Posted 20th of March 2020 by Thomas Meany
Testing saves lives. Every person caring for a vulnerable individual needs daily testing. Every hero working at the front lines in hospitals needs daily testing. Every bus driver, postal worker, and shop keeper who takes risks to keep our society going needs daily testing. This is a once in a century pandemic and we need action.
We need to urge policy makers in the UK and elsewhere to permit “emergency use authorisation” guidelines so that we can lower the strict standards currently required and accelerate test deployment.
There are four main options for testing
1. General Immunoglobulin tests (IgG and IgM) test.
When we have an immune response immunoglobulins (specific immune system proteins) are released by immune system cells. Immunoglobulin M (IgM) and IgG are the first defence and the main immunoglobulins present in the blood in response to infection.
These tests are extremely cheap and widely available. They indicate if you are have or recently had an infection (anything from a bacteria, virus to food allergy). They don’t indicate what has caused the infection. Unfortunately the tests you hear about that are being “shipped” for blood testing are still just IgG and IgM tests, sadly with obscene markup due to crisis (e.g., Biomerica). These are just the same test strips used to test for food allergies.
Massive and widely available test strips could be an immediate low-cost way to test care workers, those at airports, hospitals, or other venues where large gatherings are unavoidable. They are our front line and this will protect them.
We need to urge policy makers in the UK and elsewhere to permit “emergency use authorisation” guidelines so that we can lower the strict standards required for these tests to ensure enough can be made rapidly available.
At open cell we are preparing to deploy up to 1 million test kits (priority for care/frontline healthworkers) once we receive regulatory guidance.
We need to do this immediately (1 week to 6 weeks). We are already late.
2. Reverse Transcriptase Polymerase Chain reaction (RT-PCR)
This nucleic acid test measures RNA present in a patient sputum sample. RNA is the part of of the virus that hijacks your cells. It is like DNA but has different nucleotides (uracil (U) rather than thymine (T)).
This is currently the only approved CDC protocol for lab testing and diagnosis. The core procedure involves extracting RNA from cells (using magnetic beads or columns) and then amplifying the nucleic acid using PCR. This step involves using “primers” and “probes” that find the particular sequence and amplify it making it measurable.
Over the last week we have worked hard to pull together the necessary resources to deliver high through nucleic acid testing. The core of this has been open source automation (using OpenTrons) and testing extraction and qPCR kits from different manufacturers. The system can currently process up to 500 tests per day and is rapidly scalable.
We will be placing our findings online throughout the weekend.
This will allow labs around the world to immediately download executable protocols for their particular extraction/assay. In addition we will publish our shipping container lab design so that labs can either replicate. If you urgently need this facility contact us. We can deploy across the UK in hours.
If you have support you can offer please contact us email@example.com. Our biggest needs are qPCR machines, liquid handlers and reagents/kits for RNA extractions and qPCR. If you have these make sure they don’t gather dust in this crisis. They can save lives. In particular closed universities are full of this equipment. If you are a university president or head of department please give.
These nucleic acid test reagents cost approximately £10 per test so if you wish to donate to this project please contact us.
This is needed immediately (1 week to 3 months) and will need to be in place until vaccines and other control measures can support social distancing.
3. Serology Tests.
This is an assay which specifically screens for the presence of COVID antibodies in blood. The body produces antibodies in response to infection (proteins that find and adhere to recognised foreign bodies like bacteria, virus in the body). Each antibody is specific to a unique receptor (antigen) present on the foreign invader.
This is an excellent assay as it will directly tell if you have had an immune response to a specific infection. The most advanced current assay targeted to COVID-19 has been developed by Zhao et al. this week. This is a hard and expensive test to do and to scale up quickly. Work is vital to progress but will take time.
This is urgent but will take time (1 month to 6 months). We need to support this work.
4. RNA Sequencing tests
RNA is the part of of the virus that hijacks your cells. It is like DNA but has different nucleotides (uracil (U) rather than thymine (T)). Advances in sequencing technology have meant it is now possible to directly sequence the RNA molecule. This is achieved using nanopore sequencing and a company Oxford Nanopore is one of the instruments most heavily used. An extremely practical paper this week by L. Cozzuto discusses a workflow with the required software hosted on GitHub.
This technique is still expensive, not fast and not particularly easily scalable (although it could be). However, it provides unprecedented understanding of viral mutations and could be an excellent compliment to qPCR.
We ask anyone working at Oxford Nanopore or using an Oxford Nanopore to consider supporting this project by donating equipment or consumables. You might also consider helping us in the lab as none of our team has expertise on this new technology.
This is not a priority for us but we still believe in the 1-6 month period we need to know what the virus is doing in case a more aggressive mutation appears.
How you can help
If you have support you can offer please contact us firstname.lastname@example.org. Our biggest needs are qPCR machines, liquid handlers and reagents/kits for RNA extractions and qPCR. If you have these make sure they don’t gather dust in this crisis. They can save lives. If you are a university president or head of department please take action.
Urge your government to act. Demand that current bureaucracy be reduced and the voice of frontline health workers heard. Demand that emergency use authorisation be enacted across Europe, demand fast tracked procurement for health services, demand funding for this. Demand action. Don’t accept the normal procedures and slow politicised discussions. Prioritise saving lives.
We have been contacted by potential donors. Thank you all. Please contact us if you wish to give. We can provide financial statements and show where your funds go. Every nucleic acid test requires £10 of reagent and we prioritise these costs. If you can give thank you. It will help.