Kerala breaks free from centralised testing, sequencing Premium

Decentralized Nipah testing at IAV enables quick response, genome sequencing, and public data sharing for better public health.

When highly pathogenic virus outbreaks such as Nipah take place, contact tracing and isolation of close contacts become critical to contain the virus spread. Public health responses can begin only when samples are tested quickly.

In a marked departure from earlier four Nipah virus outbreaks in Kerala, on July 20, samples for Nipah testing were sent to NIV Pune and also to the State government’s Institute of Advanced Virology (IAV) in Thiruvananthapuram. The Institute of Advanced Virology, which became fully functional in 2022, tested the sample in four hours and conveyed the Nipah positive test result to the health department by 9 am. Kerala waited till evening for Nipah virus confirmation by the National Institute of Virology (NIV), Pune before making an official announcement of the outbreak.

Even before Nipah was confirmed by NIV, Kerala swung into action to prevent virus spread based on the result from the IAV lab — it set up a control room in Malappuram, the epicentre of the latest outbreak, put in place a 30-bed isolation ward at the government medical college hospital in Manjeri, and imposed travel restrictions in two panchayats. Also, the Nipah patient’s route map was published on July 20 night. 

Last year, Kerala was permitted to undertake Nipah testing on its own only on September 20, 11 days after the outbreak began and after 323 samples were tested for the virus by NIV. In the latest outbreak, besides the index case, the Institute of Advanced Virology has been testing all the samples of close contacts. In each case, the testing was completed in four hours and the State government was notified immediately. In contrast, it takes about 24 hours to know the result when samples are sent to NIV.

The Institute of Advanced Virology is a BSL-2 facility and follows BSL-3 practices. For Nipah, the lab has a class-3 biosafety cabinet that has an enclosed 100% negative pressure facility, which is used for virus inactivation, says Dr. E. Sreekumar, Director of IAV. A BSL-3 facility is needed only when the virus is isolated, cultured and tested on animals, and not for Nipah testing. The IAV lab is equipped to test 83 viruses, including Nipah, Zika, Chandrapura virus and influenza. “In a single sample, we carry out 30-35 tests so we are able to identify the pathogen,” says Dr. Sreekumar.

“Contrary to many outbreaks where diagnosis and confirmation have been delayed due to the requirement to ship samples to NIV, as in the case of many of the ongoing outbreaks in multiple States, the decentralised model as seen in Kerala can enable quick response to emerging pathogens,” says Dr. Vinod Scaria, a senior consultant at the Vishwanath Cancer Care Foundation. Considering the frequent outbreaks, testing and genome sequencing of emerging diseases need to be decentralised at the State level and excessive reliance on NIV has to end to enable quicker public health responses.

The importance of decentralised testing was brought to the fore recently in Gujarat that had sent samples to NIV Pune following the outbreak of acute encephalitis in children and yet remained clueless about the cause of deaths in many cases. Three weeks into the outbreak, the Gujarat government on July 18 decided to instead send the samples to the Gandhinagar-based Gujarat Biotechnology Research Centre, which is equipped with a BSL-2 lab facility to carry out whole genome sequencing to identify the virus that is causing the deaths, Ahmedabad Mirror reported. Similarly, as NIV was overwhelmed with Zika samples, the Pune Municipal Corporation in early July was considering sending samples to BJ Medical College in Pune for quicker test results.