With a multiplicity of tests, a problem will arise with the reporting and interpretation of total testing numbers.
The recent entry of the Covid-19 antigen diagnostic test has provided much excitement, but little understanding. How does it compare with the standard ‘real-time RT-PCR’ test? How should the test results be interpreted? What actions should flow from a negative result? Who should be preferentially tested? These questions need examination as we set out to determine how this test is best used in our setting, and the caveats that accompany its interpretation.
The RT-PCR test is a nucleic test that detects the replication of viral RNA. The sample is usually collected from a throat or nasal swab. The antigen test looks for viral proteins from a similar specimen. Both tests look at different parts of the virus. The former takes several hours for processing and reporting while the result is available for the latter within a few minutes. This makes the antigen test seem an attractive option as we ramp up testing.
How does the antigen test compare with RT-PCR in terms of accuracy? Here, we look for sensitivity (ability to pick up infected cases) and specificity (ability to exclude uninfected cases). The specificity of the antigen test is reportedly around 99%. That means a positive test result can be highly relied on to diagnose an infection. Sensitivity, on the other hand, is reported to be between 50-80%. That means the antigen test can miss several Covid19 cases.
Therefore, the guidelines issued by the Indian Council of Medical Research (ICMR) recommend that a positive antigen test should be taken as definitive evidence of the viral presence in the person tested. However, a negative test should be followed by a further verification test in the form of an RT-PCR, which has a higher sensitivity. This is meant to reduce the number of truly infected persons who are missed by a less than perfect test.
How accurate is the RT-PCR test itself? Reported sensitivity from China, for identifying truly infected cases was 72% for sputum samples, 63% for nasal swabs and 39% for throat swabs. The sensitivity varies according to the efficiency of the sampling technique, which determines the ability of the healthcare worker to collect an adequate sample. Another factor that influences test sensitivity is the time of sampling, as the viral load is low very early in the infection and also late in the infection when the person has recovered.
Because of these reasons, clinical assessment, X-Rays and, on occasions, CT scans of the chest are often used to make the diagnosis when the RT-PCR test is negative. The lead agency for the test in the US, Laboratory Corporation of America clearly states: “Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Negative results must be combined with clinical observations, patient history and epidemiological information”.
If RT-PCR itself has a relatively low sensitivity (compared to a composite clinical diagnosis) and the antigen test has a lower sensitivity than RT-PCR, are we likely to end up with many false negatives when we use the antigen test initially? With RT-PCR, we may be looking at a 60-70% true positive case detection rate in a good sample yield scenario. If the antigen test picks up only 60% of those, we are likely to miss more than half of the true positive, virus-afflicted cases.
More important is the need for verification testing with RT-PCR in all cases who have a negative antigen test result. Test positivity rates with RT-PCR, among all persons who are tested on the basis of current criteria of eligibility for testing, vary widely among states and between high intensity and low-intensity areas in a state. A test positivity rate of 15% in a population with RT-PCR would mean that the test has detected 15 infected cases out of 100 tested on suspicion. An initial antigen test would pick up 6 to 8 of 100 tested since it is less sensitive than RT-PCR. The remaining (over 90 out of 100) would need an RT-PCR verification test, according to the present guidelines.
The antigen test does cut short the time to diagnosis and can be used in persons with a strongly suspect clinical profile of harbouring Covid-19 infection. It may also be used for quick assessment in persons requiring emergency medical care, though many are likely to test negative.
As a confirmatory RT-PCR test will take time, it may be better to proceed with all precautions, without delaying treatment, even as the RT-PCR test is under process.
With a multiplicity of tests, a problem will arise with the reporting and interpretation of total testing numbers. Officials, as well as media, are now reporting daily testing numbers, with the same avidity and urgency as stock markets report the rise of Sensex and NASSCOM indices. Even now, we do not know how many of the daily reported RT-PCR tests are first time tests and how many are repeat tests. With over 90% of antigen tested individuals having to undergo further testing with RT-PCR, we will see a huge rise in overall test numbers. These numbers should not be confused with the number of people tested, as many would be tested twice—once with the antigen, and again with RT-PCR.
Even though the specificity of the antigen test is reported to be around 99%, does this high true positivity rate invariably mean active infection? It was thought regarding RT-PCR too. Then came a series of reports from South Korea, China and Europe that repeat RT-PCR tests were puzzlingly positive for long in some persons with good clinical recovery and documented immune response. A detailed evaluation led to the conclusion that these are false-positive test results arising from the detection of ‘dead viruses’. Will the antigen tests also yield such false positives due to detection of dead viral fragments? We do not know as yet, as the antigen tests have only recently entered the Covid-19 diagnostic arena. One more puzzle to be solved in the still-evolving story of this intriguing virus which could well be the Riddler of the microbial world.
The author is President, Public Health Foundation of India. Views are personal