Synthetic Biology (and beyond) Community response to COVID-19

Posted on by Christina Agapakis

Many organizations across biotech and synthetic biology are working hard to develop new diagnostics, vaccines, and therapeutics against COVID-19. Here is a running (non-comprehensive!) list of some of what we’ve seen so far, with a focus on these areas:

Data
Research tools
Community resources and accelerators
Diagnostics
Environmental testing
Therapeutics
Vaccines
Manufacturing and scale-up

If you are working on something you’d like to share, could use support for, or if you know of other great projects missing from this list, please email covid-response@ginkgobioworks.com.

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Data

There are many excellent resources for open public health, virology, and immunology data that are supporting efforts against COVID-19.

 

Viral biology

 

Viral tracking and evolution

  • 🧬 Ares Genetics — Next generation sequencing of virus to track evolution
  • 🧬 Nextstrain – Real time tracking of viral evolution

 

Public health tracking

 

Immune response characterization

 

Clinical trials data

 

Other data and news aggregators

  • 📲 COVIDbase — Curated list of projects, news, and data
  • 🖥 Github — Open collaboration resources
  • 🗞 SynBioBeta — News and Town halls
  • 📈 Tableau — COVID-19 Global Data Hub
  • 🗞 WEF — How are companies responding to the coronavirus crisis?


Research tools

Molecules derived from the virus—nucleic acids like RNA or DNA, or proteins—are valuable tools for COVID-19 R&D, forming the basis of diagnostics as well as being essential for developing and testing new vaccines and treatments. These companies are offering antigens, antibodies, RNA, and DNA for COVID-19 research.

Research test kits — qPCR

 

Research test kits — Immunoassays

 

Nucleic acids

  • 🧬 Arbor Biosciences — Free hybridization capture kits for NGS
  • 🧬 GENEWIZ — DNA sequencing and synthesis
  • 🧬 Ginkgo Bioworks — Synthesized viral cDNAs for protein expression
  • 🧬 IDT — DNA for diagnostics and vaccine development
  • 🧬 Paragon Genomics — Research and Surveillance panel
  • 🧬 SGI-DNA — $50,000 co-funding grants for collaboration supporting diagnostics, vaccines, and therapeutics
  • 🧬 Twist Bioscience — RNA controls and NGS panels

 

Antigens, antibodies, and enzymes

 

Software

 

Community resources and accelerators

 

Diagnostics

At this stage in the pandemic, widespread testing is essential to slowing the spread of the virus. Many organizations, from hospitals to academic labs, startups to multinationals have stepped up to develop, manufacture, and scale up testing kits. Check out the FDA’s page tracking diagnostic tests for more information and FindDx.org for an exhaustive list and this document for a detailed background on how these tests work.

Nucleic Acid Tests

 

Immunoassays

 

CRISPR based diagnostics

 

Other diagnostic tests 

  • 🌡 MiProbes — Rapid test to identify viral proteins

 

Testing hubs

 

Automation and scaling protocols

  • 🤖 Hamilton
  • 🤖 OpenCell — Scaling up testing infrastructure
  • 🤖 OpenTrons — Scale up of testing automation
  • 🤖 Salis Lab — Protocols for massively parallel testing
  • 🤖 Zymergen — Supporting automation for testing at the Chan Zuckerberg Biohub

 

Environmental testing

Testing for the presence of virus on surfaces and in other environments like sewers can help track and monitor for the spread of COVID.

 

Therapeutics

A large number of new and repurposed medicines are making their way through preclinical research and clinical trials to get to the patients that need it most. This list is biased for biologic drugs, such as antibodies, rather than small molecule therapeutics that could treat infection. Many of these therapies use antibodies, often derived from the blood plasma of patients that have recovered from coronavirus, to help the immune system of patients fight the virus directly.

Antibody therapies in development

  • 💊 AbCellera — Developing antibody therapy with Eli Lilly
  • 💊 CytoDyn — Phase 2 trial antibody therapeutic
  • 💊 Emergent BioSolutions — Plasma-derived antibody therapy
  • 💊 Kamada — Plasma derived IgG therapy
  • 💊 La Jolla Institute — Coronavirus Immunotherapy Consortium
  • 💊 Regeneron — Plasma derived antibody therapy
  • 💊 Takeda — Plasma derived IgG therapy
  • 💊 Vir — Developing antibody therapy with Bingen

 

Rapid antibody discovery

 

Other therapeutics 

 

Vaccines

In the long term, vaccines are essential for eradicating the thread of dangerous pathogens. Many groups are in the process of developing and testing several different kinds of vaccines. Vaccines train the immune system to recognize the virus so that it can be ready to clear the virus at the first sign of infection. Vaccines can be made from a number of different biological molecules: DNA, RNA, proteins, virus like particles, or live attenuated virus. Check out the WHO landscape of candidate vaccines for more.

Live attenuated virus vaccines

 

Virus-like particle (VLP) vaccines

 

Non-replicating viral vector vaccines

 

mRNA vaccines

 

DNA vaccines

 

Protein vaccines

 

Other vaccines

 

Adjuvants


Manufacturing and scale up

Once a new antiviral therapeutic or vaccine is developed and tested, it needs to be scaled up for delivery.

 

Are we missing something? Please email covid-response@ginkgobioworks.com.

Posted By: Christina Agapakis