All day in his lab, Sudhi Payyappat leads a team of 20 in carefully examining dozens of sewage samples collected from wastewater treatment plants across New South Wales (NSW) state in Australia. It’s certainly not the most appealing job in the world, but the results he churns out on a daily basis hold significant ramifications: they help millions across Australia in steering clear of the coronavirus.

A methodology developed by Payyappat, a Kerala-born microbiologist settled in Sydney, in March last year has been adopted across Australia for its testing of waste-water to locate fragments of SARS-CoV-2 and thus detect hidden cases within the broader community. His methodology is founded on the premise that a person infected with coronavirus will start ‘shedding’ the virus within three-four days through his faeces. The ‘shedding’ can also occur while coughing, showering, sneezing or brushing one’s teeth. Such virus fragments, travelling through toilets and sewer pipes, end up in sewage treatment plants. Samples taken from the sewage treatment plants subjected to intensive testing in labs can help the local health departments in detecting the presence of the infection within a community even before a person with symptoms shows up.

“I was really surprised by the sensitivity of this method. If one person is shedding the virus in a catchment of a 20,000-30,000 population, we will be able to pick it (virus) up in the treatment plant. It has a huge economic potential as it is equivalent to monitoring that many people. It has helped in containing the spread of the infection,” said 50-year-old Payyappat, who has been working as a technical specialist with Sydney Water, a government-owned statutory corporation, for the past 20 years.

“Once we make a detection in a sample, we immediately give the results to the department of health. They subsequently put out an alert through the media that the remnants of SARS-CoV-2 was found in a particular catchment. It means the virus is present in the community. The department asks people in that catchment to go and test for Covid even if they have mild symptoms,” he said.

The biggest advantage of the testing of sewage, he stressed, is that authorities can tell if someone is infected in the community even before they start showing symptoms.

“Once you get the virus, you may show symptoms only from 6 or 7 days onwards, or you may be an asymptomatic carrier. But you start shedding the virus within three days. That gives us plenty of time to arrest the spread of infection. Another advantage is that if the infection is already present in the community, through sewage testing, we can see if the numbers are increasing, decreasing or stabilising,” he said.

Payyappat, who hails from Thrissur district in Kerala, was incidentally visiting the state when the first case of Covid-19 in India was reported in Thrissur on January 30 last year. It was a medical student who had returned from Wuhan and subsequently tested positive for the virus. In February, after his return to Australia, when he heard that a percentage of people infected with the virus shed it though their stools ending up in the sewage system, it struck him that this was right up his alley: after all, for two decades, he has been running research projects in the area of molecular biology.

“We have an organisation here called Water Research Australia (WRA). It created a research programme called Collaboration on Sewage Surveillance for SARS-CoV-2 (ColoSSoS). I am part of the research programme. When I got the early successful detection, I passed on the information to other partners. They adopted my method which is being run across the country now,” said Payyappat.

The early results of the 50-year-old’s project induced confidence in March-April, around the time when Sydney reported a spike in cases. A hundred-odd samples, collected from the city’s sewage treatment plants and stored at minus 80 degrees, were used to validate the assay. When the results of those samples were compared with the actual epidemiology data in that area to see how many people were clinically affected, sure enough, there was a strong correlation.

But as effortless as the process may sound, to extract the genetic markers of Covid-19 from a sample is an incredibly complex and highly intensive one, underlined Payyappat. The samples, in little jars, collected by personnel on the field are transported to the lab in refrigerated conditions with temperature not exceeding ten degrees. The samples then go through a complex three-stage analysis, starting with concentration, followed by extraction of the virus nucleic acid and finally detection through QPCR. These days, his team tests about 150 samples in a week.

“Since we don’t have as many cases in Australia as other countries, one of the challenges was when the waste water comes to the treatment plant, there’s massive dilution happening. Obviously, the virus gets diluted that way so we needed to have a sensitive method that will pick up very low numbers. The second challenge was that sewage is a hard, difficult matrix. It can contain industrial waste and chemical compounds which can interfere with the detection of the virus. Extracting virus nucleic acid from those low number of viruses present in the sample in a way that all these inhibitors are not carried along was tricky,” said Payyappat.

With the success of Payyapat’s model in Sydney, the testing regime has been expanded to other states of Australia. He’s currently working on devising a monitoring programme for Covid waste-water surveillance for Thailand.