30 million people, one coronavirus testing lab: Crisis in eastern Uttar Pradesh

On Sunday morning, June 7, the chief medical officer of Jaunpur district sat in his office, shooting muffled instructions to his staff from behind his N-95 mask.

“Arrange 10 mattresses quickly,” he told a man who tentatively stood next to his desk. “We need to prepare 100 beds immediately.”

“Why have 25 thalis fallen short?” he asked irately on the phone. “How much food did you cook?”

“Get the RO [water purifier] fitted,” he instructed another member of his staff.

From thermocol to line sample boxes to copper pipes needed to prepare a hospital ward, Ramaji Pandey, the chief medical officer, was busy clearing purchase orders.

“Baaraat aayi hai, vyavastha karni hogi,” he quipped. The wedding party has come, arrangements have to be made.

He was referring to the migrant workers pouring into the district on trains, buses, trucks, mostly from Mumbai, Delhi and Gujarat. “More than 2.5 lakh migrants have returned,” he said. “And this is the number for which we have a record.”

Their return had led to a sharp rise in coronavirus cases in Jaunpur. The district had only 18 cases till May 15. Twenty one days later, the number had shot up to 284 – of these, 249 were migrants who had returned from Mumbai.

With 301 confirmed cases, as of June 9, Jaunpur has the highest number of coronavirus cases of all the districts in the region, higher than even neighbouring Varanasi, 60 km away.

What happens when a new virus enters one of India’s oldest cities and poorest regions? We bring you a week of dispatches from eastern Uttar Pradesh, in and around Varanasi, where the lockdown is lifting at a time when coronavirus cases are rising.

Pandey said there was no reason to worry about the rise in coronavirus cases in Jaunpur. The two months of lockdown had been used to beef up capacity in the district. From creating a small Covid-19 ward within the district hospital premises initially, to turning shelter homes into wards, and taking over an entire newly-built hostel in the Purvanchal University by the end of May, the district authorities had steadily expanded beds. “Even if the number of patients goes up to 1,000, we can manage,” he said.

But these were mostly beds in first-level treatment centres, for patients with no symptoms or mild symptoms. The district was still building a 50-bed second level treatment centre for patients needing oxygen and ventilators. For third level treatment – intensive care – patients would have to travel to Varanasi.

Jaunpur has an estimated population of 52 lakh, up from the 45 lakh recorded in the 2011 census.

Before the epidemic started, the district hospital had four ventilators. Now, it has eight. “We have 17 ventilators as back-up in the private sector,” said Dr GC Dwivedi, the joint director of health services who had been sent to the district as the nodal officer. “Until now we haven’t had to use ventilators or oxygen for even a single patient.”

But one area where shortages have already shown up is testing.

Jaunpur does not have a Covid-19 testing lab of its own. Barring Varanasi and Gorakhpur, none of the 17 districts in Purvanchal have a lab equipped to do bulk reverse transcription polymerase chain reaction tests. All they have are TruNat machines used for testing diseases like tuberculosis, which have been redeployed for Covid-19 testing. Jaunpur acquired one on June 6. “It is for emergency testing, say, someone needs to get a surgery done,” said Pandey. “It can test upto 25 samples a day.”

To put this in perspective: on the morning of June 7, Jaunpur had the results of more than 2,000 samples pending. It had tested 6,510 samples and received results for just 4,421.

“There is no problem here. Everything is good,” said the young man, waving his hand in the air. “Sab badiya hai, ek dum taka tak.”

“Bas report aa jaaye, hum ghar jaaye,” he continued. “All we want is the report comes and we are allowed to go home.”

Said a woman: “We have no other problems, doctor sahab. Only the report is a problem.”

“Aaj aayegi, kal aayegi, parson aayegi,” another man chipped in. “It will come today, tomorrow, the day after. That’s all we keep hearing.”

A small group had gathered on the balconies of the Srinivasa Ramanujan Hostel in Veer Bahudar Singh Purvanchal University, the main Covid-19 facility in Jaunpur, to speak to the nodal officer, GC Dwivedi, who had come to visit. In the group were men, women and a baby, all of whom had tested positive for coronavirus. None of them had any major symptoms. They insisted they were absolutely normal. “No fever, no cough, no cold, not even bodyache,” said a man.

Dwivedi, who stood on the ground floor, looked up and addressed them. “Please understand, we too are hassled. Aapko rookne ka koi shauk nahi,” he said. “We have no interest in detaining you. We also want you to recover and go back home soon.”

“But the place where we have sent your reports, wahan zyada bheed ho gaya hai,” he continued. “It is facing an overload. It can test 1,000 samples in a day. But 2,000 samples of our district alone are pending.”

The young man, aged 30, wasn’t satisfied. “I have been here since May 21,” he told this reporter. “You can see how long that is.” It was 17 days.

He had returned from Mumbai on May 13, travelling four days in a truck. The next day, he voluntarily went to the nearest government health centre to get a medical check-up. “Shanka mitaane ke liye,” he said. To remove all doubts.

When he told the doctor he had a brief spell of mild fever on the journey, the doctor decided to have him tested for Covid-19. His nasal and throat swabs were taken on May 16. The results came on May 21: he had tested positive. The same day, an ambulance picked him up from the village and brought him to the Covid-19 facility. The next test was done on May 27. But 10 days later, he was still to get the report.

A middle-aged woman from Ghazipur, a neighbouring district that is sending its patients to Jaunpur, had also been tested for the second time on May 27. She too had not received her report.

Said Dwivedi: “We are still awaiting the reports of 44 patients for whom the 12-day follow-up tests were done.”

He tried to reassure the group that the test results would now pick up speed – earlier, Jaunpur was sending samples to the Banaras Hindu University in Varanasi, which was overwhelmed with samples pouring in from all over the region. Now, Jaunpur has been officially linked to the Postgraduate Institute of Medical Sciences in Lucknow, he said. He did not mention that the Lucknow lab initially refused to accept the 500-odd samples that Jaunpur wanted to send, prompting the chief medical officer to ask his staff to camp outside the lab till they accepted the samples. Eventually, Dwivedi stepped in and phoned his counterparts in the state capital who persuaded the lab to take the samples.

At the Covid-19 facility, Dwivedi spared the group these details. He simply repeated that the delay had happened because of a backlog at the Banaras Hindu University. But a man pushed his way to the front of the balcony and said: “Sir, we want to believe you, but why aren’t the reports coming in a chronological sequence? The results for samples taken on June 2 have come, but not of those taken on May 30, May 31, June 1. How do we accept that this is simply a matter of overload?”

Professor Gopal Nath heads the Virus Research and Diagnostic Lab at the Institute of Medical Sciences, Banaras Hindu University. The lab has a regular staff of nine scientists and technicians. But currently as many as 45 people are working on coronavirus testing in the lab. “These are technicians from other departments: pathology, biochemistry, anatomy, trauma centre,” said Nath. “We have trained them in biosafety.”

Until June 4, Friday, the lab was catering to ten districts, with a population of over 30 million. It had tested nearly 20,000 samples.

But when 1,700 samples arrived in a single day on June 4, Nath called the state health authorities and asked them to divert samples from Jaunpur and Azamgarh to Lucknow, which is further away but has more capacity with seven labs.

Even working round-the-clock in three shifts, said Nath, the lab does not have the capacity to test more than 1,000 samples in a day. The capacity constraint isn’t machines, he explained, but manpower. Every box of Covid-19 samples that arrives at the lab must pass through multiple processes, from unpacking, sequencing, labelling, deactivation of the live virus, RNA extraction, to placing the master mix in the PCR machine.

Often, the samples arrive from districts mixed up, he said. “Suppose there are six collection centres in a district. They send us samples in one bag. Now, every centre has 25 samples with serial number 1 to 25. So there are multiple one, twos, threes in the bag, which we have to sort out, rearrange, carefully check the name of patients…We cannot just arrange the tubes they have sent.”

But the biggest problem, he said, was “managing data”. The lab must enter data into two separate portals – one of the Indian Council of Medical Research, the other of the Uttar Pradesh state government. “There are 52 points we have to enter in the ICMR portal,” he said. “From age, sex, address, PIN code, patient history, symptoms, etc.”

But wouldn’t this information have been entered at the time of sample collection? “The districts sent us a hard copy of the SRF (Specimen Referral Form),” he said. “We have to enter all the data online.”

“Ideally, there should be just one portal,” he emphasised. “And the district should enter the patient data, with the lab focusing on the results.”

Even with three data entry operators, the lab was finding it difficult to cope. Despite having the technical capacity to test 1,000 samples a day, it was taking 48 hours to produce the reports, he said. Sometimes, an entire datasheet would get left out, as had happened with the May 27 samples taken in Jaunpur, he said.

It was simply unrealistic of the Uttar Pradesh government to expect one lab in Varanasi to process samples from ten districts, Nath emphasised. “You have to raise parallel labs by yourself,” he said. “You cannot depend only on BHU. That we are a big institution and we cater to all this population. It is not possible.”

The last few weeks have been harrowing, he said. Team morale was low. The pressure was immense.

“A DM [district magistrate] called and shouted at me. He said you are not competent at your job. I asked him if you are given ten districts, will you be able to manage. He claimed yes. I said no, you are not god.”

Nath continued: “Why don’t district hospitals have such labs? Even medical colleges are not having these labs. Who is responsible for this? The person who is working is being pressurised, but the question is the government had four months, why didn’t it establish at least one lab in every district?”

He rued the fact that health and education had never been a priority in India. “The major health challenge in the country is infectious disease,” he said. “Yet, there aren’t enough expert microbiologists. Even medical colleges don’t have any.”

“Administrators, politicians, they are putting pressure on us. Why are they not looking at themselves, what they have done,” he said.

“This is a failure of the policy makers,” Nath concluded.

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.