Testing is key to fighting coronavirus – so why does India have such a low testing rate?

It is the world’s largest lockdown ever: 1.2 billion Indians have been ordered to stay at home for 21 days. The government has said the extreme measure is necessary to break the chain of transmission of the coronavirus, though public health experts point out that all this does is give the country some time to build capacity to fight the virus in the coming months.

One major capacity is the ability to test and detect cases.

Gagandeep Kang, a clinical scientist who heads the Translational Health Science and Technology Institute, an autonomous government institute, said that testing was crucial to gauge the extent of community transmission in the country. Community transmission is said to take place when the source of infection for a large number of cases in an area cannot be traced: when individuals pick up the infection without having travelled to countries where the virus is circulating or having been in contact with known confirmed cases.

Testing would also give Indian authorities a sense of the trajectories of transmission. “That will better inform models and allow us to make predictions about where we need to be emphasising stronger responses,” Kang said during a web conference.

But India has so far among the lowest ratios of testing in the world. Does India lack testing capacity? What is stopping the country from testing more?

Scroll.in spoke to officials of nine state governments, three government labs, one private lab, several independent microbiologists and the Indian Council for Medical Research.

A country’s testing capacity is contingent on a range of factors: the availability of testing kits, laboratory preparedness and human resources. Yet, some Indian states have managed to test more than others with comparable resources.

This is because while a larger number of testing kits does mean that a state can carry out more tests, the mere availability of kits does not directly translate into high testing numbers. This is a consequence of India’s testing modalities.

In fact, as this report explains, India might be underutilising its testing kits by not widening the scope of tests. And social stigma attached to coronavirus is making things worse.

India’s testing graph

First, a look at how many tests the country has done so far.

This is how it compares with the rest of the world.

India’s testing protocol

As Scroll.in has reported previously, India’s initial testing protocol for coronavirus was narrow: till March 19, the country was only testing symptomatic patients with international travel history and those who had come in contact with laboratory-confirmed Covid-19 cases.

This meant it was not even testing all those who fell under the government’s own definition of a “suspect case”. While the government said that any hospitalised patient with pneumonia-like symptoms whose condition cannot be attributed to any other cause is a suspected case, testing guidelines only allowed for testing of hospitalised patients with travel and contact history.

When asked about the conservative approach, ICMR senior scientist Nivedita Gupta told The Indian Express that it was a “rational” decision “not to exhaust... testing capacity in futile testing”.

But as the number of cases rose, facing a barrage of criticism, on March 20, the ICMR revised this regime to extend testing to all hospitalised patients with pneumonia-like symptoms.

The availability of testing kits

While the number of tests have gone up since the criteria was relaxed, concerns still remain that India is not testing enough.

The most widely-offered explanation by public health experts for the country’s conservative approach is that India simply does not have enough testing kits.

Even two state governments seemed to back this view. On March 16, Chhattisgarh health minister TS Singh Deo wrote to the Centre complaining about the “limited supply” of testing kits.

Then, on March 23, as Opposition leaders asked West Bengal chief minister Mamata Banerjee to step up testing for the novel coronavirus in the state, she said she could not even if she wanted to. She claimed the state had just 40 testing kits.

Banerjee said she had flagged the shortage to Prime Minister Narendra Modi in a meeting on March 20, following which the Indian Council of Medical Research had sanctioned 90 more kits to the state. The kits, she said, were yet to arrive.

But the Centre has consistently pushed back against this view: on March 17, ICMR scientists said India had 1.5 lakh testing kits. One million probes – an integral part of the testing kit – had been ordered from Germany and another one million probes had been requested from the World Health Organisation, they added.

It is important to note here that one testing kit does not test one sample alone. (More on the science of testing later.)

The constraint on testing, if there was any, said Rajni Kant, director of the ICMR’s Regional Medical Research Centre, was the number of laboratories – not kits. “Forget about the testing kit,” he said, “Testing kit is only a requirement to do the test.”

On average, the government laboratories roped into coronavirus testing could test upto 90 samples every day, Kant said. “That is the clear-cut conclusion,” he said.

What Kant meant was this: that even if the ICMR were to supply states with an infinite number of testing kits, the labs would not be able to utilise them.

That is why, Kant said, the network of laboratories was being expanded. “We have involved private labs too now,” he pointed out. As of March 25, 144 laboratories have been authorised to test for the virus, 25 of them private facilities.

But if test kits were indeed a non-issue, why has the ICMR roped in private manufacturers to ramp up production of the kits? As of March 26, the government has given licenses to 18 private companies to sell testing kits in India.

“We are doing what is required,” Kant said, refusing to explain this.

The science of the test

The answer perhaps lies in the science of the test. To identify the novel coronavirus, most countries including India, employ the real time RT-PCR or reverse-transcriptase polymerase chain reaction test on the swab sample of a suspected patient.

The test uses multiple cycles of cooling and heating – a chain reaction – to amplify a small amount of DNA. The presence of a fluorescent dye in the medium makes the DNA glow, helping pathologists identify the pathogen. (For a more granular step-by-step explanation, read this).

A testing kit contains various chemical components, said Ajanta Sharma, lead microbiologist at the Guwahati Medical College and Hospital, the main testing centre in the North East. Vital among them are reagents that include a pair of “primers”, which contain copies of DNA that matches the DNA of the novel coronavirus, and fluorescent reporter “probes”.

But the testing kit by itself is not enough to carry out a PCR test. The lab needs to have a PCR machine where the kit is mounted.

In one run of the machine, multiple swab samples can be tested. A testing kit can be used for multiple runs, but the most optimum use of reagents that make up the kit is to “test samples in bulk”, said Sharma. “If you run the test in small samples, say five-six tests per run, with every run, you lose some reagents,” said Sharma. “But we cannot keep waiting for an optimal number of samples in a situation like this.”

On March 22, when ICMR chief Balram Bhargava said that India had the capacity to conduct 20,000 tests per day, he was referring to the maximum theoretical capacity taking into account the number of available testing kits and labs.

The problem of fewer samples

But India’s narrow testing criteria, instead of saving limited resources, might actually be leading to their sub-optimal use.

Because not enough samples are being collected, the number of samples being tested with one kit in most states is possibly much less than the maximum theoretical capacity.

Chhattisgarh health minister TS Singh Deo alluded to this in his letter to the Centre. “The restrictive [testing] criteria has resulted in the limited use of available testing kits,” he wrote.

States with fewer samples are, therefore, likely to exhaust their kits much faster as they are not using the full potential of each testing kit.

That seems to be the reason why the ICMR has been slow to expand its laboratory network – and they are still largely centered around disease hotspots.

For instance, on March 25, Mizoram reported its first Covid-19 case. However, the confirmatory test was not done within the state. It was done at the Guwahati Medical College and Hospital, located almost 500 km away. Mizoram is yet to get a Covid-19 testing facility. Apart from Mizoram, two other states in the North East, Arunachal Pradesh and Nagaland, have no testing centres. The region so far has two confirmed cases: one each in Manipur and Mizoram.

That, microbiologists say, is a smart strategy considering India’s resources.

“If you have too many testing centres, you are wasting your test kits which are limited in number,” said a microbiologist at a government facility in eastern India. “So it makes sense to have centralised facilities where you can make optimum use of the kits.”

This is the model private laboratories also seem to be employing. “We have 204 labs, but tests will be done in only two of our labs,” said Arvind Lal of Dr Lal PathLabs, one of the private facilities authorised by the government. “In fact, right now, it is only being done in our Rohini Lab in Delhi.”

But public health experts point out that the best solution would be to collect more samples to ensure every testing kit is utilised well.

What is restricting sample collection?

For weeks, the narrow testing criteria kept the number of samples collected limited.

But now not only has the ICMR expanded the criteria, the infusion of private labs has prompted local authorities to encourage more tests.

The Mumbai municipal corporation, for instance, has set up a helpline asking people with pneumonia, fever, cough, shortness of breath, to call and request for home tests. This means even those who are not hospitalised can get tested – but the catch is they will have to pay for the service, which is restricted to private labs.

These private labs, however, are reporting their own set of troubles.

Arokiaswamy Velumani, the managing director of Thyrocare, one of the private laboratories designated by ICMR to collect and test samples, said shortage of personal protection equipment for technicians was making it difficult to cap the test prices at Rs 4,500 as mandated by the government. For every sample collected, the technician must wear fresh safety gear and discard it at the end of the procedure.

Many people wanting to get tested backed out when they realised the sample collectors would show up at their doorstep in safety gear – they did not want their neighbours to know.

Besides, the stigma attached to the virus means private labs have found it difficult to get staff for the job. Sample collectors who volunteered to do the job were repeatedly stopped by the police on the road.

Dr Lal PathLabs, too, was struggling to collect samples because of travel restrictions. “For outstation patients, we take his swab, put it in the viral transport medium, then put it in normal proper conditions between 2 degrees and 8 degrees of temperature, and maintain the cold chain in the transport box [during the journey],” said Lal. “That is what we did during the swine flu crisis.”

However, with flights not operational in the country, transporting samples from their over 500 pick-up centres across 29 states the country was not possible. As of now, Dr Lal PathLabs has only one functional testing facility in Delhi.

To overcome some of these bottlenecks, some countries have improvised. South Korea, which relied on aggressive testing measures instead of drastic lockdown measures to stabilise the rate of infections, set up drive-through test clinics. Medical workers in PPEs test patients in their cars itself, mitigating the need to disinfect waiting rooms. Health workers can test up to 10 people an hour using this method.

Singapore, another country which has managed to contain the spread of the virus, began testing all influenza-like and pneumonia cases at the first stage itself.

Testing in both countries was entirely free.

Concerns over equity

In India, with private labs charging Rs 4,500, most Indians are likely to depend on the public system. Velumani said that several people refused to take the test after they realised it was not free.

Public health experts said while it was a welcome step that the government had allowed private players to test and manufacture, the state remained central to India’s fight against the virus. The ICMR needs to keep ramping up the availability of testing kits and simultaneously expand the network of state laboratories, said Poonam Muttreja of the Public Health Foundation of India. “Let the rich go to the private sector and the poor to the government and the poor are far too many,” she said.

Differences across states

To return to the question we started with: is the shortage of testing kits then coming in the state’s way of testing more people as the West Bengal chief minister claimed? If so, are states planning to buy kits directly from the private sector instead of depending on ICMR?

We asked nine states. Most said the ICMR had sent them enough kits. Even a state as small as Sikkim said it had 100 of them. West Bengal and Chhattisgarh, the two states which had flagged shortages earlier, now said they had 500 kits each.

How do the number of available kits square with the number of tests?

Let us begin with Kerala, the state reporting the highest number of confirmed cases. In terms of tests, the state leads the pack in India by a fair margin. Till the evening of March 24, the state had done 4,516 tests (for scale: Maharashtra, which at that time, had 24 more confirmed cases had done less than 1,000 tests).

V Meenakshi, the state’s additional director of public health said the state still had enough kits, all of them provided by the ICMR. Meenakshi said the state was not looking at procuring any more from the private manufacturers as yet. Given Kerala’s heavy testing numbers, the state seems to be making full use of its kits: a win-win situation.

Maharashtra, on the other hand, is likely to have underutilised a higher number of kits for fewer tests. Yet, the state is not contemplating ordering kits from the three private companies, said Anup Kumar Yadav, the state’s commissioner of health and family welfare. “We are hoping that the private labs would buy their own kits,” he said.

Rajasthan, another high-testing state with more than 1,500 tests so far, also had an adequate stock at its disposal, said the state’s lead microbiologist Bharti Malhotra. “We have around 3,000 kits,” she said.

Still, the state’s additional chief secretary of medical, health and family welfare, Rohit Kumar Singh said the state’s labs had been asked to procure more from the three-approved private companies. “The idea is to test as much as we can,” he said. “As it is very difficult to enforce social distancing among the poor.”

Bihar had also set the wheels in motion to procure from the private companies, said Manoj Kumar, Mission Director of the state’s National Health Mission program. “We have asked our medical equipment purchasing corporation to place orders,” said Kumar.

The state, Kumar said, had 1,500 kits across three labs – 500 in each.

On the other hand, even states which have barely tested, said they had enough kits for the foreseeable future. Shailesh Kumar Chaurasia, director at Jharkhand’s health department, said the state had “sufficient” ICMR-issued stock. Jharkhand has tested less than 100 people till March 25.

Assam, which has tested around 251 samples as of March 26, had 2,000 kits in reserve, said Lakshmanan S, director of the state’s National Health Mission program. He added that the state had not yet placed orders for reinforcement from the private companies, but was “working on it”.