The coronavirus pandemic has changed the landscape of life science by consuming the majority of research opportunities for the near future. But it is also giving researchers unprecedented opportunities for collaboration, innovation, and creation of new knowledge.
And with unprecedented opportunities comes unprecedented resources–many of which are free to use. From Slack channels to SOPs, here are 9 tools to help any researchers hoping to setup testing labs, optimize a workflow, or otherwise participate in this global science project.
With over 13,000 researchers from all over the globe, this is the world’s biggest conversation about scaling up COVID-19 testing. It’s full of collaborative discussions on everything from troubleshooting RNA extraction workflows and scoping out vendors to overcoming sample and supply chain logistics and filing for an Emergency Use Authorization with the FDA. You can join the conversation, too; just click the link above and email [email protected] for a 24-hour invitation.
An extensive guide from the Innovative Genomics Institute (IGI) about how to set up a CLIA-certified SARS-CoV-2 testing lab. IGI is a group of researchers at the University of California, Berkeley and the University of California, San Francisco, and they pulled together a diverse, interdisciplinary team that worked around the clock for 3 weeks to scale up coronavirus testing in the Bay Area. Their guide includes tips on everything from their specific automation workflows and protocols to personnel training and compliance guidelines.
A step-by-step guide from the Crick COVID19 Consortium about how they created a diagnostics lab in an academic setting with outside partnerships. A collaboration between University College London Hospitals, Health Services Laboratory (HSL), the Institute of Cancer Research, and the Francis Crick Institute, the Crick COVID19 Consortium created this testing setup in a little over 2 weeks. Their downloadable guide covers everything from lab safety information and Category 2 sample inactivation guidelines to RNA extraction protocols and creating homemade buffers.
Open access from the Broad Institute about their Clinical Research Sequencing Platform (CRSP) for SARS-CoV-2. A collaboration between researchers at Massachusetts Institute of Technology (MIT) and Harvard University, the Broad Institute uses their platform to run a Real-time Reverse Transcriptase (RT)-PCR diagnostic assay. For any researchers in search of a testing facility, Broad Institute has opened access to theirs. Their instructions include guidance for specimen collection and shipping guidelines, as well as an FAQ on diagnostic testing and assay fact sheets for patients and providers.
A slate of tools from Synthego for genomics researchers to enhance speed and efficacy in developing COVID-19 diagnostics and treatments. These tools include a custom Cas13 guide for RNA collections and multi-arrayed CRISPR sgRNA gene knockout libraries targeting 330 human genes that interact with SARS-CoV-2 proteins. They have a link to all these tools, as well as the published testing data they used to create them, on their site.
A proof-of-concept of a SwabSeq NGS diagnostics workflow from Octant. A biotech company using proprietary technology combining synthetic biology, genome engineering, next-generation sequencing, and computational tools, Octant created a protocol to scale up COVID19 sequence-based testing that is simple, cheap, and sensitive. It’s called SwabSeq and their lab notes document includes everything from protocols and testing code to data charts and internal notebooks.
A proof-of-concept of a massively parallel NGS diagnostic assay from synthetic biology researcher Howard Salis of Pennsylvania State University. Salis published a preprint detailing how Massively Parallel Diagnostic Assays (MPDA) can leverage next-generation sequencing to simultaneously carry out thousands of viral RNA measurements in a single assay and process up to 19,200 patient samples per workflow. His preprint details his workflow combining viral RNA extractions, Reverse Transcriptase (RT) using patient-specific primers with unique barcodes, and a single pooled Polymerase Chain Reaction (PCR) followed by Next-Generation Sequencing (NGS).
A slew of blueprints, protocols, and other resources from OpenCell. A company providing biotech startups with mobile, affordable shipping container lab space OpenCell is leading the way in UK testing, rapidly scaling high throughput testing facilities that can process up to 10,000 tests per day.
A workflow and testing system, including reagents, from Zymo Research. A company providing biomedical tools and services, they’ve pivoted to tackle the coronavirus pandemic. They created a complete COVID-19 detection workflow that handles sample collection, RNA extraction, and RT-PCR-based detection. They also developed a joint COVID-19 testing system with Opentrons and would be happy to support any researchers interested in onboarding their workflow onto an Opentrons OT-2.
If you would like to implement the Opentrons system in your own lab, or be invited to the global Slack channel, please contact [email protected].