Soon all 52 labs to confirm COVID-19 cases, but what about sequencing?

Coronavirus photo

Finally, by March 13, to avoid delay, all 52 labs will be able to confirm novel coronavirus cases without sending samples to NIV Pune for confirmation. Similarly, it’s time India empowers national labs to undertake whole genome sequencing of SARS-CoV-2 and other viruses/bacteria.

The global recognition of the Pune-based National Institute of Virology’s “demonstrated expertise” to diagnose the novel coronavirus (SARS-CoV-2) came as early as February 6 when the World Health Organization recognised it as one of the 15 labs for reference testing support for national labs and troubleshoot their molecular assays used for diagnosing cases.

The number of COVID-19 cases remained constant at three for nearly a month in India but is now growing steadily. Anticipating such a scenario, the number of labs that can screen COVID-19 samples has been steadily increased. Besides the 52 labs belonging to the Viral Research and Diagnostic Laboratories (VRDL) network of the Indian Council of Medical Research, 10 labs under National Centre for Disease Control have now been included for testing COVID-19 samples.

All 52 labs can confirm cases

Till recently, all the 52 labs were allowed to only screen the samples; only NIV Pune was authorised to confirm positive cases. With more suspected cases piling up, a long delay in confirming positive test results would have become inevitable for NIV. So, in a welcome move, ICMR has per-empted such a scenario. “Four-five days ago, 13 labs were authorised to confirm positive cases without sending samples to NIV Pune. Another 17 labs will be authorised to do so on March 11 and the remaining labs on March 13,” says Dr. Nivedita Gupta of ICMR. With the 10 labs under NCDC regularly confirming positive H1N1 cases each year, one can expect that soon these labs also would be authorised to confirm positive COVID-19 cases.

Unfortunately, several national labs have not been brought up to speed to perform other vital functions during an outbreak.

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Sequencing the genome

NIV Pune is the only lab in India which has a biosafety level-4 (BSL-4) facility to culture pathogenic, novel viruses, and study the origin of novel viruses and provide a comprehensive characterisation of viruses by sequencing the entire viral genome. NIV has sequenced the SARS-CoV-2 genome collected from two patients from Kerala.

When the entire genome is sequenced it helps researchers understand the arrangement of the four chemicals entities or bases that make up the DNA or RNA. The differences in the arrangement of the bases make organisms different from each other. Sequencing the genome of novel coronavirus will help understand where the virus came from and how the virus has spread.

In the last decade or so, many national laboratories have developed the expertise to sequence the entire genome of viruses and bacteria using the latest equipment — next-generation sequencing (NGS). About a dozen labs have a BSL-3 facility to inactivate the virus and sequence the genome using the advanced equipment. In addition, they have the expertise to undertake such work.

While culturing a pathogenic bacteria or virus should be done only in a BSL-4 facility, a BSL-2+ or BSL-3 facility is sufficient for diagnosing and sequencing the genome. The reason: the virus is inactivated (and hence cannot infect or spread) before the genetic material is isolated for sequencing. And when next-generation sequencing is used, the genome can be sequenced directly from the clinical sample without isolating the virus, thereby reducing the risk of spread.

It is therefore puzzling why India relies solely on NIV Pune for undertaking genome sequencing. If there’s a compelling need to have all hands on the deck to sequence the genome, it is now.

While NIV sequenced two of the three COVID-19 samples collected from Kerala in late January-early February, it is not clear if more samples have been sequenced. Contrast this with how other countries have responded.

Many of the 263 sequences shared with the Global Initiative on Sharing All Influenza Data (GISAID) — a public platform started by the WHO in 2008 for countries to share genome sequences — are by universities and hospitals. In mainland China, many of the sequences are shared by the Centers for Disease Control and Prevention (CDC), which is present in all the 31 provinces. At 90, China has posted the most sequence data on GISAID, followed by the U.S. (37).

Unutilised expertise in India

“We have the experience of handling H1N1 samples during the 2009-2010 outbreak. We tested around 75,000 samples. We have a BSL-3 facility and the latest sequencing equipment. We are ready to help out if ICMR reaches out to us,” Prof. V. Ravi, Head of the Department of Virology at the National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, says about sequencing.

“It is time for team building and not the time to work in silos,” says Dr. Chitra Pattabiraman from NIMHANS. “If we are not given an opportunity to develop these skill sets and not encouraged to participate, then how are we ever going to get good at it?”

In 2018 Nipah virus outbreak in Kerala, a lab outside NIV — Manipal Centre for Virus Research (MCVR) — successfully proved that given an opportunity it could not only diagnose the novel virus but also partially sequence it. The Manipal Centre confirmed Nipah virus in 17 of 24 samples it received from Kerala. The first sample was diagnosed in just 12 hours after the Centre received it; NIV confirmed the result of only the first sample.

Unfortunately, since April 2019, the Manipal Centre has been directed to restrict itself to processing of samples of pathogens specific to BSL-2 facility. It is not even one of the designated labs to test for novel coronavirus.

Virologist Prof. Gagandeep Kang who is the executive director of the Translational Health Science and Technology Institute (THSTI) however feels that given the number of coronavirus cases in India is still under 60, NIV’s capacity to sequence has not been overwhelmed.

While agreeing that many labs/institutions in India have the ability to sequence viral genome, Prof. Kang emphasis that sequencing is useful to know where the virus strain came from and to see if the strain is evolving but does not inform immediate strategy to control the outbreak or its spread.

With the latest sequencing equipment widely available in many research labs and the cost of sequencing falling, researchers are using genome sequences for genomic epidemiology. This becomes possible as scientists already know the number of mutations that arise on an average in a month in the case of the novel coronavirus, its incubation period and the average time between cases in a chain transmission (serial interval). Using these, it has become possible to identify the index case even when the source of infection is not known, and to find the link between two seemingly unconnected outbreaks.

How China built capacity

China was completely unprepared when Severe Acute Respiratory Syndrome (SARS) struck in 2002-2003. The outbreak infected over 8,000 people globally and killed nearly 800. The bird flu (H5N1) outbreak that followed in 2003 underscored the need for influenza detection and response in China. This led to a collaboration between the Chinese National Influenza Center (CNIC) and the Atlanta-based CDC in 2004 to build capacity in influenza surveillance in China.

For the next 10 years the collaboration developed human technical expertise in virology and epidemiology, comprehensive influenza surveillance system, strengthening analysis and dissemination of surveillance data, and improving early response to influenza viruses with pandemic potential. By 2014, the national influenza surveillance and response system included 408 labs and 554 sentinel hospitals. Today, there is a CDC in each of the 31 provinces in mainland China.

The infrastructure and capacity-building put into place by China for influenza surveillance stood in good stead when H1N1 pandemic struck in 2009.

Though China bungled initially, there is much India can learn from how China was able to largely contain the COVID-19 epidemic. As on March 10, 80,754 people have been infected and 3,136 people have died in mainland China alone.

Published in The Hindu on March 11, 2020

2 Thoughts

  1. Dear Dr Modak,

    If you like or not, it doesn’t matter. Your suggestions are always against sequencing! Though worldwide scientists are using sequencing to understand every aspects of biology, eg developmental biology using singlecell RNAseq.

    Sequencing is needed to understand science behind virus transmission. For diagnostic everyone understands that realtime PCR can solve the issue.

  2. Right now there is need for rapid diagnostics and help for needy poor rather than expensive sequencing which isn’t going to add much value. Rare samples from the cases of severe attack may be sequenced.

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