Science & Technology

Fast and portable tests can diagnose COVID-19 and track variants

NIRVANA field test kit. Credit: Mo Li / KAUST

A field test called NIRVANA can detect and sequence at the same time SARS-CoV-2, Influenza and other viruses.

Clinicians using the new virus screening test can not only diagnose COVID-19 (new coronavirus infection) It only takes minutes on a portable pocket-sized machine, but you can also test for other viruses, such as the flu, which can be mistaken for a coronavirus. At the same time, they can sequence the virus and provide valuable information on the mutation and spread of COVID-19. The new test, named NIRVANA, was described online on March 31, 2021 by a multi-institutional team of journal scientists. Med..

“It’s a virus detection and monitoring method that doesn’t require expensive infrastructure like other approaches,” says Juan Carlos Izpisua Belmonte., Co-author and professor at Salk Institute for Biological Expressions. “One portable test can do the same thing as someone else using two or three different tests on different machines.”

Worldwide, more than 100 million people are infected with SARS-CoV-2, the virus that causes COVID-19. So far, an astonishing 500,000 Americans have died in COVID-19. Testing the population is the key to stopping the spread of the virus. In addition, it is important to track the spread of new SARS-CoV-2 mutants, some of which may respond differently to treatment or vaccine.

Today, the standard approach for determining whether a nasal swab is positive for COVID-19 is to perform a polymerase chain reaction (PCR) test to detect genetic material from the SARS-CoV-2 virus. is. However, if the sample is negative, the patient and clinician may be causing coronavirus-like symptoms unless they perform separate PCR tests with different swab samples for other viruses. Does not get information. Also, if the sample is SARS-CoV-2 positive, it will not learn the COVID-19 variant that the patient is infected with unless another series of tests is performed. They require large and expensive next-generation gene sequencing machines.

Juan Carlos Izpisua Belmonte and MoLi

From left: Juan Carlos Izpisua Belmonte and MoLi. Credit: Juan Carlos Izpisua Belmonte

Last summer, Mo Li, an assistant professor of biological sciences at King Abdullah University of Science and Technology in Saudi Arabia, was wondering how his expertise in genetic engineering and nanopore sequencing could be used to combat the COVID-19 pandemic. .. Lee, who previously spent six years as a Salk postdoctoral fellow at the Izpisua Belmonte Lab, found that a combination of a gene detection approach called isothermal recombinase polymerase amplification (RPA) and real-time nanopore sequencing was more useful, faster, cheaper, and now. More portable than the COVID-19 test approach. He worked with Izpisua Belmonte to investigate.

Unlike PCR, which circulates between low and high temperatures for separation DNA Strands and RPAs that copy them use proteins rather than temperature changes to achieve the same in just 20 minutes. This technique allows researchers to copy longer DNA and examine multiple genes at the same time.

“I quickly realized that I could use this technology to detect not only SARS-CoV-2, but other viruses at the same time,” says Li.

In a new treatise, Li and Izpisua Belmonte describe a small portable device that can simultaneously screen 96 samples using the RPA assay. They called the method NIRVANAnAnopore sequence ISothermal rBees vIlal aAmplification of nReal-time ears aanalysis. “

Scientists have designed NIRVANA to simultaneously test samples of COVID-19, influenza A, human adenovirus, and non-SARS-CoV-2 human coronavirus. In just 15 minutes, the researchers report, the device begins to report positive and negative results. And within 3 hours, the device confirms the results for all 96 samples. This includes a sequence of five regions of SARS-CoV-2 that tend to accumulate mutations leading to new variants, such as the B.1.1.7 variant identified in the United Kingdom. ..

Li and Izpisua Belmonte were found in 10 samples known to be SARS-CoV-2 positive, 60 samples with unknown SARS-CoV-2 status, and urban sewage samples containing the SARS-COV-2 virus. I tested NIRVANA. In all cases, the assay was able to correctly identify which virus was present. Sequencing data also allowed us to narrow down the origin of SARS-CoV-2 in positive samples. For example, differentiation of strains from China and Europe.

“The design of this assay is so flexible that it is not limited to the examples shown so far,” says Li. “We can easily adapt it to tackle another pathogen.

Researchers say the NIRVANA workflow is small in size and highly portable, so it can be used for rapid virus detection in schools, airports and ports. It can also be used to monitor wastewater or streams for the presence of new viruses.

“The pandemic provided two important lessons. One is to test broadly and quickly, and the other is to know variants. Our NIRVANA approach is not limited to current pandemics, but can occur in the future. We also offer a promising solution to these two challenges for pandemics, “said Izpisua Belmonte, Chair of Roger Guillemin at Salk. Belmonte needs market analysis to determine the initial cost of commercialization and whether the constant adjustment of tests needed to reliably detect new variants and new viruses of interest is worth it. I add that it will be.

Reference: Chongwei Bi, Gerardo Ramos-Mandujano, Yeteng Tian, ​​Sharif Hala, Jinna Xu, Sara Mfarrej “Simultaneous detection and mutation monitoring of SARS-CoV-2, and multiple respiratory viruses with rapid field deployable sequences” Co-infection “Concepcion Rodriguez Esteban, Estrella Nuñez Delicado, Fadwa S. Alofi, Asim Khogeer, Anwar M. Hashem, Naif AM Almontashiri, Arnab Pain, Juan Carlos Izpisua Belmonte, Mo Li, March 31, 2021 Med..
DOI: 10.1016 / j.medj.2021.03.015

In addition to Izpisua Belmonte and Li, the other author of this study was Salk’s Concepcion Rodriguez Esteban. King Abdulaziz University of Science and Technology (KAUST) Chongwei Bi, Gerargo Ramos-Mandujano, Sharis Hala, Jinna Xu, Sara Mfarrej, Yeteng Tian, ​​Arnab Pain; UCAM Universidad Católica San Antonio de Murcia Estrella Nunez Delicado; Anwar Hashem of Abdulaziz University. And Knife Almontashiri from Taibah University.

The work described in the current treatise was supported by a competitive research grant from King Abdullah University of Science and Technology.

Fast and portable tests can diagnose COVID-19 and track variants Fast and portable tests can diagnose COVID-19 and track variants

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