When a disease outbreak occurs, the first stage of the response is detection. In both the Zika and COVID-19 outbreaks, WHO identified effective diagnostics as vital tools in disease management in order to accurately identify the viruses, monitor and control their spread.
For diseases caused by infection by viruses such as Zika and SARS-CoV-2, diagnostics are particularly important to rule out other infections that present with similar symptoms and evaluate the severity of the patient’s condition. As with many viral infections, a wide spectrum of symptoms can occur, for example milder cases of COVID-19 include a cough, fever and, in some cases, a runny nose and headache – all of which are similar to that of the common cold and seasonal flu. Zika virus symptoms are also similar to closely related diseases such as Dengue, Yellow Fever, West Nile, and Japanese and Tick-borne Encephalitis.
It is crucial to diagnose accurately, not only to track the number and spread of cases, but also to administer the correct treatment. Treatments for Zika virus include aspirin and similar anti-inflammatory drugs, however these standard fever treatments can exacerbate negative outcomes for patients suffering from other closely related diseases, and can even trigger haemorrhage in patients suffering from Dengue Fever. This amplifies the need for specific, rapid diagnostic testing to rule out other diseases that may be symptomatically and/or genetically similar to the target disease.
In February 2020, leading global health experts met at WHO headquarters to identify research priorities for COVID-19 to control the pandemic, with the first of eight immediate needs agreed being to “mobilise research on rapid point of care diagnostics for use at the community level.” (2019 Novel Coronavirus Global Research and Innovation Forum: Towards A Research Roadmap, WHO).
The particular focus on point of care (POC) testing is due to the technology’s ability to provide quick and accurate diagnosis without the need for specialist equipment. This not only reduces the time taken to identify an infected individual, but also facilitates earlier quarantine and effective treatment, away from susceptible people. POC tests also provide a valuable alternative to standard laboratory testing techniques, such as Polymerase Chain Reaction (PCR); the current initial front-line response. In times of crisis, test reagents and laboratory capacity are in limited supply and so to alleviate this strain, the successful development and application of alternative laboratory systems, and non-laboratory testing techniques, including immunoassay-based point-of-care and consumer self-tests, is vital.
Immunoassays, and specifically lateral flow assays (LFAs), are widely used for POC diagnostics due to their ability to combine rapid results with cost-effective testing devices, achievable by non-specialists. Although LFAs are typically based on antibodies, the engineered characteristics of Avacta’s Affimer® reagents offer benefits across immunoassay diagnostic technologies, addressing a number of drawbacks including bottlenecks in assay development and production, cost to manufacture, signal sensitivity and specificity, difficult assay targets, and assay shelf-life and storage. In a pandemic situation, one of the primary advantages is enabling a faster response to outbreaks.
Identifying Affimer reagents against a novel virus
Affimer proteins are highly specific, rapidly developed alternatives to antibodies that can be implemented in a variety of test formats. Avacta is currently working in collaboration with our partners at Cytiva and Adeptrix to develop Affimer-based diagnostics for the SARS-CoV-2 virus across all three diagnostic markets: POC, consumer and laboratory-based tests.
The first stage in developing diagnostic tests in response to a disease outbreak is to identify reagents, that are highly specific to the target. Avacta’s first step is to screen Affimer proteins against the target protein (e.g. SARS-CoV-2 spike proteins) within phage display libraries, in order to identify Affimer molecules that exhibit high specificity binding. Once these high affinity Affimer molecules are identified, they are cloned into an expression vector and purified over the course of a week.
In response to the Zika virus outbreak, we developed three Affimer molecules capable of binding to a recombinant form of a secreted Zika virus NS1 protein, within just 13 weeks of receiving the virus target. The binders are capable of detecting Zika infection at the early, acute stage (for which there is no validated antibody available), allowing for rapid diagnosis, and early treatment and control of further spread. These Affimer reagents are extremely specific, and therefore do not bind to similar viruses such as Dengue, preventing false positive results.
In the case of the SARS-CoV-2 virus, a large number of Affimer reagents that are capable of highly specific binding to the SARS-COV-2 virus spike protein were identified within just four weeks. The reagents do not cross-react with other very closely related viruses, such as SARS and MERS.
Affimer reagents have critical advantages over antibodies, in terms of both assay development and production time. They can also be mass produced, without compensating on batch consistency, making Affimer reagents more cost effective and reliable than antibodies.
Implementing Affimer reagents in a test format
Following generation of Affimer reagents, the next stage is to implement them into a test form. Currently for COVID-19, we are working with Cytiva to develop POC and consumer LFA diagnostics, to detect the SARS-CoV-2 virus spike protein from saliva samples, which are less intrusive for patients than nasal and throat swabs. In addition, with Adeptrix we’re developing a laboratory-based test to provide an alternative to PCR lab testing, offering greater testing capacity to meet the high demand for accurate, high performance diagnostics.
The Adeptrix high-throughput bead-assisted mass spectrometry (BAMS™) test format runs on the already installed base of mass spectrometers in hospitals and laboratories, making use of equipment that is already present but not yet being utilised for COVID-19 testing. On June 9th 2020, we announced this test has reached prototype stage and can detect the SARS-COV-2 spike protein in model samples in the concentration range appropriate for a clinical diagnostic test. On 24th June we announced positive initial data from the first Affimer-based rapid test strips.
As with all diagnostics, the new Affimer-based LFA and BAMS tests must undergo validation and go through the clinical approval process prior to distribution for public use. Furthermore, in general, POC tests must be validated in the appropriate populations and settings before being recommended by a government, and can therefore have a longer development process than standard laboratory diagnostic tests.
By applying the technical benefits of our Affimer platform, we are able to respond quickly to disease outbreaks and initiate test development sooner than by relying on antibodies. This work supports global efforts for effective disease management, which is particularly important whilst vaccines and effective treatments for the virus are still in development.