As COVID-19 continues to spread, bottlenecks in supplies and laboratory personnel have led to long waiting times for results in some areas.
In a new study, University of Illinois, Urbana-Champaign researchers have demonstrated a prototype of a rapid COVID-19 molecular test and a simple-to-use, portable instrument for reading the results with a smartphone in 30 minutes, which could enable point-of-care diagnosis without needing to send samples to a lab.
“If such a device and test were available, we could test for COVID-19 at public events, auditoriums, large gatherings and potentially even at home for self-testing.
The results could be sent back to the appropriate public health system for coordination,” said Rashid Bashir, a professor of bioengineering and the dean of the Grainger College of Engineering at Illinois.
Bashir co-led the study with electrical and computer engineering professor Brian Cunningham and mechanical science and engineering professor Bill King.
Typical tests for SARS-CoV-2, the virus that causes COVID-19, take a sample from a patient with a long nasopharyngeal swab, put that swab into a substance called viral transport media, and send it to a lab for a multistep process of extracting, isolating and multiplying the telltale RNA inside the virus.
This RNA multiplication process, called RT-PCR, requires several temperature fluctuation cycles, specialized equipment and trained personnel, Cunningham said.
As reported in the Proceedings of the National Academy of Sciences, the Illinois team used a simpler process to analyze the viral transport media, called LAMP, which bypasses the RNA extraction and purification steps.
“LAMP only needs one temperature – 65 C – so it is much easier to control,” said graduate student Anurup Ganguli, the first author of the study.
“Also, LAMP works more robustly than PCR, especially when there are contaminants in the test sample. We can just briefly heat the sample, break open the virus and detect the genetic sequence that specifically identifies SARS-CoV-2.”
The researchers compared the LAMP assay with PCR, first using synthetic nasal fluid spiked with the virus and then with clinical samples. They found the results were in agreement with PCR results, and they documented the sensitivity and specificity of the LAMP test.
Then, the researchers incorporated the LAMP assay onto a small 3-D-printed microfluidic cartridge that has two input slots for syringes: one for the sample-containing viral transport media, one for the LAMP chemicals. Once the two are injected, they react within the cartridge.
“We use modern, high speed additive manufacturing to make these cartridges. The entire thing can be quickly scaled up to hundreds of thousands of tests,” King said.
“Production scale-up is typically the biggest obstacle for commercial applications of microfluidic cartridges, and we can overcome that obstacle using this new approach. Modern additive manufacturing is elastic and scalable, and it can be ramped up very quickly compared with legacy manufacturing technologies.”
The team is working with Fast Radius Inc., a Chicago-based technology company King co-founded, to manufacture the microfluidic cartridges.
The cartridge can be inserted into a hand-held portable instrument with a heating chamber, which heats the cartridge to 65 degrees Celsius for the duration of the reaction, and a smartphone cradle for reading the results. In approximately 30 minutes, a positive result will emit fluorescent light.
“The reader illuminates the liquid compartments with light from blue LEDs, while the phone’s rear-facing camera records a movie of the green fluorescent light being generated,” Cunningham said.
The researchers demonstrated the portable device with additional clinical samples, and found the results matched those of the standard PCR lab procedure.
The researchers are exploring whether the assay would work with saliva samples to eliminate the need for nasopharyngeal swabs, and collecting more patient data as they consider next steps for regulatory approvals, Bashir said.
Two preprints published within the last week suggest that the science is already here to make a simple, easy to read COVID-19 test a possibility.
One study is from a group of researchers at Weill Cornell Medical School in NYC—the epicenter of the epidemic in the United States. The other is from a group at the Technion – Israel Institute of Technology in Haifa, Israel.
At the heart of the technique reported in both papers is loop-mediated isothermal amplification, or LAMP. Developed by a Japanese group of researchers at the Osaka University Medical School in Japan two decades ago, LAMP is performed in a single tube, at a constant temperature for very little cost, to detect DNA. The technique amplifies DNA quickly—with high specificity and efficiency.
LAMP relies on DNA polymerase and a set of four to six primers, designed to recognize a total of six distinct sequences on the target DNA.
One of the inner primers initiates strand displacement and amplification. A strand displacing DNA polymerase displaces the two original DNA strands while creating a new strand. A separate primer then displaces the newly made strand, and a loop is formed due to complementary sequences on the primers.
The process of displacement, amplification, and forming loops continues until the DNA forms a dumbbell structure. It is the accumulation of these amplification byproducts that can be easily detected. (For a visual explanation on how LAMP works, please see the video at the end of this article.)
Add to the above protocol a reverse transcriptase step, and detection of RNA can be done in a similar way—using RT-LAMP.
The work from Isreal is published as a preprint in MedRxiv. The title of the preprint (a paper that has not yet gone through the peer review process) is “SARS-CoV-2 On-the-Spot Virus Detection Directly from Patients.”
The authors developed RT-LAMP for the detection of SARS-CoV-2 RNA directly from clinical diagnostic swabs of human patients, without RNA purification steps. They spent time adjusting the protocol, tweaking it for SARS-CoV-2 specifically. After the first round of tests, there were no false positives, but the rate of true positives was very low. They continued adjusting conditions, to find the optimal conditions. Once the protocol was validated on nasal swabs, they moved on to saliva samples. Using a very small set of self-collected samples—from three different confirmed patients and one suspected negative subject—the confirmed patients were found positive in both RT-LAMP and RTqPCR from saliva, and the suspected negative subject was confirmed negative.
“The simplicity of detecting SARS-CoV-2 without an elaborated RNA extraction and purification step and the fact that this method can significantly reduce the number of professionals required for SARS-CoV-2 detection tests” are what Naama Geva-Zatorsky, PhD, professor of nanobiotechnology & nanomedicine at the Technion – Israel Institute of Technology, and senior author on the article, finds most exciting.
Geva-Zatorsky added that they envision the RT-LAMP test used as a surveillance test for a large number of people in the community. “Detection is key,” the authors wrote. “We believe,” they continued, “that a simple and easy detection method, preferably one that can be performed and interpreted on-the-spot could relieve some of the current limitations, and help execute an efficient and safe exit strategy from lockdowns.”
LAMP tracks SARS-CoV-2 around NYC
The Mason lab at Weill Cornell reported last week the development of a similar LAMP-based colorimetric test that can identify the presence of SARS-CoV-2 from both oral and nasopharyngeal samples.
This COVID-19 pandemic, they wrote, highlighted a pressing need for “rapid, scalable diagnostics that can detect SARS-CoV-2 infection, interrogate strain evolution, and map host response in patients.”
Their work was published in a preprint last week in bioRxiv titled, “Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).”
The team designed and optimized the rapid LAMP assay to detect SARS-CoV-2 infection from nasopharyngeal swab specimens and oropharyngeal swab lysates. When tested for efficacy on 201 clinically-annotated samples, the assay had 99% specificity and 95% sensitivity.
The team then developed a large-scale shotgun metatranscriptomics platform to comprehensively profile nasopharyngeal swab samples collected from patients with RNA-seq.
Both technologies were used to profile 338 clinical specimens tested for SARS-CoV-2 and 86 environmental samples collected from high-transit areas in the NYC subway in early March 2020.
In doing this, they created a broad molecular picture of the COVID-19 epidemic in NYC.
Using LAMP for COVID-19 testing is “a great idea that just needs to be tweaked and optimized,” noted Chris Mason, PhD, associate professor at Weill Cornell Medical College and senior author on the paper. Both studies, noted Mason, show that it has “real potential for broad and easy use.”
The authors of the medRxiv paper wrote that the next steps needed to bring this to the clinic are “further adjustment of the protocol on saliva samples, tested on a large cohort, and compared to the standard method.”
Its simplicity and low cost, they added, will increase the ease to continuously monitor suspected subjects. With further development, they asserted, this method can be applied to medical clinics, points of entry, nursing homes, workplaces, and more, and can even be easily adjusted to other emerging pathogens as well.
More information: Anurup Ganguli et al, Rapid isothermal amplification and portable detection system for SARS-CoV-2, Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.2014739117