Rapid test reliance may slow Covid-19 fight
Testing for the coronavirus disease (Covid-19) in Delhi has become heavily reliant on antigen tests, which experts say are not as reliable as RT-PCR tests and end up skewing crucial data that could hamper the city’s fight to contain the virus. At least seven of every 10 tests conducted is an antigen test.
A high dependence on antigen tests, which throw up more false negatives (they identify infected people as uninfected), leads to two major problems – under-detection of cases, and tilting data metrics such as positivity rate and case distribution.
There has been a slow rise in daily cases in Delhi over the past three weeks -- from a weekly average of 997 daily in late July to a current weekly average of 1091 daily cases. And while the positivity rate is well off its June peaks of 30%-plus, it has risen from around 5.7% in late July to around 6.6% now. On Wednesday, Delhi registered 1,398 cases. To be sure, the situation in the Capital is far better than it was -- and also among the best in the country (especially in a large urban area).
Across the country, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) tests, considered by experts and authorities as the “gold-standard” for tests, remain the preferred method of testing accounting for nearly 60% of samples tested in the 15-day period between August 2 and August 15, according to an HT analysis.
The biggest advantage of antigen tests is that they provide results within the hour and are relatively cheap. These kits are designed to detect antigens (substances in human bodies that stimulate an immune response) and can be performed in mobile stations and don’t necessarily need labs. But the downside is that they have a far higher chance of returning false negatives , and thus can let cases slide under the radar. When time is a constraint , and test results are needed almost in real-time, there is nothing as good as an antigen test although rapid molecular tests such as RT-PCR ones are being developed.
The real-time reverse transcription polymerase chain reaction (RT-PCR) is the most definitive test available. It is used for the detection of nucleic acid from Sars-CoV2 and is based on PCR, a process that duplicates and amplifies genetic fragments of the virus, so that these become easily detectable. The downside is that the process, from sample collection to results, for these can generally take 24-48 hours and needs dedicated machines. Add the logistical delays and tests could take three to four days. In the US, in some states, they were taking 8-12 days.
Delhi’s big turnaround, in early July, was achieved on the back of a sharp increase in testing, and rapid antigen tests played a role in that. The tests were justified then because causes were rising exponentially, especially in containment zones, and there was a need to test people quickly, and isolate them. Delhi also did the smart thing of asking people with mild infections to stay at home instead of admitting themselves to hospitals -- and using up valuable hospital bed inventory.
The Delhi government insists that it has relied on antigen tests only to increase testing in the Capital due to limitations on scaling-up of RT-PCR tests. Delhi’s deputy chief minister Manish Sisodia, in an interview to HT on July 1 said: “This is the benefit of rapid testing — you can do it at a large scale. You cannot scale up RT-PCR to that level.” Delhi started scaling up the tests mid-June. In the first week of June, Delhi was testing 5,500 samples a day, nearly all RT-PCR. By early August, this number had jumped to nearly 20,000, but with a far larger scale of antigen testing.
While this strategy was important for the Capital at the time when cases were rising and containment zones increasing, moving away from it is equally important in order to get a true understanding of the spread of the virus in the city and identifying the best way to eradicate it.
On July 28, Delhi high court questioned the state government over its decision to heavily employ antigen tests to ramp up its testing. The HC said that the Delhi government was only conducting only 6,000 RT-PCR tests daily when it has the capacity to carry out 11,000.
For the 15-day period between August 2 and August 17, HT analysed testing data from the 13 states, which (officially or unofficially) released antigen breakup of testing numbers, in order to analyse the growing role of rapid tests in the country. In Delhi, 70.2% of all tests conducted were antigen-based tests. Odisha was the only state that had a higher proportion of antigen tests: 75%. More worrying than this percentage was that the average number of RT-PCR tests conducted in this period has remained at around 5,000 in Delhi despite the 11,000 capacity. At its peak, Delhi conducted 9,619 RT-PCR tests on June 29, but instead of scaling that up, it has scaled down.
“The tests in Delhi are being conducted strictly as per ICMR guidelines. The RT-PCR tests are demand-based and readily available at all flu clinics, labs and in all hospitals. Anyone who has corona-like symptoms can visit any of these centres and easily get an RT-PCR test done. Not a single instance has been reported where a person who wants to get an RT-PCR test done has been unable to do so. Earlier, when the cases were high more people were visiting these centers to get themselves tested. Now since the number of cases has significantly dipped in Delhi the number of RT-PCR tests has also fallen down accordingly,” the chief minister’s office said in a statement on Wednesday.
“In the case of antigen tests, the government is going to the people with antigen kits for testing them. The government has created testing facilities within localities, schools, dispensaries etc. where it is encouraging people to get the rapid test done. The ICMR protocol mandates rapid tests to be done within smaller localities. This is a uniform protocol followed not only by Delhi but also by all the states. And like in the case of RT-PCR tests, the absolute number of antigen tests have also declined since the number of Covid cases has significantly dipped in Delhi. The ICMR guidelines also mandates that if anyone tests negative for antigen testing but is showing symptoms, the person should go through an RT-PCR test. This is strictly being followed in 100% cases,” the statement added.
Concerns about relying heavily on antigen tests have been flagged by experts. “Due to the fact that antigen tests have a relatively higher chance of false negatives, it is crucial that repeat RT-PCR tests are done. This is something I don’t suspect is being done regularly, especially if we look at the proportion of antigen tests in some states,” cautioned Dr T Jacob John, former professor of virology, Christian Medical College, Vellore, Tamil Nadu.
His reference is to what experts globally as well as ICMR recommend -- following up antigen tests with RT-PCR ones. This newspaper suggested another alternative in a column -- two antigen tests, using the same or different kits, conducted on two samples from subjects simultaneously, with those whose test results showed a discrepancy being asked to go for a RT-PCR test.
Interestingly, some other heavy testing states on this list such as Tamil Nadu that have a near-zero reliance on antigen tests. As of Tuesday, Delhi (1,337,374 total tests) remains one of the regions with the highest testing rates with over 67,000 samples tested per million population, against the national average of 23,800. Tamil Nadu not only has a higher total number of tests (3,845,803) but is also close on tests per million — over 50,000. Not one of these tests is antigen. Another state, Rajasthan, has also used only RT-PCR tests. It has conducted over 25,000 tests per million of its population.
According to ICMR’s June 14 “Advisory on Use of Rapid Antigen Detection Test for Covid-19”, the sensitivity (or the ability to detect true positives) of antigen tests ranged from 50.6% to 84%. This means that as many as half of the “negatives” given by antigen tests may be incorrect. This is why US’s drug regulator FDA says that antigen tests “cannot definitively rule out active coronavirus infection. Antigen tests are more likely to miss an active coronavirus infection”.
Experts caution that heavy reliance on antigen tests can end up heavily skewing crucial Covid-19 data points such as positivity rate. “If we see a drop in case numbers today, we will not know for sure if that is because the epidemic is plateauing, or just because we are now using antigen testing. I’m not saying that this is the case; I’m worried that we may not know if it that was really happening. We won’t know what the real situation is,” said Dr Satyajit Rath, retired scientist, National Institute of Immunology.
This means that in the case of heavy antigen-testing regions like Delhi, despite the absolute number of tests increasing, due to the relatively high chance of false negatives with antigen tests there may be cases that are being missed. As a result, there is a chance that the impression that the region appears to be testing widely and has cases under control may end up being incorrect.
“To muddy these waters even further, the RT-PCR versus antigen testing numbers and proportions are not uniform within a state as well. In a state, it’s not as if all districts are using a same proportion of antigen tests. And because not only are all districts unequally hit, they are being tested differently, we can’t even compare the numbers from two districts because we don’t know how skewed the numbers are because of the varying proportions of antigen and RT-PCR tests,” Rath added.
“In an ideal situation, all antigen-negative results would be rechecked with RT-PCR tests. But if that is the ideal situation, most samples would go back for RT-PCR tests. Then why are we using antigen tests to begin with?” Rath asked.
ICMR’s guidelines says symptomatic people whose antigen tests turn up negative should be tested using RT-PCR, but it isn’t clear if that is happening.
But there’s a bigger problem: many of those infected are asymptomatic.
(With inputs from Sweta Goswami)
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