On December 16, 2023, India confirmed its first JN.1 strain Covid-19 patient, a 79-year-old woman in Kerala. Within the next 10 days, neighbouring Karnataka reported 34 cases, 20 in Bengaluru alone, and three deaths.

In the laboratory of the Tata Institute for Genetics and Society in Bengaluru, scientists knew of the sub-variant JN.1’s presence in the city around December 10, well before doctors started to see an increase in the number of patients presenting with influenza-like symptoms, in the case of JN.1, sore throat, congestion, cough, fever, fatigue, nausea, diarrhoea, and body ache.

They knew this because they had been analysing wastewater samples from 28 sewage collection points across Bengaluru for Covid-19 since January 2022.

Over four years since the pandemic first hit India, how has the public health system re-oriented to prepare for such health emergencies, which multiple studies (see this, this and this) predict are likely to be more frequent? Critical information that could be gained from sewage surveillance for quick action is missing, thanks to a paucity of funds, and while India has improved its hospital infrastructure including the number of beds and ventilators, experts say this has not been matched with a corresponding increase in manpower.

The case for wastewater surveillance

Covid-19 samples are taken as swabs from the throat. However, the virus is also known to live and replicate in the gut, leading to a high viral load in excreta, making wastewater sampling and analysis an effective way to predict whether a community is on the verge of an outbreak. Essentially, when the concentration of the virus in wastewater shows an increasing trend, an outbreak in the community may be imminent.

“Increases in the concentration of the Covid-19 virus in wastewater occur in advance of any increase in the number of cases confirmed clinically because the shedding of the virus in excreta starts when the person is still asymptomatic, so, well before the individual approaches a doctor and gets tested,” explained Farah Ishtiaq, principal scientist at TIGS.

In the Americas, Covid-19 genetic material was seen in wastewater 56 days before the first clinically confirmed case, and 90 days before the first clinically confirmed case in Brazil.

The Centre for Cellular & Molecular Biology, Hyderabad, a constituent laboratory of the Council of Scientific & Industrial Research, has also monitored wastewater samples for Covid-19 in Hyderabad, Kolkata, Delhi, Chennai, Prayagraj, Mumbai and 13 cities in Maharashtra, with similar outcomes.

“Our work has shown that wastewater surveillance can provide a 1-2 week advance warning for Covid-19,” Archana Bharadwaj Siva, senior principal scientist at CCMB, told IndiaSpend.

Govt not allocating funds

Sewage samples can be tracked for their Covid-19 viral load as well as put through genomic sequencing to identify new and emerging variants of concern.

Across 72 countries worldwide, sewage samples from more than 4,648 sites continue to be routinely monitored for the genetic material causing coronavirus.

“Such surveillance assumes greater usefulness as an epidemiological tool that can be integrated into the public health surveillance system in highly populated regions like India, where there is also a lack of reliable data on disease burden,” said Ishtiaq.

TIGS’s surveillance of Covid-19 in wastewater in collaboration with Biome Environmental Trust, the National Centre for Biological Sciences and the Bangalore Water Supply and Sewerage Board, has been funded by a grant from the Rockefeller Foundation in the US. The CCMB’s surveillance of Covid-19 in wastewater has been funded by the Rockefeller Foundation, CSIR and the SBI Foundation in Mumbai.

Siva estimates that analysing the Covid-19 viral load at a sampling site costs about Rs 400-500 per analysis (for the pipeline from sample processing until data generation). Such tests should ideally be done weekly. Analysing a sample for different variants costs about Rs 6,000 per analysis for the same pipeline.

Currently, India’s Integrated Disease Surveillance Programme monitors 12 diseases by laboratory testing, and the country allocates about 2.77 percent of its health budget for epidemiological surveillance, risk and disease control programmes. For the surveillance of wastewater for Covid-19 to be made a routine practice in cities across India beyond time-bound studies, IDSP’s list must be expanded beyond a few communicable diseases and the spending must be increased, according to Shambhavi Naik, head of research at Takshashila Institution, an independent centre for research and education in public policy.

IDSP uses laboratory-based surveillance to track emerging outbreaks, said Naik. “However, two kinds of new technologies need to be embraced: novel molecular diagnostic methods that allow laboratories to track diseases faster and more accurately; and digital technologies that can scan publicly available information to identify potential hotspots of outbreaks. All of this and putting in place appropriately trained personnel in the government departments will cost money.”

A senior government officer who IndiaSpend spoke to expressed scepticism for introducing sewage surveillance as a routine practice in large cities because the equipment and the kits are from overseas, and so, he felt the practice would burden the health system. He felt that the surveillance should focus on diagnostics. 

When IndiaSpend pointed out that testing necessitates people to come forward, which is hardly happening now that Covid-19 is no longer seen as a pandemic, and the work by TIGS and CCMB shows the utility of wastewater surveillance, he said the outcomes so far are “not very significant”. Therefore, such surveillance shouldn’t be introduced until India makes diagnostic kits domestically and even then, hepatitis may be the virus that is most useful to monitor for India. India is already the world’s largest importer of medical diagnostic kits.

Making informed public health decisions

Apart from Covid-19, wastewater surveillance can help identify trends in the occurrence of several other disease-causing viruses, and also bacteria and parasites that live in the gut and hence, are found in excreta, pointed out Siva. “The IDSP closely monitors the poliovirus. Other potential pathogens to track are adenoviruses, hepatitis A and E viruses, rotaviruses, E. coli, salmonella, shigella, ascaris, and giardia.”

“Some other potential uses of wastewater surveillance are to monitor antimicrobial resistance through genome analyses and the illicit use of narcotics, and detect the presence of antibiotic and other pharma residues,” she added.

CCMB is analysing the AMR profiles for the various cities aforementioned under the Rockefeller-funded project.

In the Prayagraj study specifically, CCMB is receiving samples from the city’s sewage treatment plant’s inflow as well as the outflow. “Testing the outflow for pathogens and AMR is as important [as testing the inflow] because treated water released from the plant percolates into the ground, and so, is expected to be safe and free of pathogens, antimicrobial genes, etc,” Siva said.

The Niti Aayog’s Vision 2035: Public Health Surveillance in India report envisages “an amalgamation of plant, animal, and environmental surveillance in a One-Health approach that also includes surveillance for antimicrobial resistance and predictive capability for pandemics”.

The document alludes to surveillance as ‘Information for Action’, because the outcome of wastewater analysis must be fed back to public health authorities in a timely manner so as to inform their decisions.

In Bengaluru, “sensitivity analysis of wastewater samples helped estimate the number of infected individuals at a citywide level, which was, at times, seen to be four times the reported cases, and identify the sewer catchment areas with the most viral loads,” shared Ishtiaq. “This information was shared with the municipal authority in real-time to make decisions on a masking mandate and to increase testing in sewer catchment areas with the highest viral loads, for the early detection of asymptomatic cases.”

What India needs to do

To ensure the outcomes of wastewater surveillance reach the right authority at the right time, Naik stressed the need for the integration of surveillance data, treatment data and the public health response. Also, “sometimes, the lack of uniform contribution from the private sector can lead to information asymmetry problems,” she said.

As an example, Naik cited the under-reporting of dengue. A study published in the British Medical Journal reported that 80 percent of patient care is sought in the private sector in India, which remains a largely untapped source of surveillance data, because those hospitals diagnose dengue using less reliable rapid test kits.

To integrate data, “some cities like Pune and Bengaluru are developing and using dynamic dashboards which map results from wastewater surveillance and other data sources with the population and demographic data across various catchment areas, besides the portal of the Indian SARS-CoV-2 Genomics Consortium,” said Siva.

INSACOG is a joint initiative of the union Ministry of Health and Department of Biotechnology with the CSIR and Indian Council of Medical Research, which brings together 54 laboratories to monitor Covid-19’s genomic variations and study if those are in any way associated with epidemiological trends. The consortium is supposedly also working to expand to sewage surveillance as a tool for the quick and early assessment of the spread of variants in a hotspot.

For accurate identification of hotspots to enable public health action, there is a need for more granular data on the sewage network, said Ishtiaq. “For instance, in Bengaluru, if the Bruhat Bengaluru Mahanagara Palike as well as the Bangalore Water Supply and Sewerage Board were to map the sewage network, we could select sites for surveillance at the ward level in the catchment areas, before sewage reaches a particular sewage treatment plants.”

Investments and funds

At the start of the pandemic in April 2020, a team of researchers affiliated with the Center for Disease Dynamics, Economics & Policy , now known as the One Health Trust, and Princeton University, US, estimated that India had 1.9 million hospital beds, 95,000 intensive care unit beds and 48,000 ventilators across 69,265 private and public hospitals. Whereas the number of government hospitals and hospital beds was sourced from the National Health Profile for 2019, the number of private hospitals and hospital beds were inferred from the percentage breakdown of hospitalisation rates across public, not-for-profit and private segments, for India and States/UTs, as available in the National Sample Survey 75th Round Report, 2019.

The estimation found great variation in the availability of beds across states. While a few of the five most populous states – such as Uttar Pradesh, Maharashtra and West Bengal – also led the bed tally, a few populous states like Bihar and Madhya Pradesh had far fewer beds for their population count, while a few less populous states like Karnataka, Tamil Nadu, Telangana and Kerala had a higher bed count per capita.

The study’s authors concluded that “accommodating the influx of Covid-19 patients will require rapid expansion of current capacity or modifications in admission policy for routine patient care”.

India saw both scenarios play out. The non-ICU bed capacity was scaled up in a matter of weeks, by creating observation and treatment zones for not-so-ill patients in stadiums in Mumbai and Delhi, for instance. Scaling up the ICU beds however, took longer. Also, about half of the ICU beds are expected to have ventilator support, and provisioning extra ventilators and oxygen supply plants took time.

By March 2022, Maharashtra, as an example, was said to have seen a fourfold expansion of its ICU beds, from 9,344 to 39,738, and ventilators, from 3,436 to 15,657, and more oxygen generation plants and liquid medical oxygen storage facilities. However, the head of a public hospital in Mumbai told IndiaSpend that no similar expansion of staff has been sanctioned since.

“For every patient on a ventilator, you need a minimum of three but actually five nurses keeping into consideration day-offs and holidays, and more doctors, all of whom should be trained in Covid protocols,” the officer said, asking not be named in view of the upcoming elections and the sensitivity of the issue.

At Delhi’s Dr Ram Manohar Lohia Hospital, a union government hospital, Ajay Shukla, director and medical superintendent, said that “the number of ICU beds, beds with oxygen support, ventilators and other related equipment has increased by more than 100 percent as compared to the pre-Covid-19 situation, so infrastructure wise, the hospital is [now] capable of handling a pandemic-like situation. However, as regards manpower, including nurses and paramedics, a formal proposal has been sent to the ministry and their response is awaited.”

At the Lady Harding Medical College in Delhi, Lekharaj H Ghotekar, head of department, General Medicine, affirmed there is an “urgent” need for more nurses, attendants, etc.

“Increased bed and ventilator capacity is needed but also trained personnel who can use these facilities,” said Ramanan Laxminarayan, president of the One Health Trust and a co-author of the aforementioned study. “The shortfall during a respiratory pandemic is also in oxygen equipment and breathing apparatus. States do need an increase in nurses and paramedics both in normal times and particularly in a pandemic situation.”

The need for continuity of general health services

The CDDEP-Princeton University team observed that the shortage of beds in India would necessitate modifications in the admission policy for routine patient care. This was poorly addressed as during the lockdown.

“Hypertensive and diabetic patients couldn’t step out to get their medicine and patients on dialysis had nowhere to go when dialysis centres closed,” the officer said. The officer estimated that many such chronically ill patients lost their lives indirectly to Covid.

“There was a need to designate certain hospitals as Covid-treating and others as non-Covid hospitals,” the officer added.

Another adverse outcome that should have been foreseen was the multiple outbreaks of measles across Mumbai after the lockdowns lifted and life resumed. The World Health Organization defines an outbreak as a cluster of at least five cases from the same area or a confirmed measles death.

“When the lockdown was called off, vaccination for measles should have been taken up on a war footing,” the officer pointed out. “I honestly don’t believe enough was done.”

This report is republished with permission from IndiaSpend.org, a data-driven, public-interest journalism non-profit. It has been lightly edited for style and clarity.