How testing sewage will help detect next wave of Covid-19 infections

Western Cape epidemiologists will start testing sewage for signs of new waves of Covid-19 infections as the province continues to see declines in cases of the virus.

Prof Mary-Ann Davis of the provincial department of health said such testing had been proven in other countries, where Covid-19 was detected in wastewater even before anyone in the local population tested positive.

Speaking during premier Alan Winde’s weekly press conference on Thursday, Davis said the province was also working on expanding its testing criteria. It was already conducting “sentinel testing” for Covid-19 antibodies on people such as HIV patients and pregnant women, as they were readily available for testing and represented a different subset of the population than would otherwise present for testing.

“They are good for monitoring trends. If we test the same kinds of patients in a month’s time they can tell us what’s happening over time, and if we’re testing people in different locations then they are useful for comparing what might be going on in different locations,” she said.

Testing was approved last week but the first results from just under 3,000 tests conducted so far showed that about 40% of them indicated evidence of previous infection.

“It was a little bit higher in the people with HIV than with the pregnant women and what was very interesting, and something we must look at a little further, is that it was higher in women than in men,” she said.

She said the tests indicated that in the population which used public health care, generally representing poorer people, a relatively high proportion of people were infected with Covid-19.

She said the mortality rates among these populations matched the new infection data.

But the stats also pointed towards the fact that these population groups had developed some sort of immunity.

“This fits with what we’ve seen in our epidemic, which is a reduction of cases despite that we are actually reducing restrictions and coming out of hard lockdown. So it’s likely that some degree of immunity in our population is contributing to that,” she said.

Only 9% of the more than 70% of beds occupied by patients in the province were occupied by Covid-19 patients by Wednesday.

And across the province there were only 18 Covid-19 ventilated cases.

Davis said the Covid-19 health response had not impacted on care for patients suffering from other diseases such as TB, HIV, or diabetes. The data showed that there were fewer non-Covid-19 related deaths during the lockdown period compared to the same period in 2019.

“This is particularly marked during the periods of strictest lockdown up to May, and that makes sense because the lockdown measures would have reduced transmission of other infectious conditions like flu which would cause mortality in our HIV and TB groups,” she said.

“Once Covid-19 deaths start to kick in we see an uptick in deaths but almost entirely due to Covid-19 in later months. So though the total deaths is pretty similar between 2019 and 2020 for the later months, this is a combination of fewer non-Covid deaths, and more Covid deaths,” she said.

Davis said it was unlikely that in the short term there would be “explosive outbreaks” in high density, most vulnerable communities, because there seemed to be a level of immunity there.

“Having said that, even in those communities there probably are people who have shielded themselves in the past months and who are susceptible, and because there is a lot of difference between population subgroups across the city and the province there will still be some groups where they would be vulnerable. Vigilance is critical to make sure we are able to detect a second wave,” said Davis.

Health officials are now saddled with the task of detecting the second wave, which may include a different form of the virus or a new virus altogether.

She said they would do molecular testing on people who had the first virus to check if new strands had evolved.

Davis said wastewater testing was not new in SA and was already used to detect polio cases and other diseases.

“Many of you may have read international articles which showed that sewage analysis was able to identify that coronavirus was circulating in an area even before the first cases were diagnosed, or that there was likely many more cases of coronavirus than were being diagnosed,” she said.

“We have a lot of skill in wastewater epidemiology. Since the start of the outbreak a number of scientists and a big collaboration of stakeholders has made progress and successfully isolated the virus from wastewater in our setting, and is improving the way to do this.”

She said a national network, including the National Institute for Communicable Diseases (NICD), had been developed to take this forward in the Western Cape, and particularly the City of Cape Town, to develop a wastewater dashboard.

“Any increases we find in the virus in wastewater will be an indication that we need to look for cases in that area and look to implement interventions,” said Davis.

TimesLIVE