New COVID-19 Saliva Test Is Born in Columbia Fertility Clinic
Researchers at the Columbia University Fertility Center have developed a rapid, one-step diagnostic test that detects SARS-CoV-2, the virus that causes COVID-19, in samples of saliva. The test has a single tube that contains all of the materials needed to provide reliable results in about 30 minutes.
Unlike commercially available tests, the new saliva test does not require expensive instruments or proprietary components.
The test was adapted from technology currently used by Columbia fertility experts to look for genetic abnormalities in embryos prior to implantation.
"This technology was initially developed to make a real difference to our fertility clinic patients, who need rapid, reliable test results to determine the next steps in their fertility treatment," says Zev Williams, MD, the Wendy D. Havens Associate Professor of Women's Health and chief of the division of reproductive endocrinology at Columbia University Irving Medical Center. "We realized that the same technology that we use to help create lives could be repurposed to help save lives during the COVID-19 pandemic. The test serves a critical need for more widespread testing to help us safely reopen economies closed by the pandemic and prevent future outbreaks."
Current diagnostic tests for COVID-19 that detect viral RNA must be shipped to a reference laboratory unless the facility collecting the samples has purchased costly and proprietary machinery and cartridges to extract the virus's RNA from the fluid in which the sample — either a nasopharyngeal swab or saliva — is placed.
The new test eliminates the extraction step and simplifies processing. Saliva is collected in a cup and then placed into a tube containing enzymes and reagents that detect the virus's RNA. The tube is then placed into a water bath or heat block to keep the sample warm throughout the reaction. Within 30 minutes, the fluid in the tube turns yellow if the virus's RNA is present and red if the virus isn't present.
Technology overcomes obstacles of testing in saliva
The new test is based on a well-known DNA amplification technique called loop-mediated isothermal amplification (LAMP), which has several advantages for point-of-care testing for SARS-CoV-2. While the traditional polymerase chain reaction (PCR) methodology used to amplify DNA requires a costly and complex thermocycler (a machine that changes temperature during different steps of the process), the LAMP test is performed at a single temperature, so it can be processed using only a heat block or water bath. In addition, the test result can be seen with the unaided eye using colorimetry.
Compounds found in saliva, and the usual buffers, enzymes, and detergents added during LAMP processing, reduce the sensitivity of the tests. Williams and his team found that alternate buffers and enzymes — along with modifications to the chemicals that recognize the virus — dramatically improved the test's sensitivity in saliva.
The new test is >1000 times more sensitive than the traditional LAMP test in saliva. The test is based on the researchers' previous LAMP test that detects the SARS-CoV-2 virus in nasal swabs. Similar to the saliva test, the nasal swab test detects the virus's RNA directly from the transport media (the fluid in which the swab is placed before processing) in one step and does not require expensive instruments or proprietary components.
New test is reliable, scalable
Williams and other researchers at CUIMC tested the LAMP saliva assay in 60 samples, including 30 samples with virus and 30 without, and in samples from 18 patients whose saliva was also tested using RNA extraction and RT-PCR.
Their study showed that the new test correctly identified all of the negative samples that also tested negative with the Roche 6800 PCR system, resulting in 100% specificity. The test also correctly identified 29 out of 30 positive samples, resulting in overall sensitivity (a measure of a test's ability to capture positive results) of 97% with no cross-reactivity with 19 other viruses and bacteria known to cause respiratory illness — including other coronaviruses.
The new test can detect as few as 1 or 2 copies of the virus in a microliter of saliva. Using traditional LAMP assays, even hundreds of copies of the virus wouldn't be detected.
Williams and his team are currently seeking regulatory approval to begin using this test with patients.
"To help stem future outbreaks, diagnostic testing must be widespread and frequent. The tests themselves need to be rapid and easy to use in the field," says Williams.
"Once we obtain regulatory approval, we envision the test being used to screen people before they board an airplane, visit a nursing home, or go to school or summer camp," continues Williams. "The test could also be a more affordable option for health care facilities in developing countries where outbreaks have overwhelmed their testing and logistical capabilities."
The research appeared in a paper titled “Field-deployable, rapid and direct diagnostic testing of saliva samples for SARS-CoV-2,” in MedRxiv on June 16, 2020.
Other authors (all from Columbia University Irving Medical Center) are Shan Wei, Esther Kohl, Alexandre Djandji, Stephanie Morgan, Susan Whittier, Mahesh Mansukhani, Raymond Yeh, Eldad Hod, Juan Carlos Alejandre, Elaine Fleck, Mary D’Alton, and Yousin Suh.
This study is supported by grants from the National Institutes of Health (R01HD100013, R01HD086327, 1RF1AG057341, and R01AG057433).