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

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 [email protected].

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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

• 🧬 Allen Institute COVID-19 Open Research Dataset — Collection of published articles and preprints on COVID-19

• 🧬 ARTIC Network — Open source sequencing & analysis protocol

• 🧬 Genome sequence

• 🧬 Immunitrack — Structures of immune stimulating epitopes from COVID-19 to aid vaccine developmen

• 🧬 Innophore — Protein structure modeling

• 🧬 McLellan lab, UT Austin — Structure of the Spike protein

 

Viral tracking and evolution

• 🧬 Ares Genetics — Next generation sequencing of virus to track evolution

• 🧬 Nextstrain – Real time tracking of viral evolution

 

Public health tracking

• 🌡 The COVID Tracking Project — testing data for the US

• 🌡 COVID Growth Rate Tracker

• 🌡 Johns Hopkins data tracker

• 🌡 Open COVID-19 Study — tracking symptoms

 

Immune response characterization

• 🖥 Adaptive Biotechnologies — Working with Microsoft to provide open data on immune response to COVID-19

 

Clinical trials data

• 🥼 Vivli

 

Other data and news aggregators

• 📈 Academic Data Science — COVID-19 Data Science Resources

• 📲 COVIDbase — Curated list of projects, news, and data

• 📲 COVID-19 Primer

• 🖥 COVID-19 Ask Miso Anything

• 🖥 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

• 🧬 Biomeme — Handheld qPCR device

• 🧬 Genscript

 

Research test kits — Immunoassays

• 🧫 Creative Diagnostics

• 🧫 Eagle Biosciences

• 🧫 Epitope Diagnostics

• 🧫 EUROIMMUN

• 🧫 Nirmidas Biotech

 

Nucleic acids

• 🧬 Addgene — COVID-19 plasmids & resources

• 🧬 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

• 🧬 SARS-CoV-2 coding sequence clones

• 🧬 SGI-DNA — $50,000 co-funding grants for collaboration supporting diagnostics, vaccines, and therapeutics

• 🧬 Sigma Aldrich

• 🧬 Synbio Technologies

• 🧬 Twist Bioscience — RNA controls and NGS panels

 

Antigens, antibodies, and enzymes

• 🧫 BEI Resources

• 🧫 Bio-connect

• 🧫 The Native Antigen Company

• 🧫 Open Enzyme Collection

• 🧫 Tierra Biosciences

• 🧫 SinoBiological

 

Software

• 🖥 AWS

• 🖥 Foldit

• 🖥 SalesForce ProGen

• 🖥 Synthace

• 🖥 TeselaGen

 

Community resources and accelerators

• 👩‍🔬 BIO Coronavirus Hub

• 👩‍🔬 The COVID accelerator

• 👩‍🔬 IndieBio Coronavirus Initiative

• 👩‍🔬 Just One Giant Lab

• 👩‍🔬 Y combinator

 

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

• 🧬 Abbott

• 🧬 Aldatu Biosciences

• 🧬 Cepheid

• 🧬 Curative

• 🧬 Hologic

• 🧬 Mobidiag

• 🧬 New England Biolabs

• 🧬 Octant Bio

• 🧬 QIAGEN

• 🧬 Roche

• 🧬 Thermo Fisher

• 🧬 Veredus

 

Immunoassays

• 🌡 Attomarker

• 🌡 Genalyte

• 🌡 Krammer Lab — Protocols for COVID serology

• 🌡 Mologic

• 🌡 Nirmidas Biotech

• 🌡 Predigen

• 🌡 RayBiotech

• 🌡 Sona Nanotech

• 🌡 Sugentech

• 🌡 United Biomedical Group

 

CRISPR based diagnostics

• ✂️ Broad Institute — Open access CRISPR testing protocol

• ✂️ CASPR Biotech — Method preprint

• ✂️ Mammoth Biosciences

• ✂️ Sherlock Biosciences

 

Other diagnostic tests 

• 🌡 MiProbes — Rapid test to identify viral proteins

 

Testing hubs

• 🌡 Battelle

• 🌡 Broad Institute

• 🌡 Chan Zuckerberg Biohub

• 🌡 Greater Seattle Coronavirus Assessment Network

• 🌡 Innovative Genomics Institute

• 🌡 UCSF

• 🌡 UK Whole Genome Sequence Alliance

• 🌡 University of Washington Department of Virology

 

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.

• 📍 Aanika Bioscience — Environmental detection for enterprise customers

• 📍 Chai Bio — RT-PCR based environmental detection from swabs

• 📍 Stemloop — Cell free biosensors

• 📍 Twist Bioscience and Mason Lab at Cornell — Sampling NYC public transit

 

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

• 💊 Berkeley Lights — Antibody screening

• 💊 Distributed Bio — Computational antibody discovery

• 💊 ImmunoPrecise Antibodies — Multi-target antibody discovery platform

• 💊 Macromoltek — Computational design of antibodies

• 💊 Prellis Bio — Antibody generating platform

• 💊 Swiftscale Biologics — Speeding the process for antibody discovery

 

Other therapeutics 

• 💊 Alnylam — siRNA based therapeutics with Vir

• 💊 CEL-SCI — Immunotherapy using peptide

• 💊 Pentelute Lab, MIT — Peptide binder to spike protein

• 💊 Voigt Lab, MIT — High throughput therapeutics discovery

 

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

• 💉 Codagenix

• 💉 Humane Genomics

• 💉 Sinovac

 

Virus-like particle (VLP) vaccines

• 💉 Medicago — expressed in plants

 

Non-replicating viral vector vaccines

• 💉 Altimmune

• 💉 CanSino Biologics — In Phase I clinical trials

• 💉 GeoVax

• 💉 Greffex

• 💉 Institut Pasteur, with Themis and the University of Pittsburgh

• 💉 Johnson & Johnson

• 💉 Vaxart

 

mRNA vaccines

• 💉 Arcturus – In collaboration with Duke-NUS Medical School

• 💉 BioNTech and Pfizer

• 💉 CureVac

• 💉 HelixNano — multi antigen mRNA vaccine

• 💉 Imperial College London

• 💉 Moderna — In Phase I clinical trials

 

DNA vaccines

• 💉 AnGes Inc. — In collaboration with with Osaka University

• 💉 Inovio

• 💉 Takis — with Applied DNA Sciences and Evvivax

• 💉 Zydus Cadila

 

Protein vaccines

• 💉 AJ Vaccines

• 💉 Clover Biopharmaceuticals — In collaborating with GSK

• 💉 EpiVax

• 💉 ExpreS2ion

• 💉 Heat Biologics

• 💉 iBio and CC pharming — Protein expressed in plants

• 💉 Ligandal

• 💉 Novavax

• 💉 Sanofi

• 💉 University of California, San Diego

• 💉 University of Queensland

 

Other vaccines

• 💉 Prokarium

 

Adjuvants

• 💉 Amyris

• 💉 DynaVax

Manufacturing and scale up

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

• 🧪 Culture Biosciences - Process optimizations and development

Other products

• 🧼 Amyris—hand sanitizer

 

Are we missing something? Please email [email protected].

Posted by Christina Agapakis

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