Human challenge studies in the study of infectious diseases
What can deliberately infecting healthy people tell us about infectious diseases? How is this useful for developing treatments, and how do we manage the risks?
On 9 September, the Prime Minister announced a moonshot plan for mass COVID-19 testing. Recently there have been capacity issues in the NHS Test and Trace programme and current technologies cannot be scaled easily to millions of tests per day. So, how is COVID-19 testing undertaken, how reliable are current tests, and what technologies or strategies are emerging that would make this moonshot feasible?
Antibody test: detects antibodies to SARS-CoV-2 virus from a current or previous infection
Antigen test: detects viral material indicating a current infection
Diagnostic test: a test that can confirm if someone has COVID-19
False negative: an incorrect result when someone with a COVID-19 infection tests negative
False positive: an incorrect result when someone who does not have a COVID-19 infection tests positive
Mass spectrometry: a laboratory technique to identify specific molecules (such as viral proteins) in samples
Mass testing: using tests in a large sample of asymptomatic people to detect those who are currently infected
Molecular test: a test that detects viral genetic material through PCR or newer laboratory techniques.
PCR test: Polymerase Chain Reaction, a type of molecular test
Point-of-care test: a diagnostic test performed at or near to the person by a trained operator (like a urine dipstick to check for urinary tract infections)
Pooled testing: an approach to testing samples from a group of people within the same test
Rapid test: while this refers to tests that can give a result in minutes rather than hours, the test may still require specialised equipment and/or trained operators
Saliva test: a test that uses a saliva sample
Sensitivity: how well a test reports a positive result for people who have COVID-19
Specificity: how well a test reports a negative result for people who do not have COVID-19
Self-sampling: describes when a person takes their own sample that is then sent elsewhere for processing and interpretation of results
Swab test and self-swabbing: a type of self-sampling that uses a technique to take samples from the nose and throat for testing
Testing people to see if they currently have or have had COVID-19 is a key element of medicine, public health monitoring and research. Detecting people with active infections is a fundamental part of any test and contact tracing system. Improving the speed and accuracy of tests that detect current infections is a research priority and the focus of recent UK Government investment and policy decisions. Until an effective vaccine is available, the Government has proposed that mass testing of the population is an approach that could limit the need for broad and repeated periods of restrictions on daily life. The annual circulation of other winter respiratory viruses also highlights the need for rapid tests that can discriminate them from COVID-19. This article explains how tests work, which ones are currently available and which are in development, how reliable the tests are and how quickly they give results, and the strengths and weaknesses of using them in different contexts.
There are two main types of test used to detect COVID-19 caused by infections with the SARS-CoV-2 virus. They either detect the virus or the immune response to it.
Tests to determine if someone has a current infection are used in several contexts. They are used to diagnose or screen for infections to allow decisions to be made about clinical treatment and subsequent actions such as whether someone or their contacts need to isolate. They are also used as a research tool so that scientists and public health bodies can monitor the prevalence and spread of infections in the population, defined regions, communities or specific groups. Examples of these uses include:
There are two main types of tests that can detect the presence of the SARS-CoV-2 virus:
Tests work by detecting the presence of either of these elements in a sample from a person. This is usually from fluid collected on swabs taken from places in the respiratory system where the virus is likely to be found (the virus can also be detected in stool and in blood). These samples are typically taken from the upper parts of the respiratory tract, commonly the nose and throat, but in healthcare settings can be taken from locations deeper down. There has also been recent interest in developing tests that can analyse saliva samples. Nose and throat swabbing can be uncomfortable, so approaches to develop tests that are less invasive are of interest, especially for children, in contexts where people will be collecting samples themselves or where the frequency of testing is high.
The type of sample taken and when it is collected is important because the level of virus present varies in different parts of the body, changes over time, and may differ with the severity of the infection and the person’s age. Virus can be detected in respiratory samples from the onset of symptoms for up to 2 weeks. Virus can also be detected in infected people who have no symptoms at all, or later in the course of an infection, by which time they are unlikely to be infectious any longer.
Test results can be processed from samples in minutes to hours. This depends on the type of test used and the capacity of the wider testing infrastructure at any given time. At present, all national testing programmes use tests that require sending the samples to laboratories, where trained staff will process and interpret the results. There is significant research activity and government interest and investment in developing test technologies so that they can:
Currently, tests with these features are only being used in research projects in the UK. These are discussed later.
Different tests use one of several techniques to identify if a sample contains SARS-CoV-2 genetic material.
Research is ongoing to develop tests that can detect viral genetic material without using RT-PCR, with more portable equipment and on other sample types, such as saliva. Newer technologies may allow for the processing of samples more quickly and without the need for laboratory processing. In theory these technologies could deliver results within an hour, with equipment that can be sited locally to the where the person is being tested, for example in a school or care home. Currently these technologies still require special equipment and a trained operator to process and interpret the results.
These tests detect if a sample contains proteins that can identify the SARS-CoV-2 virus. The test equipment or kit contains antibodies that bind to the viral protein if it is present in the sample. A positive result can then be visualised by seeing a fluorescent glow or a dark band on the test kit. These tests do not necessarily have to be carried out in a laboratory. This type of test can give fast results without the need for any laboratory processing or analysis, and is similar to how a pregnancy test works. Antigen tests can be made cheaply and so are well-suited to being used in very large quantities. The company Abbott has developed an antigen test that was approved in August by the US Food and Drug Administration. It is worth noting that the FDA makes it clear that a negative result does not necessarily rule out infection. Data from Abbott reports that sensitivity and specificity is 97.1% and 98.5%, respectively (see How reliable are tests? for definitions). As is expected it has lower sensitivity than PCR, so while it is not a good test to inform decisions about caring for a patient in a hospital, this and antigen tests like it could be useful in population surveillance.
So far antigen tests for COVID-19 have been designed to only be used by a trained operator, who will take the sample, process it if needed, and interpret the result. In general antigen tests tend to be less sensitive than molecular tests, so if someone has a small amount of virus in their body the test might not pick it up. This could lead to a false negative result (someone has an infection, but the test says that they don’t). Researchers are working to improve the sensitivity of these tests. However, some researchers suggest that test sensitivity should come second to the ability to test frequently and obtain results quickly, in the context of infection surveillance.
The amount of virus in the body (viral load) changes over the course of an infection. The viral load in the respiratory tract peaks in the first week and can be detected for up to 2 weeks. Research indicates that live virus (which can cause an infection) is unlikely to be present 10 days after symptoms begin. However, viral material that cannot cause an infection can still be detected over an even longer period, sometimes up to 2–3 months. Therefore, highly sensitive tests such as RT-PCR can potentially detect viral genetic material from someone after the point when they cease to be infectious. In this case less sensitive antigen tests may be a better option for screening approaches, since they will detect people with higher levels of virus who are more likely to be infectious. This is not straightforward because there is uncertainty about what viral load constitutes infectiousness.
Some tests can offer more information than simply indicating if the virus is present or absent. For example, they may provide information about the quantity of virus that is present.
As with any diagnostic test, data about how confident we can be about their accuracy and reliability is crucial. Depending on the context in which the test is used, different test characteristics may be more important than others. The accuracy of testing also depends on what proportion of the population have an infection at any given time. Although high quality tests are available, none can claim 100% accuracy. This is because there is no gold standard reference to diagnose COVID-19 and no agreed shared standard against which manufacturers can report the comparative performance of their tests. This has meant that public health agencies have had to develop their own reference standard, and then evaluate the performance of commercial tests against it, in order to give governments a clear idea of how tests perform.
The ability of a test to detect very small amounts of virus is important and this will vary between tests. Some samples may contain less viral material than others and the amount of virus in the body changes as an infection progresses. Tests also need to be able to react only to the SARS-CoV-2 virus and not to other viruses that may also be present in a sample, especially other coronaviruses.
When the accuracy of tests is discussed the most important terms used are:
These figures are cited by manufacturers when they describe the accuracy of their tests. However, several factors influence overall accuracy when tests are used operationally in real settings outside the controlled conditions of a laboratory. When levels of infection in the population being tested are high, a test with a high level of sensitivity will be very good at identifying people with an infection but less good at detecting people that do not. Conversely if the level of infection in a population is low, then a higher specificity becomes more important because it will be better at identifying the people that don’t have the infection than it is at detecting the people that do.
These differing characteristics mean that no one test is best suited to all the possible purposes they can be used for. The way in which they will be used also has implications for the accuracy of results. Tests with high sensitivity work well when there is a high chance that the person is infected. An example of this would be the testing approach used in the test and trace programmes across the UK that seek to confirm a diagnosis of suspected COVID-19 in people that come forward for testing on the basis of having symptoms, or of having had close contact with an infected person. Specificity is much more important if tests are used to screen very large numbers of mostly healthy people. While there may be a greater degree of tolerance for false positive and negative results in a mass screening programme, the implications of incorrect results are significant because, even for a test with high sensitivity and specificity, large numbers of people would get a false positive (and be required to self-isolate) or a false negative (and potentially go on to infect other people).
RT-PCR tests carried out in laboratories can analyse samples in a few hours, and this can be expedited using automation. The main delays result from the logistics of the wider testing infrastructure such as transporting samples, the availability of materials, or the processes that return the results.
Developing molecular and antigen tests that can give results more quickly without the need for laboratory processing is a government priority. There is ongoing development of technologies that use portable equipment that can be located at or closer to the testing site in order to process results more quickly. These are commonly referred to as point-of-care tests, or sometimes called rapid point-of-care tests, near patient tests or rapid tests. Point-of-care tests could be deployed in different ways:
Point-of-care tests are designed to give a result within a window of about 10 minutes to a couple of hours. In a health setting this type of test allows health professionals to triage patients quickly. The wider use of such tests was outlined by the Prime Minister on 9 September as the underpinning technology for a mass testing programme. In this approach, rapid tests could be used in multiple non-healthcare settings such as schools, prisons, travel hubs, and cultural and sporting venues as a way of screening people to check if they have a current infection.
The Government defines a rapid point-of-care test as one where a sample is taken at home or in a pharmacy with a result within about 10 minutes. There are currently no rapid point-of-care tests approved for use in community pharmacies or at home. Some of the technologies that have received government investment are discussed later.
An important part of evaluating point-of-care tests is to determine whether they are as accurate as RT-PCR testing carried out in laboratories. Such a review of research on rapid point-of-care tests has been carried out by the research organisation Cochrane on tests available in multiple countries. From 22 relevant studies of rapid tests included in the review, the accuracy of different test types were compared:
These comparisons were made against RT-PCR. One of the key uncertainties highlighted is how tests will perform in clinical practice or other settings. None of the studies included samples from people without symptoms so it is very difficult to determine how reliable they would be if used in groups of people who are infected but have no symptoms, or in a mass testing programme in which most people tested are uninfected.
As other respiratory viruses begin to circulate now and throughout the winter, having tests that can discriminate between COVID-19 and infections caused by other viruses is particularly important. This is because many respiratory viruses cause similar symptoms such as fever and coughing. A particular concern this winter is the simultaneous circulation of SARS-CoV-2 and seasonal influenza.
Point-of-care tests to discriminate between influenza and other common respiratory viruses (such as respiratory syncytial virus, RSV) have been used in previous winters and there are already some tests that can check for SARS-CoV-2, different influenza strains and RSV. Rapid point-of-care tests are ideal for this purpose since they would enable a health professional to make an accurate diagnosis quickly and give a patient the right advice about treatment or self-isolation. The US Food and Drug Administration has approved the use of a test for influenza and SARS-CoV-2. The latest developments in the UK on technologies to meet this need are discussed later.
The UK Government has invested in research to develop new tests that are faster, more accurate and offer improved convenience to those needing them. Government funding for COVID-19 research is largely distributed through UK Research and Innovation (UKRI) and the National Institute for Health Research (NIHR). In June, UKRI contributed £1.3m to a national research programme to evaluate tests – the COVID-19 National DiagnOstic Research and Evaluation Platform (CONDOR). CONDOR, co-funded by NIHR and other charitable funding, has developed a single process to evaluate the performance of new diagnostic tests in the setting in which they will be used (GP surgeries, care homes and hospitals). This is important because the reliability of tests used in real settings can differ from the performance that is recorded in controlled laboratory conditions. Apart from test performance, information from the CONDOR studies will be important in working out where the test will have the greatest impact, and which test is best suited for the setting in which it will be used and for what purpose. For example, rapid testing would be very important for identifying infections quickly in high-risk settings like care homes.
Test manufacturers can submit their diagnostic tests for evaluation. A Government webpage gives details about how many tests are under evaluation, with further detailed technical information about individual tests.
The Government is expediting regulatory approval for tests through a fast-track process, so that those that meet specified standards can be brought into use in different settings more quickly.
The Government is supporting innovation for improved testing technologies, both laboratory-based and more recently for tests that can be carried out at scale and at the point-of-care. The Government is also exploring whether other samples can be used, such as saliva rather than nose and throat swabs. Several companies mentioned in a recent Government statement are working on this:
The Government has invested in point-of-care testing technologies; research is underway to see how well they work in testing programmes in a range of settings:
A test developed by OptiGene uses a technology to amplify viral genetic material (LAMP) that does not require a laboratory. Data about the test’s accuracy have been reported in a paper that has not yet been peer-reviewed: the sensitivity and specificity of the test are 97% and 99%, respectively, when nose and throat swabs are used. The researchers are also studying the test’s ability to detect infection using saliva samples but data about how well this works are not yet available. Trained operators are needed to run the test, which can give a result in about 20 minutes.
The Government has funded 450,000 LamPORE tests for use in adult care settings and labs. The manufacturer is Oxford Nanopore. Results can be obtained in 60–90 minutes from swabs or saliva samples, using portable machines. The manufacturer claims that up to 20,000 tests per day can be run on desktop sized machines or 2,000 a day on palm-sized machines. Results on the accuracy of the tests on nose and throat swabs were released in a paper that has not been peer-reviewed. The sensitivity and specificity are 99.1% and 99.6%, respectively. Data about accuracy in saliva samples has not been published. A trial using saliva tests is running in Southampton in four schools. Data from these studies are expected in early October. They are also working to develop the test so that it can detect influenza and other respiratory viruses.
The Government has also funded a new point-of-care test in hospitals, using 5,000 DNA machines called Nudgeboxes. The manufacturer is DnaNudge, a spinout from Imperial College London. The test gives results from nose and throat swabs in about 90 minutes, and in a small evaluation study in a hospital setting involving healthcare workers and patients, the reported sensitivity and specificity were 94% and 100%, respectively. Data on the test’s performance when used at scale and in other point-of-care settings are not yet available. The test requires trained operators.
On 9 September, the Prime Minister announced the Government’s intention to implement a mass screening programme to identify people who are not infected. The proposed purpose of such a programme would be to enable people who are not infected to have fewer restrictions on their daily activities. This approach is also called universal testing or population-based screening. It would operate by offering regular testing using technologies that give rapid results. The emphasis in the announcement was that this would be contingent on the availability of rapid tests that could produce a result in 20–90 minutes, using saliva or nose and throat swabs. Such an undertaking would require a vast expansion of diagnostic capacity involving new technologies for which the evidence base is incomplete but developing. While the technologies described above may contribute to this increased testing capacity, they all share similar constraints to laboratory testing because they need special equipment, trained operators and logistics for delivering samples and returning results.
The technology best suited to mass screening is antigen tests because they are cheap and can be made in large quantities. The trade-off for using this cheap and rapid technology is that their lower sensitivity means that they are less accurate at identifying people who do have an infection. This could result in many people with an infection being told that they do not. The World Health Organization recommends that a person who has symptoms but tests negative with an antigen test, should be offered a follow up confirmatory RT-PCR test.
There are other approaches to testing asymptomatic people that can use resources more effectively. One example is pooled testing, sometimes called group testing. In this approach samples from a small group of people (‘a pool’) are combined and analysed with one test run. If the test is negative everyone tested in the pool does not have the infection. If there is a positive test for the pool, then follow up individual sample testing is used to see who in the pool is infected. The efficiency of pooled testing depends on the proportion of people likely to be infected: when this is high then more pools will report positive and need follow up tests. Public Health England states that pooling is ineffective if 10% or more of the people in the pool are likely to be infected. The European Centre for Disease Control and Prevention has published guidance for countries on approaches to using pooled testing for infection surveillance. Modelling techniques can also be used to work out how pool-based testing can be most effective, according to local circumstances.
Pool-based testing is being used in some UK universities. Cambridge University’s asymptomatic screening programme pools students in the same household. Students in pools that test positive are then offered individual tests to confirm the result.
A key factor when considering using pooling is whether any viral material present is diluted to such a degree that the test is unable to detect it (leading to false negatives). Follow up testing for positive pools also takes extra time, which could impact how quickly results are available. Research is ongoing to determine the limits of pooling for SARS-CoV-2 tests. Several studies have reported that pooled testing can be efficient using samples from five people or samples from eight people. Pooling can involve different methods and levels of complexity and so an evaluation of the pros and cons would be necessary to understand if it can offer real benefits. An article in the British Medical Journal highlighted that advice on this type of population screening is normally provided by the UK National Screening Committee, which advises the UK Government and devolved administrations about all aspects of health screening. NSH England and Public Health England published guidance for laboratories on procedures for pooled testing in September.
A sub-group of the Scientific Advisory Group on Emergencies (SAGE) published an analysis of mass testing in a consensus statement on 31 August, reflecting on the technological, epidemiological and behavioural aspects and how such a programme should be distinct from but linked to test, trace and isolate programmes.
What can deliberately infecting healthy people tell us about infectious diseases? How is this useful for developing treatments, and how do we manage the risks?
How do our bodies defend against Covid-19? Read how immune responses differ across people, variants, reinfection, vaccination, and current immunisation strategies.
Research studies involving thousands of people have allowed scientists to test which drugs are effective at treating COVID-19. Several drug therapies are now available to treat people who are in hospital with COVID-19, or to prevent infections in vulnerable people becoming more serious. This briefing explains which drugs are available, the groups of people in which they are used and how they work. It also outlines the importance of monitoring the emergence of new variants and drug resistance.