COVID19 Molecular Diagnostics Briefing
Jeffrey Ladish, Edward Perello, Sean Ward, Tessa Alexanian
Abstract: This document is designed for novices to biotechnology and pandemic response. The goal is to introduce various categories and molecular methods for diagnosing COVID19, outline companies and academic groups developing diagnostics, and to inform decision-making about maintaining the resilience of nations against the rapidly spreading viral disease.
COVID diagnostics are a diverse bunch and not all tests are created equal. Tests can vary in their turnaround time, cost, specificity, accuracy, and scalability. Here follows a crash course in the various molecular detection methods of note for COVID-19, and their suitability for use in a large- scale diagnostic programme.
The authors assume the following recommendations are under consideration by the readers in government and healthcare settings, which the content has been designed to support discussion around:
1. Consider temporary regulatory waivers of validated kit components of supply limited assays and domestic manufacture of alternates.
2. Consider at the minimum the parallel usage of multiple alternative diagnostic technologies for surveillance purposes while collecting a data package and regulatory fast path to consider their usage for diagnostic purposes as well.
3. Strongly consider supply chain risks in solutions and invest in domestic manufacturing capacity, including the potential temporary repurposing of existing infrastructure at the university or commercial level. That may require temporary waivers or reductions of containment level, facility accreditation, training, insurance, and documentation requirements.
Readers should be aware of the non-exhaustive list of diagnostic tests available and known to authors at this link
Note: this is a LIVE document, a composite of several parallel works by the authors, which remains in progress and will be updated regularly based on redlined elements.
EVERYONE CAN COMMENT | WE ARE SEEKING TRANSLATORS
REQUEST EDIT ACCESS OR OFFER TRANSLATION TO: [email protected]
Jeffrey Ladish - [email protected]
Edward Perello - [email protected]
Sean Ward - [email protected]
Tessa Alexanian - [email protected]
Acknowledgements: Samira Nedungadi, Megan Palmer, Maximilian von Zeffman, Andreas Stuermer, Elliot Roth
Types of Test
COVID diagnostics are a diverse bunch and not all tests are created equal. Tests can vary in turnaround time, cost, specificity, accuracy, and scalability. Here follows a crash course in the various molecular detection methods of note for COVID-19, and their suitability for use in a large- scale diagnostic programme.
Broadly speaking there are three functional categories of testing for COVID19:
1. In-house lab-based diagnostic testing (lengthy, up to several days for a test, often used for clinical confirmation and clinical decision-making)
2. In hospital rapid clinical diagnostic tools (fairly fast, but detect the symptoms, not the virus itself) and require secondary lab confirmation
3. On the spot rapid diagnostic testing (RDT) (provides results within a few minutes to hours, often used for decision-making by healthcare and public workers)
It should be noted that these represent a spectrum, and that hybrid systems exist which lie somewhere between the two former categories (explained below).
Several molecular methods for detecting COVID19 in patient samples are available for use:
1. Polymerase Chain Reaction (PCR)
2. Serological testing for antibodies
3. RNA sequencing
4. CRISPR-based diagnostics
5. Additional PCR techniques
Some of the molecular methods are more commonly used for in-house diagnostics, whilst others are typically used as the preference for RDT. The suitability depends largely on the workflow used to obtain a sample, extract relevant elements from the sample, prepare it for a molecular assay, and then obtain the assay readout.
Choosing a Test
For each kind of test, the following questions are important for both the clinical response and the contact-tracing response efforts:
* What patient samples are needed to run the test?
* Nasal / buccal swab, blood, sputum
* What does this test tell you?
* Simple “positive” or “negative” result?
* Information about viral load or immune response?
* Information about the progression of the infection?[a]
* How long does it take to get a result?
* How soon after infection can you get a true positive result?
* How long after infection can you get a positive result?
* What are the false negative and false positive rates?
* What equipment or personnel are needed to administer the tests?
* What are the bottlenecks to testing capacity?
* How complex is the test to perform at scale?
Simple tests are ideal, and the greater the number of steps required, the greater the requirement for specialised equipment and staff, and the more complex the method is.
A rule of thumb is that more complex methods require dedicated equipment and a lab, and more work for a user, who may need training or would benefit from having automated sample prep and testing to achieve high-throughput diagnostic capability. More complex does not mean better in terms of information provided by the test.
However, the rule of thumb has exceptions - for instance there has been extensive work done to miniaturise some complex processes that are traditionally considered lab-based into field-portable products. Unfortunately market penetration of field-portable products of lab-based molecular diagnostics remains limited for many types of test. The majority of installed capacity remains in labs.
What Would We Like to See for COVID Diagnostics and Their Use?
Ideally, field-based RDT would be available for COVID, with the tests having a high SENSITIVITY to the presence of the pathogen and being able to detect infected patients be