Category: Governments

Empowering the DRC to form the foundation for a biosecurity and bioeconomy platform

Today, we are pleased to announce that we’ve entered into a Memorandum of Understanding (“MOU”) with the intent of developing and implementing new biosecurity capabilities in Democratic Republic of the Congo. We’ve entered this MOU alongside the Institut National de la Recherche Biomédicale (“INRB”).

The goal of our planned partnership is to support DRC’s public health institutions as they work to address biosecurity challenges in the region. We, through our biosecurity and public health unit, Concentric by Ginkgo, plan to collaborate with the INRB to equip these institutions with biosecurity tools and training. We also plan to provide the secure data infrastructure they need to leverage automation, data analysis, bioinformatics capabilities, and other critical genomic sequencing technologies. Our collaboration aims to empower the DRC to form the foundation for a biosecurity and bioeconomy platform that serves the people of the DRC and the surrounding region.

Enabling and advancing biosecurity initiatives for all

We recognize the importance of international collaboration and cooperation to promote global health security as biological threats emerge. Low-resource areas often lack the infrastructure to monitor and respond effectively to biological threats, putting the people of these regions at a heightened outbreak risk. Investing in pathogen monitoring infrastructure in areas such as the DRC is essential for building systems that are capable of detecting and responding to emerging infectious diseases.

We’re thankful for the opportunity to collaborate with the INRB. Our aim is to continue to build upon a global weather map of critical infrastructure for tracking the spread and evolution of infectious disease, creating a safer and more secure world.

Effective pathogen monitoring and data sharing capabilities can empower government officials, community leaders, and other stakeholders to make informed public health decisions. In the long-term, these capabilities can also be leveraged to form the foundation for a sustainable regional bioeconomy.

“Continued collaboration is imperative to protect public health against emerging pathogens, in the DRC and around the world. We look forward to our partnership with Concentric, which will allow us to bring cutting-edge technology and a holistic approach to advance the DRC’s biosafety capacities,” declared Professor Jean-Jacques Muyembe, Director General of the INRB.

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

Monitoring for COVID-19 variants at Kigali International Airport

We’re excited to announce that we’re partnering with the Rwanda Biomedical Centre (RBC) on a one-year pathogen monitoring program at Rwanda’s Kigali International Airport (KGL) to identify new and emerging viral variants.

Adding a new node to our pathogen monitoring network

Concentric by Ginkgo and RBC will collaborate to detect the virus on arriving international flights. We’ll sample aircraft wastewater and collect nasal swabs from travelers on a voluntary, anonymous basis. Our aim is to provide critical early warning public health insights to help inform strategies in Rwanda and beyond.

Ginkgo and RBC will work together to establish KGL as a new node in a global network of pathogen monitoring infrastructure, complementing the insights generated from Concentric’s existing travel biosecurity programs at several major international airports in the U.S. The program builds on Ginkgo’s previously announced MOU to develop and implement biosecurity capabilities in Rwanda.

A public health radar to inform targeted response strategies

Mitigating the risk of biological threats, including emerging viral variants, remains a global imperative that necessitates a robust early warning system. This pathogen monitoring program at Kigali International Airport will act like a public health radar, providing leaders with near-real-time data to inform targeted response strategies. We are excited to be partnering with the Rwanda Biomedical Centre—to stay ahead of the next variant or pathogen of concern, we must take an international approach to biosecurity.

RBC is Rwanda’s national health implementation agency, established in 2011 to improve the health of the Rwandan population by providing high quality, affordable and sustainable health care services. Ginkgo will support the end-to-end collection and analysis workflow with materials, training and logistical support, digital platform and data reporting, as well as bioinformatics and decision support services; RBC will contribute on-the-ground operational support for sample collection, testing, and sequencing.

Prof. Claude Muvunyi, the Director General of the Rwanda Biomedical Centre said, “As we continue to feel the impacts of emerging variants and pathogens, we recognize the need to create a sustainable public health and biosecurity infrastructure in Rwanda and internationally. We are thrilled to launch this program at Kigali International Airport in partnership with Ginkgo to enhance our biosecurity capabilities.”

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

New technologies to detect engineered DNA

We’re proud to announce the completion of IARPA’s Finding Engineering-Linked Indicators (FELIX) — a program created to augment and improve current biodetection and biosurveillance capabilities. The program was a collaboration between the Intelligence Advanced Research Projects Activity (IARPA; the research and development arm of the U.S. Intelligence community), Draper (a nonprofit engineering innovation firm), and Ginkgo.

We’ve developed a suite of new computational tools for FELIX, while Draper has developed a new experimental platform to help detect and identify when samples include genetically engineered biological systems. The results from the program will be presented on October 17, 2022 at 11am on YouTube.

Current methods for detecting signs of biological engineering are typically costly, slow, and capable of detecting only a subset of all possible genetic modifications. In collaboration with IARPA, Ginkgo developed an initial set of computational tools called ENDAR (Engineered Nucleotide Detection and Ranking) that assist trained analysts to identify genetic engineering in next generation sequencing (NGS) datasets. This software aims to make it possible for scientists to detect engineered DNA at scale.

Breakthrough for biosecurity

“Through their work on the FELIX program, Ginkgo and Draper have achieved two major breakthroughs for the biodetection community,” said David A. Markowitz, Program Manager at IARPA. “The ability to detect genetic engineering in complex biological samples has long been a moonshot goal, and these new capabilities are poised to transform national biosecurity efforts.”

Designed to work across a range of biological organisms that may be found in complex, multi-species environments, ENDAR tools and methods could provide early alerts to the presence of engineered organisms and help expedite appropriate responses, thereby mitigating adverse consequences.

Ginkgo has a core belief in the promise of engineered biology—a thriving bio-based economy that delivers benefits to society, the environment, and our health. We care deeply about securing that vision by ensuring that biology is engineered and deployed responsibly. Working with IARPA, we’ve developed a fundamentally new biosecurity capability that will enhance our ability to detect, characterize, and respond to biological threats. We’re excited to explore opportunities to deploy ENDAR as an integral component of our global biosecurity platform.

Draper’s contributions to FELIX, under its contract with IARPA, include development of a lab-based genetic test, a custom bioinformatics pipeline that contextualizes DNA sequencing data and miniaturized microarray hardware all with the goal of characterizing otherwise impossible to detect genetic engineering. Potential applications include biothreat detection, environmental monitoring, and food inspection.

“At Draper, we believe that advances in gene editing technology are creating new opportunities for biosecurity,” said Laura Seaman, Principal Scientist and Machine Intelligence group leader at Draper. “Under the FELIX program, we have developed a device and associated lab and computational methods that are sensitive enough to pick out an engineered organism in a complex environmental background containing millions of natural organisms—the signal-to-noise ratio is a significant improvement over current methods.”

The event featured a panel with participants including, Catherine Marsh, IARPA Director; David A. Markowitz, IARPA Program Manager; Joshua Dunn, Head of Design, Ginkgo Bioworks; Laura Seaman, Principal Scientist and Machine Intelligence Group Leader, at Draper; and Erin Rosenberger, Senior Member of Technical Staff, Biological Microsystems Group, at Draper. During the panel, the panelists will discuss the program findings and also feature a demo of the research results.

Watch a livestream of the presentation of results from the FELIX program on October 17, 2022 at 11am here.

Find the full press release here along with all of the latest news from the Ginkgo team.

What will you grow with Ginkgo?

It’s been an intense and inspiring few weeks as our DNA synthesis team, Biofab, has been working hard to produce the first batch of SARS-CoV-2 protein constructs. This week, we sent the first 288 plasmids to Addgene and BioBricks Foundation, for distribution to academic and industrial labs.

The first set of plasmids consists of SARS-CoV-2 annotated proteins in E. coli and yeast vectors, with various C-terminal tags, suitable for protein expression and purification. We expect to send more from this set to Addgene and BioBricks Foundation each week, as well as mammalian expression constructs, additional Spike protein constructs for expression and VSV pseudotyping, and plasmids containing viral DNA. Check this repository for the full set of sequences already deposited and in our synthesis queue.

You should be able to access these sequences shortly from Addgene and BioBricks Foundation. If you have questions, other ideas, or a project that you think could benefit from access to Ginkgo’s foundries, please reach out to [email protected].

Project Update: Read about our progress on this project here!

Our mission is to make biology easier to engineer—that hasn’t changed for the ten years we’ve been building Ginkgo. The ability to read, write, and design DNA code is having profound positive impacts in medicine, agriculture, and manufacturing, from engineered cell therapies that can target a person’s cancer cells, to probiotics for plants that can reduce the need for nitrogen fertilizers, to sustainably grown materials.

We are working to unlock the enormous power of biology: its ability to grow sustainably, to process information, and adapt to changing environments. But we’re not naive to the potential risks. We understand that as it becomes easier to engineer biology, it will become easier to engineer the part of biology that’s dangerous to humans, animals, and plants—the pathogens and parasites that can infect us. Since researchers synthesized the polio virus in 2002, it has been technically possible to chemically synthesize viruses that infect humans

To date, the work done on synthesizing viruses has been intended for medical research and other peaceful purposes, but there is a concern that someone could theoretically produce a virus or other pathogen with the intent to harm. The intentional use of pathogens to harm others is abhorrent and something that I believe that we should never do under any circumstances—as a company and as human beings. The international community agrees with me on this: 180 countries including the United States are parties to the UN Biological Weapons Convention, which was first signed in 1972 and states that we are “never in any circumstance to develop, produce, stockpile, or otherwise acquire or retain: Microbial or other biological agents, or toxins…that have no justification for prophylactic, protective or other peaceful purposes.”

As the technology for synthesizing DNA code improves, groups from governments, industry, academia, and civil society have been developing frameworks for monitoring and assessing the safety and security of these new technologies. For example, we are a part of the international gene synthesis consortium, which developed standards for screening orders made to DNA synthesis companies. Our Head of Design, Patrick Boyle, was also recently on a panel convened by the National Academies of Sciences, Engineering, and Medicine to assess the risks of intentional misuse of synthetic biology.

Today we’re announcing Ginkgo’s biosecurity initiative that directly addresses some of these potential threats from engineered DNA sequences. Our current work on biosecurity focuses primarily on detecting potential threats using software that analyzes DNA sequences.

As part of IARPA’s (the Intelligence Advanced Research Projects Activity) Fun GCAT program, we are developing software to monitor DNA synthesis. This software is intended to ensure that no one orders DNA sequences that could have a pathogenic function. Think of this like a malware detector in computer programming—“programs” being written in synthetic DNA will go through the detector software, which will flag any sequences of concern before they are synthesized. The custom software we’ve developed for designing DNA sequences in our foundries is a useful start for a project like this—we need to be able to predict the function of enzymes based on their sequences in order to design new functions in our engineered microbes. Rather than predicting if an enzyme sequence could be used to produce, say, a fragrance or vitamin, here we’re applying the same types of algorithms to predict whether a given bit of code could be potentially harmful.

Unlike computer viruses, however, new biological viruses can also evolve in the wild. When a new virus emerges, researchers quickly sequence it to understand where it came from and how to best treat it and develop vaccines against it. We’re addressing this as part of another software-based biosecurity initiative, IARPA’s Finding Engineered Linked Indicators (FELIX) program. Here we are using deep learning to identify if the sequence of a new pathogen developed naturally or was engineered by humans. We’re leveraging our experience engineering the world’s largest library of engineered DNA sequences to help us train the software to detect whether something has been engineered.

Beyond developing software to guide the detection of threats, synthetic biology can also be important for responding to emerging diseases, for example making rapid response vaccines. It’s been almost a decade since the Venter institute partnered with Novartis on rapid synthetic DNA based vaccine development and the technology has been exponentially improving since then. Working alongside other companies, universities, and government agencies, we’re excited to be part of groups involved in developing tools to prevent, diagnose, and treat current and emerging diseases.

Ginkgo is the leading developer of genetic engineering tools we have an obligation to ensure that these tools are responsibly used. We are inspired by the words of Andy Weber, the former Assistant Secretary of Defense for Nuclear, Chemical & Biological Defense Programs under President Obama and a valued advisor to us here at Ginkgo on issues of biosecurity: we believe that while synthetic biology may lead to new risks, that these new tools also actually “offer the opportunity to take the global threat of biological weapons off the table.” By helping to develop software that can detect any threats before they materialize and develop the tools that can rapidly respond to emerging infectious diseases—natural or engineered—we hope to continue to drive the responsible growth of synthetic biology and realize its enormous potential for good.

For more on this story, check out Rebecca Spalding’s article in Bloomberg: “The DNA Cops Who Make Sure the World’s Deadliest Viruses Aren’t Rebuilt.“