From saline gargle to genome sequencing, a big leap for Neeri lab

Nagpur: With an impressive turnaround time of 1.5 days and delivering over 1,500 whole genome sequencing (WGS) results, CSIR-Neeri’s environmental virology cell lab has not only shared the huge genomics burden of India but set a new benchmark among the scientific diaspora. Its capability of dedicatedly declaring results within the shortest duration is being looked at with awe at the national level while its crisp reporting pattern has been adopted by several premier labs.
Besides Neeri lab, ICMR’s National Institute of Virology (NIV), CSIR’s National Chemical Labaratory (NCL), Indian Institute of Science Education and Research (IISER), National Centre for Cell Science (NCCS) – all from Pune – and Mumbai’s Kasturba Hospital are also performing genome sequencing in the state.
Initially, the Neeri lab established a WGS facility to cater to Nagpur’s population but its speedy delivery of results — rated as the fastest among all facilities — attracted the attention of state as well as national surveillance authorities. The Indian SarsCov-2 Genomics Consortium (INSACOG), established under the department of biotechnology, Ministry of Science and Technology, allocated 11 districts of Maharashtra as well as state of Tamil Nadu for WGS.
The lab led by scientist Krishna Khairnar joined the Covid fight soon after the pandemic began in March 2020. It took off the overall load of Nagpur and delivered RT-PCR results the same day. Many people from Vidarbha districts didn’t mind travelling to Nagpur to get a Covid test done at Neeri. Later, it introduced saline gargle RT-PCR which saved the pain of swab insertion.
Though working with a modest team of five project associate and one data entry operator, project leader Khairnar’s own international exposure made it look easier. Khairnar had been a faculty at University of Toronto.
“Very few labs possess such kind of exclusive skills,” said a researcher.
As a research institution, Neeri started genotypic surveillance on its own in October 2020 when it collaborated with CCMB Hyderabad. “As it was taking long time to deliver results to Nagpur, we thought of starting this facility here itself. We have been successful in doing that. Nagpur is now Atmanirbhar,” said Khairnar. The project cost is estimated at Rs45lakh, while WGS is said to be a costly affair.
Dr Rajesh Karyakarte, state coordinator for genome sequencing, said Maharashtra has done the highest number of genome studies in India. This was mainly due to the MoU between Maharashtra government through DMER, Mumbai, with CSIR-IGIB, Delhi, that led to sequencing of almost 19,000 SARS-CoV-2 samples. The next impactful sequencing was done by Pune-CoG, a consortium of five INSACOG labs in Pune. The genome sequencing activity of Pune-CoG is coordinated by BJGMC.
ICMR-NIV, DBT-NCCS, CSIR-NCL, and DST-IISER are the other four labs, these labs together sequenced more than 5,000 samples and were able to pinpoint Omicron’s entry in Mumbai and Pune.
“Three standouts in this Covid fight were Kasturba hospital lab, which took care of Mumbai, CSIR-NEERI for Vidarbha, and Pune-COG for rest of Maharashtra,” he said.