NEW YORK ─ As COVID-19 raged through the world in 2020, diagnostic developers scrambled to develop new tests to detect SARS-CoV-2, the virus that causes COVID-19.
While PCR technologies became the de facto choice for detection, becoming a household term in the process, other newer technologies emerged to complement current detection methods and, in some cases, with the goal of improving on them.
The array of emerging technologies included electrochemical, plasmonic, and nanowire-based biosensors; host response tests that used different types of biomarkers; and new ways to make and develop antigen, antibody, and PCR-based tests.
Along with PCR-based tests, rapid antigen tests, and to a lesser degree antibody-based tests, are the most commonly used to identify patients who may have, or had, COVID-19.
"There is no easy way for new technologies to compete with PCR for COVID-19 testing, but given the demand for testing there is a need for additional technologies," Harvard University Wyss Institute Senior Staff Scientist Pawan Jolly said in an interview.
Despite being regarded as the gold standard for COVID-19 testing, PCR-based testing has its limitations, though.
"Doing PCR testing in a remote setting at the point of care is still tricky and expensive, so we're seeing alternate testing methods, including for antigen tests and some that are based on novel technologies," Jolly said.
One example is a protein biomarker-based host-response test, FebriDx, developed by Sarasota, Florida-based Lumos Diagnostics, which is helping to mitigate concerns about the accuracy of antigen tests and providing a way to quickly triage patients presenting with symptoms of SARS-CoV-2.
The assay had been developed for use by physicians interested in reducing the overuse of antibiotics in outpatient settings, but doctors are now using it with patients suspected of having SARS-CoV-2 in hospitals and clinics, Robert Sambursky, president and CEO of Lumos, said in an interview.
Doctors are using the 10-minute fingerstick blood test as a triage tool to quickly help separate people with a viral infection, which could be SARS-CoV-2, from those with a bacterial infection, which could require an antibiotic. The test identifies patients who have clinically significant infections by combining measurements of Myxovirus resistance protein A and C-reactive protein.
"FebriDx provides a fast way to move patients through an outpatient or emergency room setting to ensure that they quickly get the most appropriate testing and the most effective treatment," Sambursky said. "Its results trigger a series of potential secondary tests to confirm the presence or absence of COVID-19, which could include antigen testing or PCR technologies."
By running a rapid host response test along with a rapid antigen test, clinicians can identify when an antigen test result has missed a viral infection and they can isolate patients until a high sensitivity PCR test is run that confirms whether there's a SARS-CoV-2 infection, Sambursky said.
Host response tests that rely on the analysis of gene expression are also in development for use in the diagnosis of patients presenting with symptoms of COVID-19. Such tests are likely to see greater market acceptance as SARS-CoV-2 vaccines are rolled out, according to Tim Sweeney, cofounder and CEO of Burlingame, California-based startup Inflammatix.
"In the near term, the rise of rapid antigen technology that can enable the testing of a large number of people frequently will likely have an impact on curtailing the pandemic, but longer term, in a post-vaccine world, it will be important to get back to hypothesis-free testing," he said. "You are going to see that the number of patients coming into the hospital with conditions such as respiratory pneumonia will increase relative to the number of patients with SARS-CoV-2."
Additionally, as more vaccines are rolled out, "overall community transmission rates should be substantially lower and at that point, it may not make sense to test every suspected case all the time for SARS-CoV-2," Sweeney said. In those circumstances, clinicians need a test such as that provided by the Inflammatix gene expression, host-response platform that would quickly determine whether there is an infection, whether the infection is viral or bacterial, and whether there could be a combination of infections.
North Carolina-based Predigen, a Duke University spinout and potential Inflammatix competitor, is also developing a gene expression, host-response test and said recently that it aims to apply for Emergency Use Authorization from the US Food and Drug Administration for a combined host-response and pathogen identification test for SARS-CoV-2 testing next year.
Lumos' Sambursky noted that while it is useful to know quickly whether a patient has a viral or bacterial infection, clinicians also need to know which patients presenting with symptoms of SARS-CoV-2 could be at the greatest risk of progression to serious complications, including sepsis.
"It's one thing to have a bacterial [or viral] infection but quite another to be at risk of rapid decompensation involving a systemic inflammatory response that requires intensive care," he said.
In that vein, Acton, Massachusetts-based Bluejay Diagnostics this month announced it inked an agreement with Tokyo-based Toray Industries to develop a point-of-care test to assess the progression of COVID-19. The minimally invasive Symphony IL-6 test quantitates levels of the interleukin-6 biomarker from whole-blood samples without pretreatment of patients who have progressing COVID-19 symptoms and have a high risk of intubation with a mechanical ventilator.
IL-6 is released early during a severe infection and can be used to help physicians determine which patients will become seriously ill and risk stratify those patients for treatment. Roche, Beckman Coulter, and Siemens Healthineers currently have EUAs for IL-6 tests.
Meanwhile, MeMed, an Israeli company with a focus on developing assays that gauge the immune response to infectious diseases, is developing two new tests that could help select treatments for COVID-19 patients, while Vancouver, British Columbia-based Sepset Biosciences believes that an early diagnostic test it is developing for sepsis would give clinicians valuable time to identify treatment strategies that could improve patient outcomes. It is participating in a multicenter clinical study that involves sequencing samples from COVID-19 patients to validate a diagnostic test that identifies those with the novel coronavirus that could progress to sepsis.
Cesar Castro, director of the cancer program at the Massachusetts General Hospital Center for Systems Biology and an assistant professor of medicine at Harvard Medical School, said tracking how SARS-CoV-2 patients respond to clinical management demands broader use of decentralized tests.
Such tracking could evaluate whether novel anti-viral or anti-inflammatory therapies are dampening cytokine storms or influencing septic-related biomarkers, he said.
Better antibody testing
Platforms that are more practical and lower in cost are needed, Castro added, including COVID-19 antibody tests deployed at scale "to triage whether front-line workers can safely return to the trenches, or similarly whether teachers can safely conduct in-person teaching."
One such technology being developed by the Wyss Institute, called eRapid, is enabling a multiplex platform that provides quantifiable results ─ calculations of the levels of antibodies in the blood. That's unlike almost all current lateral flow technologies used to detect SARS-CoV-2 antibodies, which tell you whether you have specific antibodies or not, Jolly said.
Being able to measure levels of antibodies is likely to be especially useful as more vaccines are rolled out and people need to quickly ascertain whether they are responding to treatment and do repeat testing, he added.
With this in mind, in December, the Wyss Institute signed a non-exclusive licensing agreement for its eRapid multiplexed electrochemical detection platform with Sydney-based iQ Group Global.
Separately, Sharnbrook, UK-based MIP Diagnostics is accelerating internal product development of molecularly imprinted polymer (MIP) technology as a basis of a biosensor that it believes can provide advantages over traditional antibody assays for diagnostic testing.
Also, Carnegie Mellon University has partnered with the University of Pittsburgh Medical Center to develop a SARS-CoV-2 test that uses a drop of fingertip blood to identify antibodies associated with the spike S1 protein and receptor binding domain. The developers said that their test can detect antibody concentrations at single picomolar levels through an electrochemical reaction within a handheld microfluidic device and provide results in less than 15 seconds.
In the test, gold micropillar electrodes are printed at the nanoscale using aerosol droplets that are thermally sintered together. That results in a rough, irregular surface that provides increased surface area and an enhanced electrochemical reaction, where antibodies can latch on to antigens coated on the electrode.
Active disease testing
Further, researchers at the University of Maryland School of Medicine have developed a biosensor that they said could be made available to test for SARS-CoV-2 alongside current molecular, antibody, and antigen tests. Leveraging plasmonic properties of gold nanoparticles that cluster around viral RNA molecules, the biosensor changes colors to indicate the presence of SARS-CoV-2 and, according to the researchers, has the potential for deployment for screening for active disease.
Cary, North Carolina-based Atom Bioworks is leveraging synthesized DNA antibodies in the development of an antigen test for SARS-CoV-2 test that it believes would cost a few dollars per kit and could be used at home to help broaden the scale of testing during the pandemic.
The company recently received funding under the National Institutes of Health Rapid Acceleration of Diagnostics (RADx) program to develop an aptamer-based detection system using its DNA-star biosensor technology and saliva as a sample. The biosensing approach uses the unique expression of spatial patterns of antigens on virus surfaces, facilitating multivalent binding to infected host cells.
Atom Bio's CEO Sherwood Yao told 360Dx that the firm recently received an additional RADx award to build a five-minute rapid COVID-19 test that uses its biosensor technology and would enable high-throughput testing. For that, the company is collaborating with Santa Clara, California-based Agilent Technologies to develop the test, and anticipates that support from the RADx organization will help it obtain EUA in the first half of 2021 and position it to produce 1 million tests per day, Yao said.
Southborough, Massachusetts-based NanoDiagnostics also has its eye on the development of technology for active disease detection at the point of care for SARS-CoV-2. The company's test runs on a compact nanowire-based diagnostic platform, called the NanoDx System, using technology that the firm has been developing for a few years to detect traumatic brain injury.
Point-of-care molecular tests
While developers continue to improve on antigen and antibody tests, room for improving molecular technologies at the point of care is also prompting technology development.
Researchers at Imperial College London and Moredun Research Institute in Edinburgh, Scotland, recently reported on the development of a proof-of-concept prototype that uses the properties of silicon to implement important functions such as target amplification and detection for use at the point of care.
They believe the prototype could provide the basis for a testing platform to detect multiple infectious diseases and circumvent challenges associated with other electrochemical detection methods and traditional PCR-based testing.
Additionally, London-based DNA Electronics is developing a sequencing platform that runs rapidly and directly from a raw sample and uses a disposable test card. The platform, based on DNAe’s semiconductor technology, would be combined with related upstream and downstream technology to create a sample-to-result system.
"Despite the large number of tests available for COVID-19, there is still a huge unmet need for a solution that has gold-standard accuracy and sensitivity, especially in a rapid cartridge-contained test," Sam Reed, CEO of London-based DNA Electronics, said in an interview. "Any solution needs to be in a form that is sufficiently robust, meaning it performs consistently regardless of where it is used and can also be undertaken with minimal training required. Such a test would make accurate tests widely available, rather than being limited to only the most sophisticated labs."
DNAe has completed proof-of-concept testing on SARS-CoV-2 targets and plans additional testing in 2021, Reed said.
It also believes emerging disease threats could drive greater use of its technology.
Several countries, including England and South Africa, have in recent weeks reported the emergence of a new, highly contagious coronavirus variant. In a bid to mitigate a surge in cases, parts of England are facing tighter restrictions.
"There is a lot of talk about mutations now, and the reality is that this virus not only will evolve but there will be new threats in the not-too-distant future," Reed said. "We believe that there will be a growing interest in more agnostic diagnostic platforms … [and] health systems will look to invest more, as an insurance policy of sorts, in platforms that will be future-proofed against emerging needs," he said.
Additionally, numerous research studies are underway to sequence the viral genome in patient samples to study how the virus spreads and evolves over time.
Developers are also researching new types of samples. During the pandemic, most used nasopharyngeal and nasal swabs and some used saliva samples for PCR testing. SARS-CoV-2 antibody tests used mainly blood, and now developers are developing testing technologies that use the human breath as a sample.
Imec, a Belgian R&D organization focused on digital and nanotechnologies, intends to deploy a prototype SARS-CoV-2 breath-based test in Brussels Airport next summer. The organization partnered with UZ Leuven University Hospital to validate the system and is currently considering different ways to commercialize the technology.
Further, Cleveland-based Canary Health Technologies and Delhi-based Divoc Laboratories have announced that they will collaborate in a clinical trial to develop a rapid breath test for the detection of COVID-19.
In another alternative to mainstream testing, the combination of CRISPR and smartphones is showing promise. At least two different research groups ─ at the University of California, Berkeley, and Tulane University School of Medicine ─ have developed new CRISPR-based diagnostic assays for the SARS-CoV-2 virus that can be read with smartphones, and can quantitatively measure patients' viral loads in addition to testing for infection without the need for separate RNA extraction or amplification.
Additionally, some researchers and studies suggest that mass spectrometry could carve out a niche within the COVID-19 testing world. Among the potential advantages mass specs could offer are rapid turnaround time, the ability to circumvent supply chain limitations, and, in the case of MALDI-based testing, a large pre-existing installed base of clinical instruments around the world.
Overall, the pandemic underscores an unmet need to rapidly diagnose infections, Castro noted, adding, "This includes the need not only for prompt interventions but also use of the most appropriate interventions involving various anti-infection options."
Moving COVID-19 diagnostic testing technology forward cannot occur within engineering silos, he warned. It requires input from numerous stakeholders, ranging from basic science researchers to public health experts.