Seven days into infection, nasopharyngeal sample may lead to false RT-PCR negatives: NIV director Dr Abraham
During a public seminar on genome sequencing of SARS-CoV-19 which was attended by the national laboratory heads from across the country including the National Institute of Virology (NIV) director Dr Priya Abraham, it was revealed that despite severe Covid-19 symptoms, a person may test negative for the infection through RT-PCR.
Dr Abraham said that there have been multiple reports in the media about RT-PCR negative individuals unable to get admission into hospital even though they are gasping for breath and are unable to get access to the oxygen because of the negative report.
“There are multiple factors which could lead to this. Due to the extreme stress due to the situation in a clinical setting, the sampling could be inappropriate; individuals may be appearing late for sampling and typically if they come after seven days into the infection the sampling from the Nasopharyngeal area may reduce sensitivity of the nucleic acid leading to a false negative of the RT-PCR. The other factors could be efficiency of the acid kits being compromised as they were not stored or transported properly and so the reverse transcription enzyme or the polymerase enzyme may lose the integrity. Also the added pressure on the laboratory staff due to the current situation as they are also being infected differs from the ideal situation,” Dr Abraham said.
The Indian SARS-CoV-2 Genomic Consortia (INSACOG) members also said that in Maharashtra they sequenced around 4 per cent or 71 sequenced samples that detected with Variants of Concern (VOC) of the 1,779 samples sequenced.
Of these 1,723 were community samples and 56 were from travellers.The INSACOG is a 10-member group which was formed by the Government of India for large scale sequencing of genome sequencing.
Dr Abraham said, “To identify the variants we have to first sequence them, then detect them, which is done through amplification process most commonly known as RT-PCR tests. Since the pandemic RT-PCR has been the gold standard for diagnosis and detection of the infection since the beginning of the pandemic. Over 99 per cent of the times, we are able to identify the virus and are able to allow us to then go on to sequence and identify the variants which are being discussed.”
She further added that normally an RT-PCR picks up variants of every kind and today the acids are approved and validated by the government are fully capable of picking up the UK variant, the double mutation variant, the Brazilian variant and also the South African variant.
The webinar was arranged by the department of biotechnology, ministry of Science and Technology, Government of India on Friday on genome sequencing of SARS-CoV-19 to highlight the importance of sequencing genome of SARS-CoV-19, and the work done by the Indian SARS-CoV-2 Genomics Consortium (INSACOG) in ascertaining the current status of the new variant of SARS-CoV-2, establishing a sentinel surveillance for early detection, and determining the genomic variants in the unusual events/trends.
Research laboratories across the country had started sequencing of the SARS-CoV-2 genome from April 2020, however these were mostly samples collected randomly across the country. The first report of a UK variant of concern was published in December 2020 and the government immediately established INSACOG which is a national multi-agency consortium for large-scale sequencing of viral genome collected in a systematic manner with complete metadata.
Ten laboratories of the department of biotechnology, CSIR, ICMR and Ministry of health and family welfare, were brought together. The National Centre for Disease Control (NCDC), MoHFW was given the responsibility to correlate the clinical aspects and coordinate collection of samples from the states. So far about 20,000 samples have been sequenced and about 1,500 variants have been identified across the country. These are mainly the UK and South Africa variant and a small number of Brazil variants.