Stemloop - Environmental SARS-CoV-2 Test

The COVID-19 pandemic has revealed how challenging it is to scale laboratory testing: it's expensive, complicated, and slow. These limitations preclude high-resolution and widespread medical and environmental SARS-CoV-2 testing.

As we move into the next phase of the pandemic, we need solutions to ensure workplace safety, get students and teachers back in school, and enable proactive monitoring of COVID-19 spread before symptomatic patients present in clinics.

1. Stemloop is solving the problems (cost, complexity, time, centralization) of laboratory testing, which is inherently reactive to symptomatic presentation of COVID-19.

2. We propose a test kit for the rapid, inexpensive, and easy on-site detection of SARS-CoV-2 for environmental applications. 

3. If scaled globally, our solution can help ensure that both lives and livelihoods are protected from the damages caused by COVID-19 by proactively identifying community spread and informing actionable mitigation strategies.

We are solving the problem of laboratory testing, which is unable to scale to meet the demand caused by a global pandemic. This is due largely because of complexity of laboratory testing, which in turn makes it costly and centralized to facilities with sophisticated equipment and technical operators. Furthermore, this also causes delays, which in some cases were as long as two weeks in various locations in the United States immediately following the declaration of a national emergency.

The testing problem is being felt worldwide, particularly in countries which did not implement strict controls and contact tracing procedures at the outset of the pandemic. The lack of widespread testing in the US along has resulted in over 2M cases, 110k deaths, and economic shutdowns which have caused nearly 40M Americans to become unemployed. 

Medical testing presents further challenges. It is inherently performed in response to clinical presentation and oftentimes well after peak infectivity. There are also privacy, regulatory and reimbursement challenges with medical testing. In contrast, environmental testing (e.g., surfaces in workplaces or community monitoring through sewage) alleviates many of these components and can more readily scale.

Our solution is a simple and inexpensive biochemical reaction that can be  used on-site, by a relatively untrained operator, to detect the presence of SARS-CoV-2. The reaction itself is freeze-dried (to avoid cold-chain storage and distribution requirements) and is provided along with a sample collection kit (non-medical swab), buffer used to break apart the virus, and a battery powered handheld device to incubate and monitor the reaction. Within an hour, results are wirelessly transmitted (via Bluetooth) from the device to a mobile device or tablet and can be optionally geotagged and timestamped.

In simple terms, the reaction makes copies of a small fragment of the viral genome and simultaneously produces a fluorescent signal, which is picked up by the low-cost portable device. 

The technology uses isothermal nucleic acid amplification and RNA synthetic biology. We have prototyped the core technology and demonstrated it's ability to detect SARS-CoV-2.

Our target population whose lives we are working to directly and meaningfully improve include the countless essential workers who are unable to work from home and must be physically present in warehouses, production plants, and other high-density workplaces that present community viral transmission opportunities. These populations are at risk and are unlikely to be offered medical testing due to the the high cost and disruptive nature of medical testing in the workplace. 

We are engaging these populations primarily through customer discovery interviews with the management layer that oversee operations. This includes health and safety officers, occupational/industrial hygienists, and facilities managers. For these customers, the primary incentive is to ensure operational continuity and risk mitigation stemming from outbreaks at their facilities.

We are also in discussion with public health departments and wastewater utilities, who are looking for methods to monitor community spread in their communities. Wastewater-based epidemiology can provide a 7 day leading indicator, which can allow preparedness (ensuring enough hospital beds and ventilators) if the virus is detected, or prevent unneeded and economically debilitating shutdown measures if the virus is not detected.

The Health Security and Pandemics challenge calls for "improved solutions for prevention, accurate detection, and rapid response." Furthermore, the challenge calls for "tech innovations that... track the spread of an emerging outbreak... by developing low-cost rapid diagnostics." Low-cost environmental detection meets these criteria through surface or wastewater detection by offering a proactive monitoring solution.

Finally, the challenge states that "we cannot treat disease outbreaks reactively." The current paradigm—medical testing—is typically done in response to active symptomatic infection. Therefore, approaches like environmental testing, which can detect the presence of virus long before symptoms emerge, offer a proactive solution.

Our solution is innovative because it proposes to be the first truly portable test kit for SARS-CoV-2 that can be used by non-experts. 

We identify two main competitors that offer environmental detection kits for SARS-CoV-2 – Chai Bio and Biomeme. 1) Chai Bio offers a lower cost RT-qPCR device and test, however their device is not portable and their device is priced at several thousand dollars. They neither solve the ease-of-use problem, nor can their technology be easily operated outside of a laboratory setting. 2) Biomeme's product is much closer to our vision of a field-deployable test that can be used anywhere, however it still requires a high degree of technical competence and remains expensive (device cost approaches ten thousand dollars). 

An additional competitor in the wastewater segment of environmental testing is BioBot Analytics. We do not view them as a direct competitor as the samples still need to be shipped (across the country if originating from the west coast) to their test facility, each test is ~$1200-1600, and results are delivered in a matter of days rather than hours.

Our core technology is powered by 1) cell-free synthetic biology and 2) RNA engineering. 

1) Cell-free synthetic biology is the use of biomolecular processes (e.g., transcription, translation, metabolism) for biotechnology purposes. It overcomes the complexity posed by biology, by eliminating the cell and reducing it to predictable and controllable biochemistry. In our application, we are using advanced biochemical reactions that run parallel processes to detect SARS-CoV-2, sensitively and specifically, and produce a measurable output.

2) RNA engineering is the design and implementation of life's "messenger" molecule. Unlike DNA, RNA is a dynamic and functional molecule. Synthetic RNAs can perform biochemical reactions (cleavage, gene regulation, etc.) and even functions like fluorescence activation.

We combine these two technologies to create cell-free reactions that uniquely use RNA to perform input (detect) and output (signal) functions for SARS-CoV-2 or other viral pathogens. Cell-free systems have the advantage that they are NOT genetically modified organisms and are not subject to import/export regulations that GMOs face. Furthermore, they are not alive and therefore eliminate concerns over biocontainment. Finally, SARS-CoV-2 is an RNA virus that uses RNA to exploit and invade living systems. We turn that on its head by countering with RNA-based technologies that can interrogate  the virus.

To mitigate risk and maximize success, we are taking a multi pronged approach and are developing several technologies in parallel. These include standard isothermal amplification techniques (NASBA, RPA, RCA), CRISPR based diagnostic technologies (Cas12 and Cas13), cell-free systems, and the use of engineered RNAs (fluorescence-activating aptamers, toehold switches, small transcription activating RNAs, etc.). We are using these methods in a variety of combinations.

We have significant technical expertise in these areas. Recent examples of our work include: 

1) a portable, equipment free sensor for the detection of plant viral pathogens (uses engineered RNA and RPA isothermal amplification in a cell-free system)

2) a portable, equipment free sensor for the detection of fluoride (engineered RNA and cell-free systems)

3) an innovative strategy for the detection of a widely banned pesticide (cell-free systems)

4) a cellular and cell-free sensor for the detection of a common disinfectant (cell-free system)

5) a generalizable and innovative platform for the detection of heavy metals, pharmaceuticals, small molecules, etc. (in press at Nature Biotechnology) – a novel approach to cell-free systems with engineered RNAs.

Evidence that our technology works was included in a previous response and is copied here. This shows an engineered RNA output that is generated during the process of isothermal amplification. Technical challenges remain - we need to improve upon its sensitivity, demonstrate that we can stably freeze-dry the reaction and enable 1-step use by a non-expert.

Laboratory based testing, especially medical diagnostic testing, is difficult to scale. This has resulted in widespread shutdowns across the world, which has long-lasting economic impacts that we are just beginning to see. As we begin adapt to the "new normal" and restore workplace activities, education, recreation, etc., we need new technologies to ensure safety and operational continuity, as both lives and livelihoods are at stake.

One approach is to regularly test employees with medical diagnostics – an approach being taken by Amazon. However, this is expensive to implement and can only occur with a twice-a-month frequency for even a large company like Amazon. Medical testing in the workplace is also operationally disruptive, personally invasive, and raises concerns over medical privacy.

An alternative and preferred approach would offer more frequent testing capability, at lower cost, while maintaining medical privacy and without disrupting operations. This can be enabled by environmental testing of surfaces and wastewater. Environmental testing is non-invasive, anonymized, and can be performed regularly to generate aggregate data. Furthermore, environmental testing has been shown to be an effective leading indicator of viral spread, enabling effective shutdown measures if and when they are needed.

Our theory of change is simple. If widespread environmental testing is deployed, we can safely monitor our communities and places where we gather. If virus is not detected in our environments, we can maintain "business as usual" status. However, if virus is detected in the environment we can implement measures to perform additional medical diagnostic testing, deeper cleaning and sanitation, and shutdowns if necessary.

From an organizational standpoint, environmental testing can protect employee health and safety. It can be implemented regularly, easily, and at lower cost than medical testing. It can prevent localized outbreaks and minimize workplace disruptions. In the long term, this would allow society to continue to progress and make informed decisions about shutdown measures that can disproportionately and negatively impact livelihoods of those that are unable to 'work from home.'

Current number of people we're serving: 0

Number we'll be serving in one year: 10 million (through community wastewater surveillance in a major metropolitan area such as Chicago)

Number we'll be serving in five years: Optimistically and perhaps naively, 1 billion through widespread environmental surveillance programs.

Our mission at Stemloop is enable anyone, anywhere, to sense the world around them. Our vision is to accomplish this with cell-free biosensors that enable democratized and decentralized testing of public health threats, including pandemic agents such as SARS-CoV-2 and toxic contaminants such as lead and arsenic. We envision a future where everyone can access the tools that make them a 'citizen scientist' — aware and proactive towards the threats that exist around them.

Immediately after developing and deploying our SARS-CoV-2 solution we plan to turn to a pathogen that is lurking in the shadows: Legionella. Legionella is a bacterium that grows in building water systems (HVACs, ice machines, cooling towers, etc.). When aerosolized it can cause a severe form of pneumonia with a high fatality rate ("Legionnaires disease"). Treatment of Legionella growth includes frequent flushing and disinfection of water systems. However, with the number of buildings that have remained under occupied during the pandemic, there is widespread potential for localized outbreaks originated from stagnant water systems.

Beyond pathogens, we envision using our platform to detect threats like antibiotics and other drugs in our environment, heavy metals and toxic ions in our water, food borne pathogens, etc. These are all public health threats which are currently identified through laboratory based testing procedures. We have innovated on several of these fronts and our goal is to get these technologies out of the lab and into the field where they are needed the most.

Technical: Our desired sensitivity is within an order of magnitude of gold standard medical diagnostic grade RT-qPCR. Currently, we are several orders of magnitude away from this. Although this can be solved with a secondary reaction, that eliminates our value proposition of ease-of-use. We are actively developing additional amplification techniques to boost our signal while minimizing noise.

Financial: While we have some non-dilutive support and an early investment, we have not yet crossed the threshold to independently support salaries for a full-time scientist. This is our most immediately hurdle that we are attempting to bridge with non-dilutive grant funding opportunities. We have lab and office space, as well as materials and supplies, covered for the next year.

Market: We are feeling intense pressure to develop and get a product to market ASAP. We expect established players will soon make their way to the market and make our path more difficult.

Cultural: While heightened bio-awareness currently exists, we are already seeing the politicization of science and active rebellion against public health measures as simple as wearing a mask. For us to have our desired impact, we need a concerted societal effort to implement widespread environmental monitoring.

Legal: While we are focused on innovation in our technology, it builds upon a rich history of other scientific innovations, some of which may still be protected. We will be performing a freedom to operate analysis but expect having to license technologies to ensure FTO.

Technical: We have risk mitigation strategies built in to our approaches and an active partnership with Northwestern University (who are developing a separate strategy which we have already optioned).

Financial: We recently closed a $50k USD investment, received a $20k sub award on an NSF RAPID grant awarded to Northwestern University, and have submitted several grant applications independently or in collaboration with partners.

Market: We have had early discussions with companies that have an existing footprint in the environmental testing market. We may partner with these companies to use their existing channels to market and distribute our product.

Legal: We have optioned technologies that our founders developed at Northwestern University and will be filing provisional patents through the company when our ideas have been reduced to practice and have the money to file.

Our current team of 5 consists of two scientific cofounders, Dr. Khalid K. Alam and Prof. Julius B. Lucks; a scientific advisor, Prof. Michael C. Jewett; a business advisor, Dr. Dick Co; and our head of business operations, Adam Cohen.

All members of our team are equity compensated. Dr. Khalid Alam and Adam Cohen are working full-time.

We are engaging with engineering contractors to build a prototype handheld device. We are also looking to make our first scientific hire.

Diversity is valued at Stemloop and we are actively working to enhance the diversity of our team.

We are uniquely positioned to deliver on this technology. Our team is spun out of Northwestern University's Center for Synthetic Biology and Center for Water Research, where we spent several years developing low-cost, rapid, and easy-to-use biosensors for the detection of public health threats. We are world leading experts and innovators in the field of cell-free biosensor technology and have field tested our innovations with real-world samples and in real-world (non-laboratory) settings. We are experts in synthetic biology, RNA, cell-free systems, and biosensors.

Recent examples of our work include: 1) a portable, equipment free sensor for the detection of plant viral pathogens, 2) a portable, equipment free sensor for the detection of fluoride, 3) an innovative strategy for the detection of a widely banned pesticide, 4) a cellular and cell-free sensor for the detection of a common disinfectant, and 5) a generalizable and innovative platform for the detection of heavy metals, pharmaceuticals, small molecules, etc. (in press at Nature Biotechnology).

We were most recently invited to submit a review article on our innovations in water quality testing for a special issue organized by the WHO/UNICEF Joint Monitoring Programme on water quality and sanitation. 

We have two strong organizational partnerships with 1) Northwestern University and 2) Argonne National Laboratory.

1) We are spun out of innovations from Northwestern University's Center for Synthetic Biology and Center for Water Research. We are co-developing the technologies being described in this solution. This was recently covered in several press appearances, including the Chicago Tribune (1, 2) and Illinois Public Radio.

2) We are members of the Department of Energy's Chain Reaction Innovations program at Argonne National Laboratory. We are deeply embedded with the structural biologists and environmental scientists at Argonne that are respectively working on SARS-CoV-2 biology and wastewater detection of SARS-CoV-2.

Finally, we have deep ties with the Metropolitan Water Reclamation District of Greater Chicago and North Shore Reclamation District and are in discussion  with them to launch a pilot project for wastewater monitoring of SARS-CoV-2.

Our environmental test kit for SARS-CoV-2 helps organizations who want to ensure safety in their environment and maintain operations by regularly and inexpensively testing their environments for the presence of the virus. Our test enables anyone to perform the test on-site, unlike laboratory based testing, which is costly, complicated, and slow.

Our product will have an upfront cost ($1000-2000) for the handheld device and limited number of tests. There is a recurring cost for additional tests ($10-20 each). 

We will partner with environmental service providers (e.g., EcoLab) with existing channels for marketing and distribution, and with a wide array of manufacturing partners to produce our test kit components.

We launched Stemloop with the support from the US Department of Energy and Argonne National Laboratory. We continue to seek non-dilutive grant support and have submitted SBIR Phase 1 proposals to both NIH and NSF. We expect this money to cover the cost of our early R&D and key scientific hires.

We are also actively fostering relationships with investors towards a seed round that we hope to fundraise later this year. We have already received a soft-offer from a local water technology investment firm and a term-sheet from a biotech focused startup accelerator. Both of these were turned down as we hope to raise on more favorable terms after we have built more value in the company. Recently, we accepted investment from Northwestern University's N.XT fund. This small investment provides us with money that we can spend at our own discretion towards non-R&D activities such as legal costs, marketing, etc.

We want to build a sustainable business and seek to generate revenue as soon as possible. Given the high cost of establishing life science R&D capabilities (outside of our current R&D agreement at Argonne National Laboratory), we believe that venture capital will be necessary.

We are applying to Solve to advance our technical and business objectives. A Solve prize will provide us with needed capital to advance our technology. More importantly, Solve's platform will provide us with exposure to a strong network of potential mentors, investors and collaborators.

As an early stage biotechnology company we believe that we need strong partnerships to succeed — we can't do it alone. While we have strong technical backgrounds with a history of innovation, we need additional technical support to advance our objectives and need support to recruit diverse talent. Furthermore, as first time entrepeneurs we are relatively inexperienced on the business side of things and are looking for mentors and partners to help us grow all aspects of our business, including hiring, legal strategies, fundraising, marketing, etc.

As we move towards a product that is ready to deploy, we will need to rely on partners to provide us with the biological materials at scale, test kit manufacturing, and distribution. These are activities that we are not well-suited to do ourselves and will lean heavily on partners to perform. We are actively growing our network to understand who we can work with.

Several MIT and Solve affiliated organizations can help us succeed. For example, The Engine, MIT Water, companies closely linked to MIT such as Ginkgo Bioworks, and the countless innovators and investors of Solve and the greater MIT community.

We are a team of scientific innovators that have developed several  technologies for the detection of contaminants and other public health threats on site, including heavy metals, antibiotics, and disinfection byproducts. Our goal in our technology development is to create tools that empower and enable anyone, anywhere, to sense the world around them. We envision a world that no longer relies solely on inaccessible laboratory based testing.

Our team will use the The Elevate Prize for Health Security to hire additional scientists to continue to develop our technology.

There is no technology that scales better than biotechnology. Our cell-free synthetic biology platform for biosensing of public health threats can cheaply scale and be deployed, for widespread detection and informed decision making. As we approach a population of 10B people, 2/3rds of which will be middle class, in urban environments, and putting demand on scare resources, new technologies will be needed for us to live sustainably.

With the future planet capital prize, our team will be able to work on some of the harder challenges that can be solved with biosensing technologies (i.e., continuous, real-time monitoring of public health threats using biomoecular systems).