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Japanese Team to Commercialize Nanopore System for Point-of-Care COVID-19 Screening


NEW YORK – Researchers at Osaka University in Japan have developed a nanopore system for point-of-care infectious disease testing that they hope will eventually be adopted for SARS-CoV-2, the virus that causes COVID-19. 

The scientists described their method in a recent Nature Communications paper and according to lead author Masateru Taniguchi, plans are underway to make the test available clinically in both single and multiplex formats.

"At this time, the device developed is for diagnosing a single sample, and if it is approved as a medical device, it will most likely be used for point-of-care testing," Taniguchi said. He said that the team is at work on a system capable of measuring 16 samples at once. "This device is expected to be used as a screening device in large-scale facilities like airports, baseball stadiums, soccer fields, and smaller facilities like schools, kindergartens, and nursing homes," he said.

The new test was developed by researchers at the Institute of Scientific and Industrial Research at Osaka University. It relies on machine learning tools to identify single virus particles as they pass through a nanopore. The developers claim the technique is sensitive enough to discriminate between SARS-CoV-2, severe acute respiratory syndrome, and Middle East respiratory syndrome. The device can process a saliva sample and deliver a result within five minutes, they claim.

As noted in the Nature Communications paper, the authors view their approach as a natural alternative to real-time PCR, the gold standard for SARS-CoV-2 testing, which relies on viral RNA extraction to achieve high sensitivity, making real-time PCR time-consuming, an issue when trying to contain a disease outbreak. Technicians are also at increased risk of contracting the disease if they are exposed to samples. "There is a need for an inspection method with higher throughput," the authors wrote in the paper.

The Osaka team's platform consists of what they dub an AI nanopore platform. This includes a nanopore module of 25 mm x 25 mm x 5 mm in dimension, enclosing a silicon nanopore chip and channel. The 5 mm x 5 mm chip contains nanopores of about 300 nm in diameter, which is comparable with coronaviruses of between 80 nm and 120 nm, according to the paper. The chips are manufactured in 12-inch wafers, with high accuracy and yield, the authors reported.

The hardware is just one component of the system. The developers also trained machine learning tools to be able to differentiate between viruses passing through the nanopore and tested the approach on a set of 40 PCR positive and 40 negative SARS-CoV-2 saliva samples. They then validated the approach on a set of 50 PCR positive and 50 negative SARS-CoV-2 saliva samples with a concentration of 2.5 pfu/μl. All were measured within five minutes, and sensitivity was 90 percent and specificity was 96 percent.

According to Taniguchi, the turnaround time was noteworthy in particular. "The fact that high sensitivity and specificity can be obtained with a short measurement time of five minutes thanks to a simple pretreatment of centrifugal filtration is an important result," he said.

Similar performance was achieved for other viruses, including SARS and MERS, meaning that the system can be used to differentiate between viruses. Since these kinds of virus samples are maintained in facilities of different levels of security restrictions, the authors noted they were not able to test viruses in parallel.

To carry out the study, the authors relied on two commercial instruments. All particles were measured using the nanoScouter, a fine particle measurement instrument sold by Advantest, a Tokyo-based semiconductor test equipment supplier. The desktop sized instrument has a nanopore sensor module for microcurrent measurement. Using the nanoScouter, the researchers were able to measure the waveform of the particles flowing through the nanopore.

The second instrument was the Aipore-One, a new system commercialized by Aipore, a spinout of Osaka University led by Taniguchi. According to Taniguchi, his group at Osaka has been working on single-molecule DNA sequencing and nanogap electrodes for the past 15 years. Concurrently, it has worked on micromeasurement technology, as well as microfabrication technology for manufacturing nanopore and nanogap electrodes. This work resulted in the development of the Aipore-One and founding of Aipore in 2018. The company currently maintains an office of six people in Osaka.

The system was originally developed for infectious disease research, enabling users to identify different viruses and bacteria, but when the COVID-19 pandemic hit, the company refocused its efforts to position the system for detecting SARS-CoV-2. The company had already started selling the device for physics and chemistry experiments.

"The new coronavirus pandemic began just as the venture company's supply chain was being built and the prototype was completed," noted Taniguchi. "As a result, we commenced the development of a new coronavirus testing device."

Following the publication in Nature Communications, Aipore is now turning toward seeking Japanese regulatory approval of the platform as a medical device, while working on a higher-throughput version capable of assaying 16 samples simultaneously. Taniguchi said his current estimate is that a singleplex version of the device could be on the clinical market in two years, while the 16-sample device should be available for nonclinical use in half a year and for clinical use, potentially, within three years.

"Perhaps it will be approved earlier, depending on the status of the infection," Taniguchi said.

Sales of the AI nanopore platform for research use will commence internationally next year, while sales for clinical use will vary depending on local regulatory clearance in each country, he added.

Since the AI nanopore is a handheld point-of-care system, it is competitive with other point-of-care devices for SARS-CoV-2 testing on the market. These, however, vary in terms of technology and scope. Cepheid, Luminex, and Qiagen all sell real-time PCR-based, point-of-care and near-patient assays for SARS-CoV-2 testing, for instance. Multiple handheld quantitative PCR systems are also in development.

While SARS-CoV-2 is its current focus, the authors noted, the platform can be adapted for emerging infections in the future. "By modifying the training data, the platform is a versatile virus diagnostic system," they wrote in the paper. Noting that influenza A and SARS-CoV-2 can present with similar symptoms, they reported that the device could easily discriminate between the two.

"When the clinical specimens collected from patients infected with each virus are used as training data, the identification result of the cultured viruses will enable the development of a device that can diagnose both viruses with high accuracy," the authors wrote.

Sébastien Balme, an associate professor at the European Membranes Institute at the Université de Montpellier in France, called the work by the Osaka group "highly promising for virus detection."

Balme, whose previous research was cited in the recent Nature Communications paper, commented that the Osaka team's machine learning approach allowed for improved accuracy of the nanopore testing approach. He noted that in the past nanopore detection has suffered from low resolution in discriminating samples, in this case, viruses of similar size.

"Probably, the main advance of this paper is the use of nanopore technology in the framework of clinical samples," said Balme. "For me, this technique is also promising because it requires a low amount of sample and thus a low amount of copy," said Balme. "The detection is in real time and requires no labeling kit," he added.