in an article published in the journal ACS Sensors, is based on CRISPR gene editing technology, which enables rapid detection of pathogens by identifying genetic sequences in their DNA or RNA enables.
Many human pathogens are currently being detected using a method known as the real-time polymerase chain reaction. Although very accurate and sensitive, such diagnoses are time consuming and require special laboratory equipment, which limits their use to healthcare and specialized facilities. SENSR was developed to simplify the SARS-CoV-2 detection process with the aim of adapting it for home use.
While the Cas9 enzyme has been used extensively in CRISPR genetic engineering research, recently scientists have used other enzymes such as Cas12a and Cas13a to develop high-precision CRISPR-based diagnostics. SENSR was developed in a similar way and is the first SARS-CoV-2 diagnostic to use the Cas13d enzyme (specifically a ribonuclease effector called “CasRx”).
The researchers believe that any Cas enzymes that may or may not complement existing systems should be studied in order to maximize CRISPR’s capabilities and expand the genetic diagnostic pipeline.
CRISPR has greatly improved our ability to quickly identify infected people, providing point-of-care testing in resource-poor environments that was not previously possible. SENSR continues to open the toolbox for CRISPR diagnostic systems and will help identify emerging pathogens before they become pandemics. “
Omar Akbari, lead study author, professor of biological sciences, UC San Diego
In developing SENSR, Akbari’s Molecular Genetics Laboratory worked with Professor Elizabeth Komives’ laboratory in the Department of Chemistry and Biochemistry (Division of Physical Sciences) to purify SENSR proteins, and Rob Knight’s laboratory in the Department of Pediatrics (School of Medicine and Center for Microbiome Innovation) to test SARS-CoV-2 samples.
SENSR is one of the latest developments in UC San Diego’s innovative approach to combating the COVID-19 pandemic. The university’s nationally recognized science-based return to learn strategy for campus safety includes Knight’s groundbreaking wastewater screening program, which enabled the early detection of 85% of COVID-19 cases on campus. With nearly 10,000 students on campus in the current academic year, the Return to Learn program strategy, which includes high vaccination rates, has resulted in a COVID-19 case rate of less than 1% and has become a model for other academic institutions.
Early tests in SENSR’s development showed detection of SARS-CoV-2 in less than an hour. The researchers note in the paper that further development is needed, but the technology has the potential to become “powerful molecular diagnostics with numerous applications”.
After all, Akbari believes that SENSR will become important in places like airports so that passengers can quickly determine if they may be carrying a virus.
“We need to continue innovating in the area of detection and protection to develop more tools so that in another pandemic we will have scalable point-of-care diagnostic systems for rapid distribution,” said Akbari.
The paper, published in ACS Sensors, brought together a mix of UC San Diego PhD students, postdocs, project scientists, and faculty members. These include: Daniel Brogan, Duverney Chaverra-Rodriguez, Calvin Lin, Andrea Smidler, Ting Yang, Lenissa Alcantara, Junru Liu, Robyn Raban, Pedro Belda-Ferre, Rob Knight, Elizabeth Komives and Omar Akbari. Igor Antoshechkin from CalTech is also a co-author.
Research funding was provided by: the UC San Diego Seed Funds for Emergent COVID-19 Related Research; a Directors New Innovator Award from the National Institutes of Health / National Institute of Allergy and Infectious Diseases (NIH / NIAID) (DP2 AI152071-01 and R21 (1R21AI149161), a DARPA Safe Genes Program Grant (HR0011-17-2-0047) ; a Director’s Pioneer Award from the National Center for Complementary and Integrative Health (DP1 AT010885), the Molecular Biophysics Training Grant from the NIH (T32 GM00832), the Return to Learn program from UC San Diego via the EXCITE laboratory (EXpedited COVID-19 Identification Environment); and the Molecular Biophysics Training Grant, NIH Grant (T32 GM00832).
Source:
University of California San Diego
Journal reference:
Brogan, DJ, et al. (2021) Development of a fast and sensitive CasRx-based diagnostic assay for SARS-CoV-2. ACS sensors. doi.org/10.1021/acssensors.1c01088.
