RT-PCR coronavirus tests and false negatives: Why is that happening?

As Covid-19 case numbers increase rapidly, and people are finding it hard to get RT-PCR tests done, get a sense of what is happening on the ground

Earlier this month, Arjun Sharma (name changed on request) visited three hospitals in Delhi with his father, trying to get an oxygen bed for him. His father had tested negative for Covid-19 on an RT-PCR test, but was showing symptoms of the disease--his oxygen levels had dropped and a CT scan showed infection and pneumonia in his lungs.

"Doctors who we consulted said that my father most likely has Covid-19 and should get admitted to a hospital to get oxygen support. But the test was negative despite his serious symptoms, and maybe this was a false-negative test result," said Sharma, a central government employee living in east Delhi.

All three hospitals which Sharma visited with his father were unwilling to admit him. They told him that if his father was Covid-19 positive, they could try to accommodate but since his test had shown up negative, they could not offer him a bed as they were keeping their beds only for those testing positive for Covid-19.

After several days of struggling, and taking the help of other civil society volunteers in Delhi, Sharma has admitted his father to a government-run hospital in east Delhi where his father has been on oxygen support since April 25.

Questions have been raised on whether the RT-PCR test, while essential for accuracy in Covid-19 detection, is returning false negatives, and this has more recently been blamed on the test's purported inability to detect new Covid variants. People who are getting tested may show symptoms of Covid-19 even though their tests give negative results. In other cases, people are unable to get tested due to the shortage of testing kits in different parts of the country, but are showing Covid-19 symptoms. Either way, the gate-keeping of the RT-PCR test is proving cumbersome for many to navigate.

On April 23, the Delhi government issued an order acknowledging that people with RT-PCR negative tests for Covid-19 were being denied admission in Delhi hospitals, despite having symptoms. "No patient requiring medical aid should be denied treatment," said the order.

Experts have long emphasised the need to test people widely, and that even people who are presenting with severe acute respiratory illness or influenza-like illness should be tested for Covid-19 since their symptoms are similar.

Other ways to tell if it is Covid-19

"It is very common, not at all rare," for patients to be infected with Covid-19 but for it to not show up on test results, said Kamna Kakkar, senior resident in the intensive care unit, department of pulmonary and critical care medicine, at Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Haryana.

"Even though the RT-PCR test is a good test, there could have been problems with how the swab was taken, whether it went deep enough to take the sample, or if perhaps the person took the test too late and the virus was no longer in the upper respiratory region but inflammation had settled in inside the lungs." All of this can result in a negative RT-PCR test, she said.

She said this is why doctors are trained to recognise diseases also by their symptoms and not just lab reports.

Given the high number of Covid-19 patients and the shortage of tests, Kakkar says that CT scans and X-rays can be some proxies, which doctors can rely on while diagnosing for Covid-19 especially since people are unable to access tests easily.

However, she said it is mostly junior doctors who meet patients when they first come to a hospital. "When a person comes with fever and shortness of breath, as a senior resident I know it can be a number of things--it could be Covid-19, heart attack, dengue, scrub typhus, chikungunya, even acid reflux. So clinical judgement here is very important, to be able to tell the difference." But since there are mostly junior doctors on the frontline, and the system is overloaded, administrators have insisted on lab parameters like RT-PCR test results in order to be admitted, she explained.

"What if we did not have reliable RT-PCR tests for Covid-19, would we not as doctors still have treated people for the disease based on our clinical observations of the disease in a patient?" said Kakkar.

False negatives

A 'false negative' in diagnostics parlance is when a person actually does have a particular disease but the diagnostic test for it fails to detect that disease.

This can happen if the technology used in the test is not accurate, or not specific or sensitive enough to pick up that disease. It can also happen because the technician performing the test did not conduct it properly, or the reagents used are of poor quality. Sometimes even if the technology is fine and the sample was taken correctly, the sample could have been transported under inappropriate conditions to a lab.

And, as we said before, false negative test results can occur if the sample was not taken at the right time in one's infection.

Any link to variants?

The Indian government has said that the presence of false negatives is also not linked to the new SARS-CoV-2 variants. The RT-PCR tests do not miss the UK, Brazil, South Africa and double-mutant variants, as the tests being used in India target more than two genes, said a press release from the government on April 16.

The RT-PCR tests for Covid-19 look out for the presence of three genes on the SARS-CoV-2 virus. These genes have not changed much and thus the RT-PCR tests which are already in use, are able to identify these genes and give positive results, said Shahid Jameel, director of Trivedi School of Biosciences, Ashoka University. "The new variants which scientists are studying are not likely to drastically impact the ability of RT-PCR tests to give positive results for Covid-19," he said.

As a way to check whether tests work, he said there should be random quality checks and surveillance of these testing kits.

On this, Arokiaswamy Velumani, chairperson of Thyrocare, a large diagnostics chain in India, said that he too is not worried about RT-PCR tests not doing an accurate job for Covid-19. "The government has asked us to send 10 positive and negative samples every month to designated government labs where our test results are verified... This is a continuous monitoring of the quality of these tests to ensure that they are accurate and we are testing correctly," he said.

When to get tested?

Another reason why people may get a negative Covid-19 test result, but may actually be positive for the virus, is if they test too early or too late in their infection. But when is the right time to get tested?

Among the many resources that the World Health Organization (WHO) has shared on testing for Covid-19, there is no specific guidance on when to get tested. IndiaSpend contacted the WHO with queries, and a spokesperson explained the following over email: RT-PCR tests are typically "highly accurate" but "lower viral loads may increase the likelihood of false negative results".

When is a viral load of the SARS-CoV-2 virus likely to be low? On this, the spokesperson said that viral loads are typically high one to three days before the onset of symptoms, or at the time when symptoms begin, and in the early days of illness for mild patients (five to seven days), and possibly longer for severe patients.

"There is no set timing on when a person should be tested, except in the case of if they develop symptoms. If a person develops symptoms, they should be tested as soon as possible," they said. Since symptoms "may develop in hours to days after exposure", they said, "there is no specific set time for testing".

Simply put, one should use their discretion and get tested at the soonest, if one has been in definite proximity with someone who has tested positive for Covid-19 or if one has started to show symptoms, and should not wait until symptoms escalate.

What about close contacts? On this, the WHO says there is no need for all contacts to be tested but they should be quarantined, and if these contacts remain without symptoms, they can be tested "as capacity allows".

In sum, "a negative test result does not guarantee that the person will not go on to develop Covid-19 in the remaining days of the incubation period", the spokesperson said. False-negatives could be due to "poor sampling or processing", they said, adding that when health systems are stressed, "the chances of human error may understandably increase".

The Indian government issued testing strategy documents, which it has updated from time to time, but not since May 2020. An advisory to states based on this strategy was issued in September 2020. Both these documents did not specify when in a person's infection they should get tested.