Q&A: Distributed biological processing can prevent pandemics 

It is possible to leverage the powers of distributed biological processing to fight emerging pathogens faster and prevent them from spreading in the future, building a global antibody defensive barrier, according to Dr. Eric Hobbs.

The company Berkeley Lights founded the Global Emerging Pathogen Antibody Discovery Consortium (GEPAD) in collaboration with Vanderbilt University Medical Center, La Jolla Institute for Immunology, Ginkgo Bioworks, and Emory University. The aim of the consortium is to accelerate the discovery of neutralizing antibodies from COVID-19 patient blood samples to find an immediate treatment, and in the longer term, enable the quickest therapeutic response to emerging pathogens.

Berkeley Lights' proprietary technology, the Beacon® system, is being used by researchers across three continents to screen COVID-19 patient blood samples and help develop a treatment and vaccine faster

The company has also found and recovered, with Ablexis and AlivaMab Discovery Services, a broad panel of unique, functionally diverse antibodies to SARS-CoV-2. They are in discussions with pharma now to see them developed further.

To gain an insight into the potential of distributed biological processing, Digital Journal spoke with Dr. Eric Hobbs (Berkeley Lights). Dr. Hobbs has been working at the intersection of biology, pharma, and tech for many years.

Digital Journal: What are the major pathogen threats?

Dr. Eric Hobbs: SARS-CoV-2 has created a global pandemic and is the focus of significant research currently. Outside of the current pandemic, the NIAID lists some of the top highest risk pathogens, with the most dangerous being those that can be easily transmitted from person to person and may result in high mortality rates. A pathogen or infectious agent is a biological agent that causes disease or illness to its host (i.e. humans), and it can be a virus, bacterial infection, or fungi, for example. Some examples of pathogens are the Ebola virus, HIV, rabies, influenza, smallpox, MERS-CoV, SARS-CoV, and, of course, SARS-CoV-2.

DJ: How can we leverage the powers of distributed biological processing to fight emerging pathogens faster?

Hobbs: First, it’s important to know that infectious diseases emerge in single locations globally. It is in that single location where all of the human immune responses to the emerging pathogen occur at the early stages of an outbreak. Unfortunately, during the COVID-19 outbreak, we have seen that today’s biopharmaceutical discovery infrastructure is highly centralized and not well suited to rapidly respond to emerging pathogens at a local level. There is a disconnect between local pathogen emergence and centralized response.

During this pandemic, some of the researchers and scientists who had access to recovering patient blood samples lacked access to state-of-the-art antibody discovery technology, while many who had access to leading technology did not have access to the patient blood samples. At Berkeley Lights, we believe that the speed and ability to respond to emerging pathogens can be dramatically improved with a solution that can be placed close to recovering patients from the initial outbreak – a solution that leverages the powers of distributed biological processing. If we leverage distributed biological processing in the future, we'll be able to react faster and save more lives in the future.

The Berkeley Lights Platform addresses this localization problem and uses distributed biological processing. This means the platform leverages automation, workflow standardization, and the ability to gather more relevant phenotypic and genotypic information for each single cell, across a number of dimensions using Deep Opto Profiling™ to enable the rapid discovery, development, and distribution of therapeutic antibodies targeting emerging pathogens anywhere in the world.

By placing the Berkeley Lights Platform at Centers for Disease Control (CDCs) and regional centers of excellence worldwide, we would enable researchers to analyze emerging pathogens directly where they appear and prevent them from spreading in the future. Our systems can be networked via the cloud to provide global access to the latest Berkeley Lights workflows and return diverse, functional antibody sequences to biopharmaceutical companies for development and manufacture of therapeutic antibodies. The Berkeley Lights Platform can also be applied to endemic infectious diseases, such as influenza and tuberculosis, in the ongoing search for broadly neutralizing antibodies.

We believe that our platform can become a key enabler of distributed biological processing, ultimately helping to fight emerging pathogens faster and more efficiently right where they appear and very early in the spread. More broadly, distributed biological processing means that we’re able to distribute and decentralize the way we approach biology and scientific research, helping researchers around the world respond locally at the point of initial infection and develop solutions for diseases across the world.

DJ: How can this technology prevent pathogens from spreading in the future?

Hobbs: Berkeley Lights technology does not, itself, prevent pathogen spread, but our platform can be networked via the cloud to access the latest workflows and enable researchers anywhere in the world to find neutralizing antibodies to emerging pathogens, right where they appear. By doing so, researchers can, at the first points of infection, start identifying local solutions and treatments to such pathogens and thereby minimize the likelihood of the pathogen spreading and becoming a pandemic.

Specifically, researchers can import live cells from recovering patients or immunized animals into the Berkeley Lights Platform, which then captures deep phenotypic, functional, and genotypic information for thousands of single cells in parallel. Within 24 hours of starting our automated workflows, the platform delivers functionally characterized antibody therapeutic candidates, which can be used to develop a treatment for the disease. We need to distribute these capabilities globally and enable the world to respond to new viruses on a local level faster and more efficiently with this technology.

DJ: What are some lessons we learned about drug discovery and vaccine development during this pandemic?

Hobbs: We already knew that vaccines take a long time to make and distribute—it can take five to ten years to get a vaccine ready for clinical trials in humans, then go to market. What we have learned is that existing timelines and processes cannot quickly defeat a fast-spreading pathogen. The long lead times to therapy and vaccine gives coronaviruses like SARS-CoV-2 the opportunity to spread across the globe to cause widespread devastation. The takeaway is that we need to move faster. If we want to find a sustainable solution to COVID-19 and future pathogens, we need to pursue new avenues, such as antibody discovery platforms that can accelerate drug discovery and vaccine development at scale and from anywhere in the world.

DJ: What are the main risks around the SARS-CoV-2 virus?

Hobbs: We are still learning about the varied and numerous effects of the SARS-CoV-2 virus on people. Obviously the risk of death, while statistically small, is very real and horrific. And we are also learning that there may be long-lasting negative health impacts on recovered patients. While for most people, the risk of becoming seriously ill from COVID-19 is thought to be low, older adults and people of any age who have underlying medical conditions may be at higher risk for more serious complications or death.

DJ: How can antibody therapies be used to limit the mortality and morbidity of COVID-19 before we have a vaccine?

Hobbs: Realistically, we probably will not have a U.S. FDA approved vaccine until 2021. Our focus at Berkeley Lights at this time is to drive antibody therapeutics research to develop a treatment sooner and limit not only the death rate but hopefully some of the serious health impacts being seen in ”recovered” patients. Our Beacon system allows researchers to screen antibodies prepared from COVID-19 patient blood in just ten hours to identify the neutralizing antibodies required to develop antibody therapeutics. Antibody therapeutics are a form of immunotherapy that use monoclonal antibodies to bind to particular cells or proteins, in this case the spike protein on the surface of SARS-CoV-2, and stimulate the patient’s immune system to attack and block the virus. A treatment or prevention from antibody therapeutics could have potentially saved the over 905,000 lives lost to COVID-19.

Since early 2020, we have been working with multiple commercial and academic institutions across the globe, enabling them to find functional, blocking, and potentially neutralizing antibodies from COVID-19 patient blood samples faster with our platform.

For example, Genscript in China leveraged the Berkeley Lights Platform to find SARS-CoV-2 binding antibodies within 24 hours of loading cells from patient blood onto our system. The Vanderbilt University Medical Center used the platform to screen cells from recovering COVID-19 patient blood and found over 500 binding antibodies in a single day. We are also working with the University of Queensland who is using our system for cell line development and to accelerate manufacturing of a potential vaccine.

DJ: Why is biotech/government collaboration to combat COVID-19, as well as for preventing future pandemics, so important?

Hobbs: Unfortunately, most countries do not heavily invest in pathogen research until an epidemic or pandemic arises. This is why, prior to the outbreak, there was not enough funding for research in this field and only now, as COVID-19 emerged, governments and companies are investing in finding a solution. But to prevent pandemics from happening again, we have to think ahead and invest in solutions now, putting the technology and systems in place that can help fight the next virus locally wherever it appears and before it spreads across the world.

Biotech companies have the cutting edge technology, brainpower, and flexibility to quickly come up with such solutions to viruses such as COVID-19, while governments have the funds to help them in their efforts. This is an opportunity for the world’s governments to acknowledge and assist the enormous role biotech and pharma companies play in this global race for a vaccine and treatment. Government needs to take advantage of how fast these companies can move and provide them with the tools and resources they need to operate quickly at scale.

Government support could allow us to build a global defense network of systems, software, and tools that would allow scientists from all over the world to work together to develop drugs and vaccines faster and more efficiently. Berkeley Lights is already placing its systems all over the globe to develop antibody therapeutics. We founded the Global Emerging Pathogen Antibody Discovery Consortium (GEPAD) to accelerate the discovery of neutralizing antibodies from COVID-19 patient blood samples to find an immediate treatment, and in the longer term, enable the quickest therapeutic response to emerging pathogens.

As we are now experiencing, the prevention and containment of infectious diseases at this scale requires cross-border collaboration. There is a need to infuse more funding into the biotech industry around the world to accelerate this process and set up the best possible defense against future emerging pathogens.