RT-PCR false-negatives continue to haunt Bengaluru hospitals

While RT-PCR tests on people showing significant symptoms of the Covid-19 disease returning negative even while CT scans confirm the infection are not new, the government-run Jayanagar General Hospital has had eight such cases in the past one week.

Two of these people have died and doctors say this is unusual given the low incidence. So many false-negatives in such a short span was not seen before, hospital authorities claim.

“All eight cases had typical symptoms of Covid-19 and required hospital admission. We conducted a CT scan in all these cases which showed the infection. However, we lost two patients,” said Dr Sudha Heroor, nodal officer for Covid-19, Jayanagar General Hospital.


BBMP is currently randomly collecting swabs of positive patients for genomic sequencing, but sequencing needs to be done on these patients to check if they were infected by a different variant, the hospital said.

Cluster cases
However, Dr CN Manjunath, nodal officer for lab and testing, state Covid-19 task force, said these could be among a cluster of such cases, and they may not be representative of all Covid positive cases.

“People who undergo RTPCR tests that throw up a false-negative result are treated as Covid-19 patients after CT scans show the infection. This is true of 5-8 % of cases across the state. Sometimes, repeat RT-PCR tests can be helpful. The syndromic approach based on CT scans and symptoms, irrespective of the RT-PCR report, is now well established,” Dr Manjunath said.

Doctors says false-negative reports can be misleading as patients tend to ignore symptoms given the heavy reliance on RT-PCR testing alone in Covid-19 management. RT-PCR is the gold standard to test for Covid-19.

Quality of kits
Dr Raghu J, senior consultant, internal medicine and infectious disease specialist at Sakra World, said false-negative RT-PCR results are seen in about 10-15 % of cases. The quality of RT-PCR kits used for the test also matters in end results, he added.

“All patients who are negative for Covid RT-PCR test, but have symptoms are advised to take a CT scan,” said Dr Raghu. “False-negative reports themselves are not confirmatory and the person’s symptoms need to be considered. We do explain this to the patient’s family. However, even in such cases, not everyone would require hospitalisation. Their symptoms, comorbidities, oxygen saturation, progression of the disease and CT severity scoring are all taken into account.”

Timing all-important
However, according to Dr Satyanarayana Mysore, pulmonologist, false-negative results can happen when the swab is taken on the ninth day after one is infected or if the swabs are tested long after they are collected.

“If the person is symptomatic and if RT-PCR results are negative for Covid, then a CB-NAAT test must be done, which can give more clarity. CT scans in such cases shows the infection and treatment should begin,” Dr Mysore said.

He said that there are a number of cases where RTPCR reports showed negative and such cases have been explained to BBMP’s nodal officer so that the government’s patient ID number could be issued. In some cases, people who have reported negative for RT-PCR have tested positive in Covid antibody tests, meaning the virus may have gone but the after-effects linger.

When contacted, Dr BK Vijendra, chief health officer, BBMP, said there is no increase in the number of RT-PCR false-negative since the pandemic hit. “The proportion of such cases has been 2-3% of the overall cases in BBMP limits. There is no increase in such cases and the role of variants cannot be established with present data,” he said.