Karnatka (SunstarTV Bureau): According to a top varsity official, after a vivid experimentation, a researcher team at Nitte University in Karnataka’s Mangaluru has discovered a new mutation in the Covid-19 genome for testing its virus strain.
Nitte senior director, Iddya Karunasagar told to IANS, “The novel mutation will have implications for the diagnostic RT-PCR-based detection of the Covid-19 virus, which is used for screening test.”
In a paper submitted for publication in the prestigious Elsevier Journal ‘Virus Research’, investigators at Nitte, a deemed to be university, said they have detected partial deletions in the gene encoding, the viral envelope protein (E-gene) in the genomes, across many states such as Karnataka, Maharashtra, Madhya Pradesh, New Delhi and Odisha.
Scientists have found antibodies that recognize SARS-CoV-2 in the blood of people who have never caught the virus. Children are particularly likely to harbor such antibodies, which might explain why most infected children have either mild illness or none at all.
The research was initiated after Anusha Rohit of Madras Medical Mission in Chennai alerted the Nitte team on some lab observations that occasionally samples may be negative for E-gene but positive for RdRp gene or N-gene, depending on the confirmatory test system.
Karunasagar said, “As most labs do screening and confirmatory tests one after the other, samples negative for E-gene will not be processed for confirmatory test and reported negative.”
Nitte researchers comprising B. Krishna Kumar, Prithvisagar and Praveen Rai under the mentorship of K. Indrani, scanned the nucleotide sequence of E-gene of 2,000 viral genome sequences from the Global Initiative on Sharing All Influenza Data (GISAID).
As Karunasagar said, “Partial deletion in one end of the E-gene was found in 34 viral genomes. The deletions in all states except Odisha were such that RT-PCR detection of the virus would not be affected.”
In eight genomes from Odisha, however, the deletion was large enough to render the RT-PCR reaction negative.
Albeit, it is a small proportion (8 out of 2,086) in the sample studied, it works out to 32,500 genomes, with large deletions in 8.4 million cases, detected across the country.
“Some of the test systems like Truenat from India and GenXepert from the US do simultaneous screening and confirmatory tests. Such systems can detect even viruses with these deletions,” stated Karunasagar.
The finding has huge implications for detection of corona virus by RT-PCR (Reverse Transcription-Polymerase Chain Reaction), which is used as gold standard for diagnosis.
“If only E-gene based screening test is used, it is possible to miss some of the cases infected with mutated virus,” he reiterated.
Noting, the need to understand the clinical implications of the mutation, the director said as the E-gene was essential for virus structure, mutation could lead to viruses with lower infectivity.
Karunasagar added, “This needs to be, however, confirmed with clinical data from individuals who have infections with mutated viruses”.