Category: Biosecurity Services

Concentric by Ginkgo recently opened its first public test center in Boston’s Seaport District. The new center is expanding access to COVID-19 diagnostic testing for workplaces and organizations of all sizes. Many organizations need employees on-site daily in order to operate. It’s crucial for these companies to have a convenient way to test employees and identify individual COVID-19 cases before they turn into widespread, disruptive outbreaks.

The test center located on the ground floor of the Innovation and Design Building is currently open to customer organizations and their participants Monday through Friday from 7:30am to 5:30pm. Any organization interested in accessing the service can contact the Concentric team to sign up. Concentric provides diagnostic testing in a comfortable setting that can be built into your team’s workday. Over time, the center will also explore offering different types of COVID-19 tests to meet a wide range of needs.

New Normal: Comfortable Testing

Concentric’s service prioritizes a test taker’s comfort and experience. We aim to make testing a familiar, easy experience rather than an unfamiliar, time-consuming activity. Individuals from customer organizations can easily request a test through our online portal, stop by the center to quickly take a test in a comfortable and private setting, and continue on with their day. The results are typically returned in 3 days or less. As public health experts have explained, the information that testing provides can help businesses identify infectious individuals with the goal of reducing transmission of COVID-19 in the workplace. The goal is to remove the stress, inconvenience, and discomfort from COVID-19 testing while providing access to testing when it’s needed.

Concentric’s Test Center is located in one of Boston’s largest business districts, which means our customers vary in size and industry, ranging from food service companies to manufacturers to large corporations. Concentric by Ginkgo offers affordable diagnostic testing options that can be accessed as needed: organizations can purchase a specific number of tests and then send employees in when testing is necessary.

Exploring the Latest Testing Innovations

Concentric by Ginkgo is exploring innovative types of COVID-19 tests in order to meet the different needs of organizations like workplaces and universities that require people on-site every day. While the majority of testing at the Seaport location is done using saliva as the collection method, we’ll soon be exploring antigen tests and shallow nasal swab methods (as opposed to deep nasal swabs). We’re consistently reviewing our processes and offerings to ensure we’re providing the best testing service to our customers.

Many organizations need to remain operational while the COVID-19 pandemic persists. Industries that support our critical infrastructure, our communities, and our ways of life all benefit from better access to testing. By removing barriers like low local test supply, lengthy turnaround times, and inconvenience, organizations can arm themselves with the knowledge they need to make better proactive and reactive decisions in their COVID-19 response plans.

For more information on how to access the testing service at the Concentric Test Center, contact us at www.concentricbyginkgo.com/idb.

In late March, a group of researchers at the University of California, San Francisco published a preprint describing a protein-protein interaction map that could find potential drug targets against SARS-CoV-2. Their study looked for interactions between every viral protein and every human protein, with the idea that molecules known to bind those human proteins might disrupt the interaction with the viral protein, therefore interfering with the viral life cycle. Several hundred hits were identified, and of those hits, over 50 protein targets had known small molecule binding partners, so-called “druggable” targets. These small molecules could potentially interfere with viral protein binding and therefore be repurposed against COVID-19. One interaction was observed between the viral protein Nsp13 and human centrosomal protein 250 (CEP250), a protein target previously predicted to be too flat for small molecule drugs to bind to it and therefore “undruggable”.

Several years ago, our team at Warp Drive Bio performed a very different high throughput screen, searching for human proteins that could bind to a novel natural product that the team had discovered. The molecule, called WDB002, is made by a species of soil-dwelling Streptomyces bacteria that was identified using Warp Drive Bio’s genome mining technology. WDB002 was found to be a strong binder to a little appreciated human protein called CEP250 — the same protein identified in the recent SARS-CoV-2 study! WDB002 first binds to another human protein, FKBP12, which then forms a tight three-part complex with a portion of CEP250.

In October 2018, Revolution Medicines bought Warp Drive Bio, and Ginkgo then acquired the Warp Drive genome mining platform from Revolution Medicines in January 2019. Today PNAS published an article authored by members of the former Warp Drive Bio team, showing how WBD002 and its related molecules can bind to the “coiled-coil” domain in CEP250, in complex with FKBP12 via binding studies and crystal structures. These coiled-coil domains are very “flat” and therefore notoriously difficult targets for drug discovery, which makes the tri-complex modality potentially useful for finding leads against other so-called “undruggable” disease targets.

As for CEP250’s role in COVID-19, we don’t know yet whether WDB002 will be useful for treating the virus, but Ginkgo is committed to finding out. Revolution Medicines has licensed intellectual property to Ginkgo to answer this question. Our team has already produced a batch of pure WDB002 from Streptomyces. Now, we are testing how it behaves in an in vitro live virus assay in collaboration with research groups that can perform these studies at biosafety level 3. It’s been exciting to be part of the story of WDB002, from when it was first discovered to exploring its potential as an antiviral. Despite the unknowns inherent in drug discovery and development, it is inspiring to witness Ginkgo’s ability to apply its platform towards vaccines, therapeutics, and diagnostics for COVID-19. We hope to share news about the WDB002 project in the coming months.

To learn more about how Concentric by Ginkgo can support you and your organization, please contact us.

Today we’re thrilled to announce the launch of Concentric by Ginkgo. Concentric offers COVID-19 testing at scale to support schools and businesses in their reopening strategies and provides end-to-end, on-site testing services for organizations that seek to make testing available to their communities.

Everybody’s health is connected. Many layers of public health response are necessary to predict, understand, control, and eventually end a pandemic. Testing is a major pillar of such a response and increased testing capacity is critical for enabling informed public health decisions and contact tracing programs. While national capacity has grown significantly in recent weeks, there is still a large, unmet need for more testing, and experts believe that millions of tests per day are needed for the United States to contain and slow the spread of COVID-19.

We’re developing large-scale testing capacity for Concentric by Ginkgo with next generation sequencing (NGS), which allows us to read, process and analyze many DNA and RNA samples in parallel on one machine. You can read more about the differences in testing methods in our white paper. We’re also working toward obtaining an Emergency Use Authorization for a COVID-19 test for our CLIA certified laboratory with the goal of scaling testing further. At the present time, to serve current reopening needs of businesses and educational organizations, Concentric by Ginkgo will work with other CLIA-certified labs offering RT-PCR based tests to make on-site testing programs available immediately.

We chose the name Concentric to highlight the interconnected communities we exist in, the different layers of proximity each of us have, and the ripples of impact that our choices send out into the world. As we grow Ginkgo, we’re excited to expand our foundries to enable more cell programming projects across many industries, now alongside Concentric.

Read more on Concentric’s efforts in our CNBC article and interview. To learn more about partnering with Concentric by Ginkgo to support your organization’s COVID-19 testing strategy, visit concentricbyginkgo.com to contact us.

There is broad agreement within the public health community that the path out of the COVID-19 lockdown is through widespread testing to catch new infections, tracing to find everyone who may have been infected, and supported isolation to prevent further spread of the virus. There is little agreement, however, that the technology and infrastructure exists today to meet that need.

With so much at stake—countless lives and billions of dollars—speed is of the essence in scaling up COVID-19 testing. We’ve put together a brief white paper providing an assessment of existing and emerging testing methods and outlines a path by which the United States can rapidly scale up the infrastructure that enables millions of tests per day.

To rapidly increase the scale of COVID-19 testing, the United States should:

• Continue to scale up testing methods already in use, such as RT-qPCR as well as isothermal nucleic acid methods, by expanding the number of testing machines and kits.
• Leverage the country’s vast genomic sequencing capacity by repurposing it to dramatically augment testing capacity.
• Invest in the development of massively distributable, cheap, point-of-use tests, such as antigen-based tests, and be prepared to deploy them as soon as they become available.
• Make testing widely available, beginning with those at highest risk, regardless of symptoms, insurance reimbursement, or other impediments.
• Scale up testing to enable screening of significant portions of the workforce and integrate screening effectively with contact tracing.

You can access a PDF version of our report here. We welcome your feedback—please reach out to us at [email protected].

In response to the COVID-19 pandemic, many groups across academia, biotech, and pharma are working hard to develop antibody therapeutics against SARS-CoV-2. Antibodies from patients who have recovered from COVID-19 may be effective in the treatment of critically ill patients, and many groups are seeking plasma donations to help those in need. In the long term, however, different approaches are needed to make effective antibody treatments available on a much larger scale.

Precisely engineered antibodies make up some of our most effective medicines. New antibodies can be based on those identified in convalescent patients, by reusing related antibodies (e.g., those effective against SARS), by screening antibody libraries, or by using computational methods to design new antibodies. As researchers discover and design new antibodies against SARS-CoV-2, many need help to rapidly produce and test these antibodies in preclinical studies. As part of our broader effort against COVID-19, we’re joining our friends at Berkeley Lights in their Global Emerging Pathogen Antibody Discovery Consortium to support the rapid development of promising candidate antibodies into useful treatments.

The consortium brings together many groups that are working to develop assays using the Berkeley Lights Beacon platform to quickly scale up the studies needed to advance new therapeutic antibodies against COVID-19 or any future emerging diseases. As a consortium member and in partnership with organizations that are designing new antibodies, Ginkgo will be using our automated high-throughput tools to reduce the preclinical development time for novel antibodies, through:

• Synthesis of large numbers of antibody genes;
• Expression of large numbers of antibodies in mammalian cells;
• High-throughput screening of those antibodies for antigen binding as well as critical functional properties including virus neutralization, antibody-dependent enhancement of infectivity, and cross-reactivity with blood proteins; and
• Optimization of lead antibodies for better stability, solubility, decreased  immunogenicity, and reduced cross-reactivity.

We have been so inspired by how the biotech community has come together so quickly in response to COVID-19, and we’re thrilled to be part of this consortium bringing together the people and tools to help accelerate a next generation of therapeutics. As with many aspects of Ginkgo’s COVID-19 response, this antibody-related work was a capability that we were developing that is now being put on an accelerated timeline.

If you’re working to discover new antibodies or other therapeutics targeting COVID-19 and would like to collaborate, please reach out to us at [email protected].

We’re inspired and heartened by the tremendous public health response to COVID-19, and recognize that a similar scale of effort is needed by the biotech community to find long-term solutions to this crisis. Former FDA commissioner Scott Gottlieb said today:

“We must get a drug and eventually vaccine. We can have treatments, antibody prophylaxis, point of care diagnostics for early detection by fall. That must be [our] focus. #COVID19 doesn’t go away. [The] [i]nitial wave will run course into summer but it’ll be back until our technology stops it.”

We’ve built our platform to enable partners across a wide range of applications to rapidly scale their R&D efforts, and we want to apply this technology today to the fight against the pandemic. To support the people building the treatments that will stop COVID-19 Ginkgo is now offering:

• $25M of no-cost foundry work towards projects that can use Ginkgo’s platform to accelerate development of point of care diagnostics, vaccines, or therapeutics. See below for details on how our technologies might be able to support these efforts.
• Connection to sources of funding from private and public sources. We are coordinating with people like Sam Altman and others on private funding efforts. If you are interested in funding COVID-19 work, we can connect you to vetted technical teams.
• Rapid sharing of R&D information as it is learned among the community of academics and companies working on solutions.

If you are currently a company or academic lab that is developing a diagnostic, drug, or vaccine and are interested in leveraging Ginkgo’s infrastructure at no cost please email us at [email protected].

Details on Relevant Ginkgo Capabilities:

Ginkgo has invested ~$400M over the last 5 years to build a 100,000 sqft automated facility that is used today to support partners like Roche and Bayer with a broad range of infrastructure for biotechnology R&D. We’ve listed some examples from our discussions with companies developing solutions to COVID-19 below, to help possible partners understand our scope. We will regularly update this list as we find additional areas of leverage we can provide to those working on COVID-19.

For the manufacturing of nucleic acid-based vaccines, we could:

• Provide process development capacity with our large bank of ambr250 fermenters for production of vaccine DNA
• Assist in developing E. coli or alternative strains for increased production of plasmid or vaccine DNA
• Rapidly discover and produce enzymes capable of improving downstream in vitro processing steps specific to the development of mRNA-based vaccines
• Use our high-throughput DNA synthesis capacity to rapidly synthesize and screen many designs for vaccine discovery and optimization

To support antibody-based therapeutics development, we could:

• Support lead optimization of promising candidate Abs, specifically using rapid DNA synthesis to generate 100s of different Ab designs and inserting these into CHO cells at a precise set of location(s) using cell lines with pre-engineered landing pads
• Screening via virus neutralization or (lack of) antibody-dependent enhancement of infectivity leveraging rapid & high throughput screening on the Berkeley Lights Beacon (an optical microfluidics screening platform that we have in-house)

To enable point of care diagnostics, we could:

• Rapidly discover enzymes capable of improving CRISPR/Cas-based nucleic acid diagnostics
• Use our protein engineering pipeline to further improve key parameters such as diagnostic specificity and selectivity, limit of detection, temperature and storage stability, and overall robustness
• Synthesize swap-in/swap-out guide RNA components for CRISPR/Cas-based devices, allowing rapid updating as new viruses need to be detected
• Scale protein expression to rapidly optimize production of the enzymes needed for device manufacture

To provide research tools, we could:

• Leverage our NGS platform to provide viral sequencing of ~10,000 samples per day. Environmental samples could be sequenced at our facility and we can partner with clinical labs to increase capacity for patient samples.
• Synthesize gene length fragments of the SARS-CoV-2 virus in a variety of expression formats and distribute via plasmid repositories to vetted and licensed entities.

More generally, we hope that our capacity for large-scale sequencing, synthesis, analytics, and cell engineering can support and accelerate efforts to develop new diagnostics, biologics, or vaccines for efforts such as those listed above and beyond. We’re looking to commit every part of our platform that can make a difference over the coming months. If you bring us an opportunity that’s not a fit for Ginkgo but can be accomplished by one of our technology partners, we’ll connect you.

We want to help connect great ideas in the community with the resources they need, whether that’s funding or access to technology at Ginkgo or elsewhere, or connections to others working on similar problems. If you have a project that needs support or are looking to contribute resources or expertise to the response and want to be connected to promising efforts, please email us at [email protected].