A year and half after the coronavirus pandemic began in India, two of five districts still don’t have a laboratory to conduct the RT-PCR or real time polymerase chain reaction test that is considered the gold standard for Covid-19 detection, data from the Indian Council of Medical Research shows.

There is no government-run RT-PCR lab in 342 of India’s 742 districts (46%), while 306 districts (41.2%) lack both government and private labs.

The largest gaps in testing infrastructure exist in the North East. Of 120 districts across eight states in the region, 99 districts (82.5%) do not have a single RT-PCR lab.

From the start of the pandemic, inadequate testing has been a matter of concern in India. In March 2020, the country had just 65 government labs for Covid-19 testing and was conducting just five tests per million population.

Since then, the testing ratio has improved to 3.5 lakh tests per million population, with 48.17 crore tests done till August 9. The number of ICMR-approved labs for Covid-19 testing has expanded to 2,808, as of July 31. But only 1,717 labs – 625 run by the government and 1,092 in the private sector – are equipped to conduct RT-PCR tests.

The remaining 1,091 labs rely on CBNAAT, TrueNAT or Molecular Nucleic Acid tests, which are more expensive.

CBNAAT, or cartridge based nucleic acid amplification test, used to diagnose tuberculosis before it was repurposed for Covid testing, works on the same technology as RT-PCR by testing RNA of the virus present in oral and nasal swabs. It gives results in 45 minutes, but the cartridge is expensive. TrueNAT, a chip based technology, also used for tuberculosis detection, is costlier than RT-PCR and can process only a few hundred samples at a time. Molecular nucleic acid testing platform uses molecular diagnostics technique to give results. It is available in only 18 labs across India.

Outside laboratory settings, rapid antigen testing is a quick and cheap way to diagnose Covid-19. It detects proteins on the viral surface and takes just 15-20 minutes to produce results. However, its sensitivity to detect SARS-CoV-2, the virus that causes coronavirus disease, ranges from 50%-84%, which is significantly lower than RT-PCR.

From second wave to third wave

During the deadly second wave of Covid-19 in the summer, the shortfall of RT-PCR facilities had led to a massive backlog of testing, even in urban India where most labs are located. The situation was far worse in rural areas. The ICMR even issued a notification on May 4 asking states to upscale rapid antigen tests.

But ICMR officials acknowledge that rapid antigen testing has serious limitations. “It performs well in symptomatic people, it does not work well for an asymptomatic population,” said Dr Samiran Panda, head of epidemiology and infectious diseases at ICMR. Ideally, RT-PCR tests should account for 70% of all tests and rapid antigen tests for not more than 30%, he said. “But this is only an advisory,” he added. “It is upto the states how they implement it.”

Epidemiologists say the lack of RT-PCR test facilities was leading to many cases being missed. “If testing is sparse, you will not get a high number of cases,” said K Srinath Reddy, epidemiologist and president of Public Health Foundation of India. “The only indication of infection then is the number of people landing up at the hospital and in cremation or burial grounds.”

Towards the end of June, the Ministry of Health and Family Welfare took stock of diagnostic preparedness in a meeting with state officials. In its presentation, the ministry noted that 327 districts had no RT-PCR facility at that point. “The Centre asked certain states to spruce up their testing facilities,” an officer who was part of the meeting said.

But with early signs of a third wave of Covid-19 already building up, experts say the delays in expanding the RT-PCR network could prove costly – particularly in the districts without lab facilities.

“The fact that our lab infrastructure is limited was raised during the second wave when cases started spreading in rural areas, but little has been done to address this issue,” said Rijo M John, health economist and faculty in IIM Kozhikode.

Regional variations

Scroll.in mapped data of ICMR-approved labs, as of July 31, and found significant regional disparities.

At least one RT-PCR facility exists in every district of Kerala, Maharashtra, Rajasthan, Tamil Nadu, Karnataka, Goa, Gujarat, and union territories Lakshadweep and Ladakh.

In contrast, there are RT-PCR labs in only eight of Assam’s 33 districts; two of Arunachal’s 25 districts, two of Meghalaya’s nine districts, three of Nagaland’s three districts, two of Manipur’s 16 districts, and just one of Mizoram’s 11 districts.

The lack of RT-PCR facilities in the North East has led to an over-reliance on rapid antigen testing in the region.

Arunachal Pradesh, for instance, uses rapid antigen tests for 90% of its samples, while the remaining 10% are processed through TrueNAT and RT-PCR. The sparsely populated hill state has just 14 people per sq km. Collecting a sample from a remote village and bringing it to one of the two RT-PCR labs in Naharlagun or Pasighat would mean a turnaround time of 10-12 days, said P Parthiban, the state health secretary.

“Even if we set up more machines, we need more microbiologists to process samples,” said Parthiban. “Currently, we have four non-clinical and four regular microbiologists for the entire state.”

In Mizoram, too, where 11 districts share a single RT-PCR lab in Falkawn, most of the testing is done through TrueNAT and rapid antigen tests. “We have proposed to set up more RT-PCR labs,” said Dr Eric Zomawia, director of the National Health Mission in the state. “If the ministry approves, we would like to install it in all districts.”

Outside the North East, six other states had more than 60% of districts without RT-PCR labs. In Madhya Pradesh, 35 of 52 districts lacked RT-PCR labs; in Bihar, 25 of 38; in Chhattisgarh, 17 of 28; in Jharkhand, 16 of 24; in Odisha, 18 of 30; and in Jammu and Kashmir, 12 of 20 districts.

In the country’s most populous state, Uttar Pradesh, 27 out of 75 districts did not have an RT-PCR lab.

Long distances, high costs

Districts that lack an RT-PCR lab are forced to send samples over long distances.

In Madhya Pradesh, for instance, Tikamgarh district relies on labs in Jabalpur, 250 km away, and Sagar, 120 km away. It takes two to four days for the results to come, said Lokendra Parmar, a local resident. Tikamgarh’s chief medical officer Dr Shivendra Chourasiya did not respond to calls or messages.

In western Uttar Pradesh, samples from Shamli district travel 70 km to Lala Lajpat Rai medical college, Meerut, said chief medical officer Dr Sanjay Aggarwal. During the peak of the second wave, Meerut was also receiving samples from Muzaffarnagar, Baghpat, Hapur and Amroha, four other districts lacking RT-PCR facilities, straining its already stretched resources. “It took 72 hours for results to come at that point,” Aggarwal said. About a month ago, the UP government sanctioned an RT-PCR lab in Shamli, but it is yet to be set up.

Several districts in eastern Uttar Pradesh, which lack RT-PCR labs, have been sending their samples to the Banaras Hindu University in Varanasi. The viral research laboratory at BHU conducted 10,000 RT-PCR tests daily during the peak of the second wave in April and May, running its over 14 RT-PCR machines for 24 hours on support of 100 staffers, said chief scientist Dr Gopal Nath.

Not only does sending samples over long distances lead to delays, it also adds to the cost.

Vedanshi Saraogi, a copywriter who lives in Katni in Madhya Pradesh, said she paid Rs 1,000 to a private nursing home in June to transport her swab samples to a lab in Ahmedabad, Gujarat, 939 km away.

Katni’s collector Priyanka Sharma said the district had tied up with two private labs – Krishna Diagnostics in Indore and Neuberg Supratech lab in Ahmedabad – for testing samples collected in the government district hospital. “Samples have also been flown to Ahmedabad from Jabalpur. But recently we are getting more samples tested from Indore labs,” Sharma said. Indore is 540 km from Katni.

Of the 52 districts in Madhya Pradesh, 38 lack government RT-PCR labs. Like Arunachal Pradesh, the state is short of microbiologists. “We have set up a laboratory in each medical college and even in one district hospital in Mandsaur,” said Mohammed Suleman, MP’s additional chief secretary (health). But the state needed “microbiologists, technicians, bio-safety level infrastructure” to run them, he added. As a solution, MP has set up 1,000 lab collection points and connected them with medical colleges and private labs to process samples from rural regions.

Uneven spread of private labs

Most of the districts lacking RT-PCR labs are predominantly rural, since private labs, which account for 63.5% of the total number of RT-PCR labs in India, are largely limited to tier-I and tier-II cities.

In MP, for instance, 80% of private labs are located in Indore and Bhopal. In UP, 50% of 77 private RT-PCR labs are located in Lucknow, Noida, Ghaziabad and Kanpur. Bihar has 38 districts and 14 private labs – eight are in Patna.

Four states in the North East – Arunachal Pradesh, Mizoram, Meghalaya, and Nagaland – do not have even a single private RT-PCR lab. Chhattisgarh has just eight private labs, while Jharkhand has 12 and Odisha has 13.

In contrast, there are 140 private RT-PCR labs in Maharashtra, 86 in Telangana, 81 in Delhi, and 73 in Kerala. Even in these states, private labs are largely concentrated in metro cities.

“When we face a pandemic of this scale, it makes sense to use private facilities,” said Professor Soumitra Ghosh of the Tata Institute of Social Sciences. “But high expense of testing is an issue and patients may not come forward for testing in that case. The government either needs to take over private labs or subsidise the testing.”

In February’s budget speech, finance minister Nirmala Sitharaman had announced that the government will set up “integrated public health labs in all districts and 3,382 block public health units in 11 states”.

“The second wave after February’s budget speech threw plans off track,” said Reddy of the Public Health Foundation of India. “It is time government fulfills that promise.”

This reporting was supported by a grant from the Thakur Family Foundation. Thakur Family Foundation has not exercised any editorial control over the contents of this article.