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Israeli Startup LessTests Uses Single-Step Pooling Software to Multiply COVID-19 Testing Capacity

NEW YORK – Israel-based startup LessTests has developed a software that can help multiplex COVID-19 testing using a single-step, or nonadaptive, pooling strategy.

The company, founded by Ruth Polachek earlier this year, has received regulatory approval from the Israeli Ministry of Health and is mainly catering to high-throughput labs. 

Demand for COVID-19 tests hasn't slowed down since the beginning of the pandemic, leading laboratories to rely on alternative and less common methods to meet capacity needs. One of those methods is sample pooling, where multiple samples are combined and tested as one. If the result is negative, the samples are all presumed negative, but if it's positive, the samples are individually retested. This double-step pooling method has become popular, particularly in areas with a low prevalence of positive cases, but becomes less effective as prevalence increases.

To counter this issue and streamline the pooling process, LessTests developed its method, which can be used in high-prevalence areas to multiply testing capacity by five, 10, or even 15, depending on a variety of factors, namely disease prevalence.

Instead of combining multiple samples into one tube, LessTests' nonadapative method splits every sample into multiple tubes, performs the test, and then uses an algorithm to determine which of the samples are positive. Although nonadaptive pooling is well known, it's not widely used, which Polachek discovered while looking into ways to help during the COVID-19 pandemic back in March.

Idan Yelin, a consultant for the company and a scientist at the Israel Institute of Technology, published a proof of concept showing that pooling could be used for COVID-19 testing in May in the journal Clinical Infectious Diseases. He said the people at LessTests "know how to overcome the barriers," including convincing institutions to use pooling at a larger scale. Yelin also noted that the method is well known but has not been applied broadly in infectious disease testing.

The company's team of mathematicians developed the software and algorithm in house, specifically for use with PCR tests. It is adaptable based on a laboratory's workflow and throughput needs, making it what cofounder Tsvika Vagman called "customer-centric."

As software engineers, Polachek and Vagman are "usually developing things that can work anywhere," Vagman said. "Our main goal was to provide a solution that will be able to integrate into any existing environment."

Vagman emphasized that their method provides more than a binary result of positive or negative but can predict the cycle threshold value of the individual sample. 

The basic two-step method, while easy to perform, also generates "quite the workload for labs," Yelin said. Automation is key to decrease that workload, and LessTests' method automates the combinatorial pooling method. Automation also can cut down on the chances for error, he noted.

Since many high-throughput laboratories have automated liquid handlers that can be programmed, the LessTests software can work with a variety of them, Vagman said. The solution and matrix are adapted to each laboratory's specific liquid handler for peak performance. "The process itself is not changed externally, we are just changing the robot road map," Vagman said.

In areas with low disease prevalence, LessTests' software can increase testing capacity tenfold, but as prevalence increases, the available capacity decreases. In many areas, once prevalence reaches between 5 and 7 percent of a population, traditional pooling isn't possible because there are too many positive pools, leading to too many retests. However, Polachek said LessTests is able to still pool samples and double testing capacity at those higher prevalence rates. "Because our platform is working across a very wide spectrum of prevalence," it could be used for diagnostic testing, screening, or surveillance, Vagman added.

But pooling isn't the only draw for LessTests' software. Analytical tools included in the software help maximize laboratory workflows, improve operations, and combine different pooling matrices, depending on the lab's location and needs. It can connect with the facility's laboratory information management system to sync with the lab's other devices and integrate more smoothly, Vagman said. 

"It's not even half of it to have a good algorithm," he continued. "You have to wrap it up with functional, user-friendly, and user-helpful tools." LessTests is focused on connecting with the labs and understand their challenges to make the method adaptable, Vagman said. 

"The algorithm is just the beginning of the story," he added. Labs can also decide the thresholds for the analytical tools and adapt the software to their own protocols and requirements, along with combining different pooling matrices as needed. If they want to keep tests at the highest sensitivity, they may not be able to reach the highest efficiency, or they can maximize efficiency by lowering sensitivity, depending on their needs and the requirements of local regulators. "We are keeping it very, very flexible and you can decide for yourself or adjust the parameters according to what you want at any given point in time," Vagman said.

To build the tools, Polachek and Vagman spent two to three months shadowing laboratory personnel and talking to them about their most common issues when testing at high volumes. The main issue they heard about was time – sample-to-result time in particular, which is what makes the shorter turnaround time of single-step pooling appealing, Polachek said. 

Another component of the time issue was how long it takes to perform surrounding operations, particularly sample prep and pipetting, which LessTests aims to address in some of its software tools, such as a stimulator that looks at a lab's production line.

"We were able to adapt our software to take into account what's important for a lab manager when planning ahead, of course, and for the team members that are actually doing pipetting and moving things from one step to another," Polachek said. 

Both Polachek and Vagman noted they are adapting the implementation process to each lab, since the company is not allowing customers to download the software directly from the Internet and implement it themselves. Instead, LessTests is going to clients and partners directly and supports them remotely in implementation. 

Although the company declined to share pricing information for the product, it offers two different payment options. Customers can choose to license the software annually for a set fee or go the revenue/savings share route, where LessTests would take "a modest part" of the lab's savings from using the software. Vagman emphasized that some labs might be able to save $40,000 per week with pooling and the other software improvements, partially because fewer supplies will be used for the same number of tests compared to regular PCR testing. Polachek said in an email that LessTests' software can lower test costs and demand for reagents by 90 percent. 

In July, the company received accreditation from the Israeli Ministry of Health to use its method in any clinical laboratory in the country, although both Polachek and Vagman noted there was some hesitance from the regulators at the beginning of the process. "We are two software entrepreneurs that are diligently developing a very innovative solution, and coming into the central Israeli biolab with this suggestion, at the beginning it was difficult to convince them to even test it," Vagman said. "Our main advantage is that we are coming from an entrepreneurship angle and we are not scientists."

"Our main mission is to bring it to market," Polachek added.

Yelin also said that labs could be hesitant to use the method at first, since "scientific evidence doesn't mean immediate adoption."

"You have to show your test is as good as what they know," he continued. 

The company is currently choosing local partners, such as laboratories and manufacturers, in every territory it hopes to launch the software that can help them through the specific regulatory processes of each region and finding early adopters, Vagman said. The goal is to perform a few installations in different areas before winter arrives, and some installations are currently in progress, he added. 

"Our strategy is to put a flag in major markets," such as Israel, India, the US, and Southeast Asia, and have a representative within each region, Vagman said.

With the flu season barreling towards the Northern Hemisphere, Polachek and Vagman are expecting demand for COVID-19 testing to rise and aim to be ready to help meet it. "We predict demand is going to be high and we want to be ready for that," Vagman said.

Currently, the self-funded company isn't looking for investors and is instead planning to rely on its revenues, although it did receive a grant of undisclosed size from the Israel Innovation Authority. The firm is also a semi-finalist for nonprofit OpenCovidScreen's COVID-19 XPrize, which has a $5 million reward for the winner.  

Although the firm began with the COVID-19 pandemic and is currently focused entirely on SARS-CoV-2 testing, Vagman noted that every liquid-based test can be done with LessTests' approach, including for diseases like malaria, HIV, sexually transmitted diseases, and dengue fever. The company also plans to continue developing additional features, such as artificial intelligence for test prediction and pipeline optimization.

"Pooling is here to stay and can add value to a lot of applications and strategies in medicine in the future," Vagman said.