Meet the scientists tracking the lousy future of Covid-19

Fifth spike in Covid-19 cases in South Africa. at the exit without overloading the country’s healthcare system. A new variant of SARS-CoV-2, the virus that causes Covid-19, could potentially change that, but there is a way that scientists can detect signs of a dangerous new version of the virus early — and can buy a healthcare system for up to a week. prepare before the sick show up at the facilities.


Looking at saliva, feces and urine that circulate in the sewer.

We’re breaking down the process with the help of people analyzing these cloudy samples collected from a wastewater treatment plant in South Africa.

What is hidden in the sewers?

SARS-CoV-2 delayed human digestive tracttherefore, the germ’s genetic material will end up in the sewer when people use the toilet.

Research shows that the number of clinical cases (infections confirmed by tests for Covid-19) corresponds to the level of virus particles in wastewater. Thus, when the concentration of virus fragments in wastewater increases, this usually means an increase in the number of infections. Similarly, when there are lower levels of viral bits in wastewater, infections are likely to decrease as well.

Because people start shedding fragments of the virus soon after they become infected, but before development symptoms, fragments of the genetic material of the virus can be detected in sewage up to 14 days before showing up in nasal swabs (and will be found in stools and urine even if someone does not show any symptoms).

So even if people don’t get tested for Covid-19, virus particles can still be found in wastewater.

If a new option is hidden, analyzes of wastewater samples, for example, carried out in South African Medical Research Council (SAMRC)) and National Institute of Infectious Diseases (NICD)can provide early warning and help policy makers prepare for a possible surge in clinical cases.

Dirty crystal ball

This is exactly what happened to the Omicron variant in November, when scientists at SAMRC and NICD noticed something was afloat.

In the last week of October in The NICD observed that levels of SARS-CoV-2 in sewage have increased in Tshwane., says Kerrigan McCarthy, the institute’s pathologist. The number of clinical cases registered in the district only began to increase in early November. When scientists analyzing nasal swab test results, the Genomics Surveillance Network (NGS), announced the discovery of Omicron on November 25, NICD could say it was a variant of Omicron that they had found in their sewage samples.

When SAMRC analyzed wastewater collected on November 23 from a wastewater treatment plant serving Cape Town International Airport, they also found fragments of the genetic material of the Covid-19 virus, called RNA, that were identical to the Omicron variant reported in clinical studies. NHS samples.

By November 30, just a week after SAMRC researchers first discovered this new variant in airport sewage, it was detected at 11 of 12 wastewater treatment plants in Cape Town.which indicated that it began to spread rapidly among people.

This information came just at the moment when cases of Covid-19 infection were registered in the city. rising slightly. By December 4, cases in the city of Cape Town jumped much more – and much higher than cases in other parts of the province.

So the wastewater analysis revealed a trend that would have taken much longer to detect from human swabs, says Craig Kinnear, manager of SAMRC’s genomics center.

But what happens next?

Laboratories that analyze the genetic sequences of the virus in test samples send their reports to the health department and tell them whether the Covid-19 virus gene sequence looks new or is changing, which could indicate a new variant.

But wastewater tracking could also be used to create a more accurate picture of Covid-19 in the future because testing rates in South Africa are dropping rapidly.

McCarthy says that when the government eased quarantine and isolation rules in February, fewer people started being tested for Covid-19.

What’s more, most people only test when they don’t feel well. said Bekisis in May. And far fewer people than before are getting seriously ill because much of the country has developed immunity to Covid-19 through natural infection, vaccination or both, so fewer people get tested.

Thus, with the decrease in the number of tests, the results of wastewater analysis are becoming more useful for policy makers.

So what does the Ministry of Health do with such information?

“If we think that the director general of health and the minister should know about it, we inform them immediately. The plans for what we do depend on what is found,” says Nicholas Crisp, deputy director general of the health department.

McCarthy says if sewage analysis shows rising levels of Covid-19, politicians should encourage people to get vaccinated and warn them about social distancing and wearing masks.

Waste water tracking

How does wastewater analysis work?

At a waterworks, scientists fill a one-litre bottle with wastewater as it enters the plant, but before it is treated. This is because the chemicals used to treat wastewater to keep the water clean enough to be released to the environment will destroy virus fragments needed for analysis.

The sample is then placed on ice and sent to the laboratory.

Here, scientists pass the sample through a fine filter to separate solids from liquid (fragments of viruses, such as the one that causes Covid-19, are found mainly in sewage sludge). The sludge is then placed in a test tube so that it can be turned into pellets in a centrifuge (a machine that spins the samples very quickly).

After that, the silt granules are mixed with water, a small amount of this mixture is sucked off and passed through polymerase chain reaction (PCR) machine, the same device scientists use to analyze nasal swab samples for PCR tests. If viral RNA is present in the sample, the PCR step will create many copies, after which the final concentration of virus per milliliter of wastewater can be calculated. (For method there must be enough copies of the viral RNA in the sample to work, so copies of the RNA are made.)

All results from the plant samples are then summed up so that the average virus concentration in the plant wastewater can be calculated.

Why poop-based prophecies aren’t perfect

However, wastewater analysis has its limits.

Because sewage samples only come from the official sewer system and exclude sewage from places not connected to the municipal network, the results cannot give an accurate picture of Covid-19 infections in the area.

Other flaw is that as people move around the city, the exact number of people served by a particular treatment plant is not fixed, so it can be difficult to track the number of infections. Rain also interferes with work because it can dilute the sample and give the impression that there are fewer infections than there actually are. (On a rainy day, it’s best to wait another week and then take another sample to see how much the concentration of the Covid-19 virus has changed.)

But despite these hiccups, Kinnear says that over time, “accumulating data gives us an estimate of the presence of SARS-CoV-2 in the community served by a particular wastewater treatment plant.”

What about the options?

Finding a new option in wastewater is a bit like putting a puzzle together, Kinnear said. At first, the pieces are scattered, and the overall picture is unrecognizable.

Since the virus is constantly mutating, wastewater samples will contain RNA fragments derived from different forms of the virus. So, in order to figure out what the complete genetic code would look like, the RNA from each sewage plant is cut into small pieces and put into a computer program.

With this program, scientists put together small fragments to form a whole chain of the virus’s genetic code. This helps them compare it to the original sequence of the virus found in Wuhan when the pandemic began in 2020.

“We can track where [in the genetic sequence] there are changes. And by different changes we can tell exactly which option [is in the water]’, says Kinnear.

An RNA virus like SARS-CoV-2 mutates quickly because it does not have a built-in mechanism for checking and correcting errors that occur during viral replication. DNA viruses, a type of virus that monkeypox virus belongs toFor example, there is a mechanism that’s why they mutate more slowly than RNA viruses.. While not all changes in gene sequence are necessarily of concern, they are still catalogued.

For now, wastewater sequences can provide strong clues that a new option is rearing its head. But to confirm that the variant is dominant, NICD scientists need to know the results of clinical trials.

Kinnear says that the SAMRC project, which uses methods slightly different from those of the NICD, is able to detect the variant without the results of clinical trials.

How South Africa might respond to the new option

What happens if wastewater analysis indicates that we may be facing a new Covid-19 problem?

If there is evidence of a new variant emerging in the wastewater, the wastewater treatment teams will report their results to the NGS, who will compare them to clinical sequences (based on nasal swab results).

Then the whole chain of communications is turned on. The scientific teams and the health department have been alerted, and if a new form of the virus appears to be of concern, the World Health Organization (WHO) is also notified. The South African public is then briefed on developments in a press briefing and health authorities alert hospitals to be prepared for a possible increase in patient numbers.

With South Africa no longer in a national state of distress due to Covid-19, the announcement of the new option is unlikely to result in lockdowns or other restrictions, but could help authorities know when to take other public health measures, for example. , increased vaccination, in place.

For example, when the Omicron variant was announced last year, a ministerial advisory committee advised the health ministry to make booster shots available to all adults.

It could also put hospitals and healthcare workers on alert so they have time to prepare for more available beds or stock up on oxygen if needed.


This story was produced by Bhekisis Medical Journalism Center. Subscribe to Newsletter.