A New COVID-19 Testing Method

An improved testing method in development at NYU Abu Dhabi could help better understand and curb the spread of COVID-19.

Researchers at NYUAD are working on developing a COVID-19 testing method that could prove to be at least 100 times more sensitive than the gold standard commonly used around the world today. The improved testing method could also help better understand and curb the spread of COVID-19.

Assistant Professor of Biology Youssef Idaghdour and Professor of Biology Kristin Gunsalus are working on developing a COVID-19 testing method that could significantly improve testing methods.

In research approved by the UAE’s Department of Health, Idaghdour and Gunsalus teams have demonstrated a testing protocol that could help provide a more accurate overview of the disease’s incidence and virus’ transmission rates.

Working with both synthetic viral RNA and clinical samples, the research team believes their results will overcome two issues that are currently prevalent in testing protocols around the world.

The first is related to the sensitivity of testing protocols that lack a 100 percent sensitivity detection rate and could lead to cases of false negatives.

Cases of false negatives present challenges in densely populated areas whereby current testing protocols might not detect viral particles in individuals carrying low doses of the coronavirus. This would deem them as free from COVID-19 and could lead to transmission of the virus.

But the method being developed at NYUAD aims to reduce that number.

“Our team has been using synthetic RNA used as a proxy of the coronavirus to test and implement the method. By enhancing  existing PCR protocols combined with the power of nanotechnology we have demonstrated the ability to detect as low as one copy of viral RNA per microliter of material tested, somewhere in the order of 100 to 1000 times more sensitive than the current gold standard,” said Idaghdour.

Follow-up work by the team validated the method by testing clinical samples in collaboration with a diagnostic laboratory in Abu Dhabi.

The other issue stems from the prevalence of asymptomatic individuals and the problem it poses in the current testing protocols used around the world. Currently, the overarching philosophy in most testing regimes is to only test when needed and most commonly after symptoms arise or in the case of exposure to infection.

This method is known as passive testing. This approach presents a dangerous situation in that those who have the virus but do not display any symptoms could place the general population at risk by sustaining asymptomatic transmission. Idaghdour suggests that countries should follow the example of the UAE by moving towards active testing protocols and frequent screening programs, whereby random representative samples of communities in the country are tested frequently regardless of symptoms to provide an indication of infection rate and prevent transmission at an early stage.

The team is collaborating with several hospitals and diagnostic centers to test patient samples in order to evaluate the newly developed methods and their ability to detect positive samples. 

“We want to determine if the standard WHO and CDC protocols which are followed in those clinics are missing asymptomatic patients. That's important because people have demonstrated that the virus can be transmitted asymptomatically,” said Gunsalus, who runs the NYUAD Center for Genomics and Systems Biology and is the director of bioinformatics and affiliated faculty.

According to Gunsalus, another important question is how a person's viral load, or the amount of virus that can be detected in a diagnostic assay, relates to their risk for severity of disease symptoms. One advantage of the new assay being developed at NYU Abu Dhabi is that it is not only ultra-sensitive, but it provides a quantitative readout of viral load, unlike standard clinical diagnostic tests currently in use. 

The costs of PCR COVID-19 testing in the UAE, approximately AED250, is still a limiting factor. But NYUAD’s testing method is scalable and more affordable and the team hopes it would prompt implementation of active screening programs without compromising sensitivity of detection.

The other aspect of this testing procedure that could make it more effective is the possibility to test up to 20 other pathogens for the same cost and to use saliva instead of  the currently used, and slightly invasive, method of nasopharyngeal swabs. Preliminary results are promising and the team is currently in the process of validating the method using clinical samples.

If successful, that could mean, with some development and a strict level of user adherence, that sample collection could be conducted at home, and sent to labs for testing –similar to the techniques used to collect genome analysis toolkits.

“While the final word is not yet in, several independent  studies have found that saliva samples can be just as effective as nasopharyngeal swabs for detecting viral particles in infected individuals. Saliva samples are easier to collect, and people can do it themselves. So we are currently comparing the results of our testing method using both kinds of samples taken from the same patients in order to evaluate the potential for adopting saliva samples for routine monitoring” said Gunsalus. 

The team is currently working to implement their assay for a university-wide testing program that would have two benefits. One is that the study will help to understand the prevalence of asymptomatic COVID-19 cases among students, faculty, and staff at the university.

“This project is also very important to our community, because it is one of the best ways to ensure the community is safe and we have measures in place that in the event of someone being positive then we have protocols can be activated in terms of self-isolation and other things,” added Professor Idaghdour.

In collaboration with the Biology Program, the Center for Genomics and Systems Biology, the Public Health Research Center and the Health Center, the overarching goal of the research team is to contribute to the wider battle against the disease.

“The role of scientists in this process is to provide the tools to achieve those goals and generate data and evidence that can inform policy making.  The pandemic has shown how vital generating new knowledge and close collaboration between epidemiologists, clinicians, scientists and policy makers is very important to combat the disease.” said Idaghdour.

This project in its nature reflects the collaborative effort of NYUAD as an institution and its lean and dynamic response that could, in large part, be attributed to the efforts by a member of the University’s senior leadership. When the pandemic first developed, Fabio Piano, who was provost of NYUAD at the time and a professor in the field of genomics and systems biology, gathered different parts of the institution to help manage the institutional response to the public health crisis.  

“The results of our COVID testing innovations are the fruits of a highly collaborative environment that developed as soon as the COVID-19 threat was clear.  These initial results demonstrate an important path to impactful innovation,” he said. 

By using the gold standard PCR testing method as a starting point, the team improved significantly on sensitivity and scalability of the method by applying some bioinformatic tools.  

“Together these results can give important insight into public health and clinical research.  Perhaps most importantly, the combination of these developments create a platform for continued innovation to help manage COVID-19 or other natural pathogens that might come in the future,” said Piano.