No coronavirus variants detected in Bengaluru college cluster

No UK, South Africa or Brazil variants of the coronavirus have been found in the Covid-19 cluster at Manjushree Nursing College in Bengaluru, according to the National Institute of Mental Health and NeuroSciences (Nimhans).

The good news came on a day the state capital witnessed the emergence of another cluster of 10 Covid-19 cases in an apartment complex in Bellandur, making it the third one to be detected in the city after the nursing college and Bommanahalli clusters.

However, only 14 of the 40 Covid positive samples from the college were found to be suitable for genomic sequencing, and only 12 of these genomes could be amplified.

Dr V Ravi, State nodal officer for genetic conformation of SARS-CoV-2 virus, told DH: "Genomic sequencing can be done if the cycle threshold (CT) value of the sample is less than 25 in an RT-PCR test. CT value is the number of cycles needed in an RT-PCR test to amplify viral RNA to a detectable level. Low CT value is an indication of a high viral load."

Ravi said the results have been sent to Delhi. "The virus that is transmitting locally is what the students have as well," he added.

Professor of Neurovirology, Nimhans, Dr Anita Desai, told DH that they were "focusing on sequencing clusters to understand if the cluster was formed because of the high transmissibility of the new variants".

"We need to sequence at least a proportion of the cases to understand what variant is transmitting," Dr Anita, who is also a member of the State Covid-19 Technical Advisory Committee, said.

She said they had also taken up the Bommanahalli apartment cluster (109 samples) for sequencing and are awaiting results.

"If the CT value is not less than 25, we get bits and pieces of the genome instead of the whole genome which may not be helpful in realising what variant it is. In a whole genome, all mutations can be studied," she added.

The Indian SARS-CoV-2 Genomics Consortium, of which Nimhans and InStem are also a part of, has proposed Rs 3.9 crore per lab for 10 labs to enable 5% sequencing of Covid samples in each state for detecting the South Africa and Brazil variants.

"This is not only the budget for manpower but also for consumables. Suppose we have a second surge, we may have to sequence 10% of the Covid samples," Dr Anitha said. "We have to keep a watch on the mutations and sustain sequencing for which more funds are required. A detailed concept note for the project with the budget has been submitted to GoI."

A meeting with the Department of Biotechnology in this regard is scheduled on Thursday.