Nagpur: Whole genomic sequencing of up to 784 samples studied and collected by the Environmental Virology Cell of CSIR-NEERI found mostly the delta (B1.617.2) type and in many cases its sub-lineage delta plus. Long before the latest SarCov-2 variant Omicron scare, SAIL at the premier research institute led by Dr. Krishna Khairnar started sequencing RNA of all daily coronavirus positive samples from the city of Nagpur from the month of June.
However, the virology cell is also involved in SARS-COV-2 sequencing of samples from Nagpur city since October 2020.
CSIR-NEERI had started the whole genome sequencing of every new covid positive sample following the request of Nagpur Municipal Corporation (NMC) – which is very less since the month of June this year itself. And CSIR-NEERI was also conducting sequencing studies from October 2020 onwards, but till the month of June, the study was confined to the samples collected from the RPTS testing centre.
Chief Medical Officer of NMC whose name is Dr. Sanjay Chilkar. He has said that the R-not count, infectious rate, and condition of the patient are also being monitored. The patients were stable even if they were found to be covid positive for delta or delta plus. Recently, only one elderly patient has passed away.
Radhakrishnan B Municipal Commissioner has said that this data regarding genomic studies are regularly updated on the Global initiative on sharing all influenza data (GISAID) portal. And apart from this with the help of its own regular government channel, NIV has also done indexing in Pune.
Whole Genome Sequencing Study
When TOI accessed Global initiative on sharing all influenza data for this city as well, the Omicron variant was not reported from the samples processed by NEERI. Delta was also the major covid variant reported in Global initiative on sharing all influenza data for samples from district Nagpur.
Dr. Krishna has also said that The SARS-COV-2 Whole Genome Sequencing Study is also a wonderful joint initiative of CSIR-NEERI, Nagpur, and CSIR-CCMB, Hyderabad.
Dr. Krishna has also said that for fairly quick detection of Omicron, RTPCR kits that use ‘S’ gene target failure (SGTF) can be a very good strategy. But it also has to go with whole genome sequencing. Even without indexing, a completely new version cannot be 100% confirmed at all. And the SGTF would have told us about the possibility of Omicron as well as a possible signal. But this needs to be further confirmed with the help of whole genome sequencing.
State Coordinator for Genome Sequencing whose name is Dr. Rajesh Karyakate. He has said that according to INSACOG up to 5% of all samples from each district were sent for genomic studies.
Dr. Rajesh has also said that even monthly 100 samples from these districts are sent to NIV Pune.