‘Human & other issues, not RT-PCR, to blame for false negatives’

RT-PCR continues to be the gold standard for Covid-19 diagnosis with 98-99 per cent of assays used in the country picking up the virus, Priya Abraham, Director of the Pune-based National Institute of Virology (NIV), an Indian Council of Medical Research constituent lab, said on Friday. If this diagnostic test was throwing up false negatives, as reported in a section of the media, that could be either because of inappropriate sampling or compromised integrity of reagents, she said.

In the extremely stressful situation in a clinical setting, sampling may be inappropriate, individuals may be appearing late for sampling, or improper transportation of the kits can lead to loss of the integrity of enzymes used for the RT-PCR test, she said. Abraham and a few other experts were participating in a webinar on SARS-Cov2 mutants, organised by the National Biopharma Mission.

If an individual gives the sample more than seven days into the illness, the sampling from the nasopharyngeal region can reduce the sensitivity of the assay, leading to a false negative result, she added. Similarly, with the number of staff doing these tests reducing significantly, as many of them are going down with Covid-19, labs are under tremendous pressure which sometimes can lead to inappropriate sampling, said Abraham.

“These are some of the departures from the ideal situation,” the ICMR-NIV director said, adding that normally an RT-PCR test can pick up variants of every kind, including the UK , South African , Brazilian, or the double-mutant strain, found predominantly in India.

Sujeet Singh, Director, National Centre for Disease Control, New Delhi, said the 10 labs that are part of the Indian SARS-CoV2 Consortium of Genomics (INSACOG) have sequenced 15,135 samples, including 1,932 from foreign travellers, and identified 1,735 variants of concern (VoC). A typical VoC is associated with an increase in transmissibility, disease severity, reduced effectiveness of treatments or vaccine, or diagnostic failures.

Variants of concern

While 73.5 per cent samples tested from Punjab were found to have a VoC, it was 40.6 per cent, 37.8 per cent and 36.4 per cent, respectively, for Telangana, Tamil Nadu and Kerala. Significantly, in Maharashtra and Delhi, which were reporting the highest number of daily cases, the proportion of these variants in the tested samples was 4 per cent and 13.7 per cent, respectively. However, the presence of the double-mutant variant was found to be high in samples from Maharashtra.

Though INSACOG was mandated to test 5 per cent of all samples in the country, the labs in the consortium have managed to analyse less than one-fifth (of 5 per cent) of the samples because of limited resources. Shahid Jameel, Director of Trivedi School of Biosciences at Ashoka University in Sonepat, said five additional labs would soon join the consortium.

The experts, however, expressed confidence that vaccines should work against the variants and reduce the severity of the disease, even if one gets infected by a mutant strain.

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