At key testing centre in Pune, 604 samples checked so far

Anuradha Mascarenhas

At ICMR-NIV (left), Director Dr Priya Abraham counts sourcing quality reagents from overseas to conduct tests as among the centre’s early challenges. Express Photo by Pavan Khengre

It’s a busy day at the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) in Pune. At the institute’s influenza centre, Director Dr Priya Abraham takes a quick round of the cordoned-off specimen processing room that holds a highly secure biosafety cabinet. It is here that the processing of nasal and throat swab samples, including of those suspected to be infected with the 2019 novel coronavirus (nCoV), is underway.

Between January 24 and February 7, 604 samples have been tested at the institute that is at the centre of the country’s efforts to deal with the nCoV outbreak. So far, three of these samples have tested positive. Across the country, over 1,300 samples have been tested at 14 other virus research diagnostic laboratories (VRDLs), including those at the apex ICMR-NIV lab.

“Around mid-December, we started following reported cases of mysterious pneumonia in China. Even before nCoV hit the headlines, we had formed an outbreak response group of ICMR-NIV doctors trained in community health (epidemiologists).

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As the numbers increased in China, we proactively ordered primers, probes and controls from Hong Kong and Berlin, where laboratories to test for nCoV globally were first set up. There were many challenges, including sourcing international quality reagents from overseas to get the tests rolling,” says Dr Abraham.

The samples arrive at the centre in a three-layered packing in a virus transport medium from across the country, and are handled carefully in the biosafety cabinet by technologists in protective gear. The samples are then separated into small portions and carefully labelled. They are then sent to another unit where nucleic acid extraction followed by the real-time polymerase chain reaction tests are conducted to detect whether the sample is positive or negative for nCoV. Every sample is checked for, besides nCoV, 18 other respiratory viruses, a process which takes about four hours.

If a sample tests positive for nCoV, it goes through three different types of real-time tests — a screening assay and two confirmatory assays — and finally undergoes genome sequencing. The positive sample, along with other negative samples, is sent to the Bio Safety Level-4 laboratory at ICMR-NIV’s Pashan centre on the outskirts of Pune, where another team of scientists conduct tests on them. “We ensure that results of both laboratories are concordant, and then we match them with our results again. We have to be really sure when a sample is declared positive,” says Dr Abraham.

After monitoring the tests, Dr Abraham joins a video conference with Dr Nivedita Gupta, senior scientist at ICMR, experts at the National Institute of Cholera and Enteric Diseases (NICED), Kolkata, and the All India Institute of Medical Sciences, New Delhi, along with other laboratories. Through the daily video conferencing exercise, scientists at ICMR-NIV discuss how to handle the samples and run the nCoV assays with other labs.

“A total of 106 Virus Research and Diagnostic Laboratories (VRDL) have been functional and 13 have been strategically placed near international airports, and are empowered to test samples at the primary level for nCoV,” explains Dr R R Gangakhedkar, the national epidemiology chief at ICMR, who is in Pune to monitor the exercise. The VRDLs then report the results of the assays done to the Pune centre, which has been providing the standard operating procedures and personal protective equipment where needed.

As the ICMR-NIV team responds to technical queries during the video conference, Dr Balram Bhargava, ICMR chief and director-general, joins in to check if the situation is under control.

With the WHO declaring the nCoV outbreak a global health emergency, the security at the ICMR’s apex laboratory has also been tightened, and samples are expected any time, during the day or at night. “Dedicated team work, commitment and inter-dependency among all units has led to a successful response to the outbreak,” says Dr Bhargava.