Variants not leading to false negative test results, says Centre

NEW DELHI: The Union health ministry said on Friday that coronavirus variants detected in India are no more likely to lead to false negative tests, following a series of reports from several parts of the country of people with Covid-19, often with severe outcomes, testing negative through RT-PCR tests.

The government said the kits used for RT-PCR tests check for more than two genes, which makes them less likely to miss a sample if it contains a variant with mutations that change the signature of genes.

“The RT-PCR tests being used in India do not miss these mutations as the RT-PCR tests being used in India target more than two genes. Sensitivity and specificity of the RT-PCR tests remains the same as earlier,” the ministry said.

The concerns stem from mutations that have in the past seen to cause tests kits to not detect specific genes. The B.1.1.7 variant, first found the in the UK, caused the kits in the country to not detect the S gene due to the deletion of amino acids at locations 69-70 on the virus’s spike protein.

Laboratory owners in Delhi say that RT-PCR test kits are updated from time to time and none use the S gene, where clinically significant mutations are seen.

“The sensitivity (ability to detect true positive) of even the gold standard RT-PCR test is 70%. Add to that the sheer volume of tests being conducted currently; there could be error in collecting or handling the samples that could lead to a false negative report. It could also be that people get the test soon after exposure or several days after the infection when viral load is low,” said Dr Rajesh Chawla, senior consultant of pulmonology at Indraprastha Apollo hospital.

Chawla added it is important that people not mix with others if they have Covid-like symptoms and have tested negative.

Doctors from hospitals such as Lok Nayak and All India Institute of Medical Sciences who also handle a bulk of patients agreed. “There are a few cases from across the country where the RT-PCR might be negative but the CT shows presence of Covid-19 symptoms,” said Dr Karan Madan, associate professor at AIIMS.

“The RT-PCR test has a sensitivity of 70%, so yes sometimes the infection might be picked up by chest CT even if the RT PCR is negative. The negative result could also be because people get tested a day after coming in contact with a positive person; they should ideally wait for four to five days before getting the test,” said Dr Navin Dang, founder of Dr Dang’s Laboratory.

He added, “We use the E gene, N gene, RdRP gene, and ORF gene for our tests. And, as far as I know, most labs use kits that test for two to three genes, reducing the possibility of missing out even the emerging mutations.”