In the Covid storm our poop doesn’t tell lies

We are in the eye of the storm. Yes, right in the middle of the third wave of this Covid-19 pandemic.  This wave is unprecedented and the scale was unpredictable. There was an expectation that we would have a milder third wave. But the rise of new mutations, most recently the delta variant, has facilitated the rapid rise in infections, breaking previous and records locally and nationally. 

In June this year, the Water Research Commission (WRC) published a science brief based on its National Wastewater Based Epidemiology (WBE) Surveillance programme with implementation partners the National Institute for Communicable Diseases and the South African Coordinating Committee of Environmental Surveillance Systems network. It reported an exponential increase in Covid-19 RNA fragments detection at one of its sentinel wastewater treatment plants serving the eThekwini municipality. This input by the Durban University of Technology (DUT) was an early warning of at least four weeks in advance of the rise of confirmed clinical cases. This was the beginning of the third wave. A rapid response with robust interventions would have mitigated the intensity of the third wave. But that was not the case and the WBE surveillance, in spite of demonstrating its effectiveness as an early warning mechanism and a complimentary instrument in managing this Covid-19 virus, was largely ignored. 

 The science community continues its work with other centres. The City of Cape Town, in partnership with the Medical Research Council (MRC), has also demonstrated its effectiveness in managing hotpots, an opportunity not exploited by many other metros and cities in our country. We must once again call on the government to fund a national WBE Covid-19 surveillance programme covering at minimum the majority of our wastewater treatment works in the critical areas, because this third wave will not be our last.

The concept of screening municipal wastewater and environmental water quality as an epidemiological tool for viruses is not new. It has been used to help inform broader infectious disease epidemiological surveillance and mitigation efforts such as the Global Polio Eradication Initiative. Environmental surveillance has also been used and recommended for other infections such as typhoid, hepatitis A and norovirus outbreaks, as well as for antimicrobial resistance, with modelling techniques used to assist both the design and interpretation of those efforts. Wastewater based epidemiology (WBE) is also commonly used in the surveillance of legal and illicit drugs and various chemical contaminants that may affect human health. Recent studies have shown that environmental surveillance of SARS-CoV-2 (the virus responsible for the Covid-19 disease) signals biomarkers (typically RNA) by means of Reverse transcriptase Polymerase Chain Reaction (Rt-PCR) and can be a low-cost solution for tracking Covid-19 outbreaks.

This is because SARS-CoV-2 is shed at relatively high titres in the stool of some individuals. Viral gastrointestinal infection, or at least shedding, can remain for some time after clearance of the virus in the respiratory tract. The detection of SARS-CoV-2 RNA in untreated domestic wastewater was first reported internationally by KWR-Netherlands and this had spurred many other countries into the pathway of WBE. More than 100 countries have some form of formalised activity. We are dealing with a remnant protein particle of the COV-2 virus and not a live virus, hence it is safe.  The detection of SARS-CoV-2 in sewage is relevant not necessarily because of the potential risk of disease spread, but rather because of the potential to determine the presence of infected individuals in a community. SARS-CoV-2 screening in raw sewage water using Rt-PCR can therefore be used as a tool to measure virus circulation in a defined population, for example a city or a smaller municipality feeding to the same wastewater treatment works.

South Africa is recognised among the world leaders in WBE surveillance because of the work of the WRC last year with several institutions, both public and private, playing a role in dealing with this pandemic. We are privileged to have the body of leading scientists and practitioners who have made WBE surveillance a shining example for the world. The second privilege we have had is that we have been able to track this virus in wastewater right from the onset of the first infections and thus have a longitudinal view of trends and patterns in many of the sentinel wastewater plants in hotpots. For example, for sentinel plants in Gauteng we can see that from March 2020, weekly samples tested positive for the presence of the COV-2 RNA the majority of the time (the red in the table; the grey and yellow lines are the clinical cases reported).

So, the team went back to the samples collected and did tests to determine the COV-2 RNA copies present. They took the samples from February 2021 onwards to demonstrate the onset on the third wave. As early as February this year, the teams were picking up an increase in the signal of the COV-2 RNA fragments, with the exception of Ekurhuleni, which started to show mid-April. In all the cases the surge was dominant from the last week of May 2021, when the clinical cases had not even surfaced. This shows the power of WBE and its early warning properties. This pattern was similarly observed in several other sentinel sites in other provinces.

There is a need to take this early warning system much more seriously. The proof of concept has been completed by the WRC and various partners in the South African Water and Health Research Community of Practice very effectively. It is time to invest in the national surveillance programme. This will not only give us the early warning system we so badly need, but also monitor the effectiveness of our various mitigation measures such as lockdowns, treatment regimes and the vaccine roll-out at community scale and in advance of the person-to-person testing.

Epidemiological curves of laboratory-confirmed SARS-CoV-2 cases, SARS-CoV-2 viral loads in wastewater and SARS-CoV-2 PCR detection results in wastewater by district, Gauteng Province, 2020-2021. The districts shown include City of Johannesburg (A), City of Tshwane (B) and the Ekurhuleni metropolitan area (C). Figure: The yellow curve represents laboratory-confirmed Covid-19 cases (left axis) by epidemiological week 2020-2021 (horizontal axis). Blue bars represent quantitative viral loads in copies per millilitre (right axis) in specimens collected in given epidemiological week 2020-2021 (horizontal axis). Table: Green squares represent negative PCR results, red squares represent positive results and black squares represent invalid results. JHB=City of Johannesburg. TSH=City of Tshwane. EKH=Ekhuruleni. WWTP=wastewater treatment plant. *Population is the approximate size of the population served by the wastewater treatment plant. Lab is the name of the testing laboratory  (Source: NICD)

From the graphs above the past few weeks are showing high counts of SARS COV-2 RNA in the wastewater streams, indicating that the level of infections are high in the areas served. The first important finding from the interpretation of the data and information on testing for Covid-19 RNA fragments in wastewater confirms that Wastewater Based Epidemiological (WBE) Surveillance is a cost-effective way of providing an early warning of the spread and increase in infections. In this case the RNA signal in the wastewater showed increases in copy numbers at least four weeks in advance before the clinical cases started to confirm increases in reported positive cases.

The second important finding is the increase in the viral loads or increase in the amplification of the RNA signal offers a very effective signal on the increases in infections, because it is able to capture the asymptomatic cases as well, which form a pathway for the spread of infections.

We continuously keep building on the science and approach and have recently incorporated the element of determining existing and new variants through the WBE surveillance programme. Preliminary results shared with the media last week of the work of the MRC confirmed the high presence of the delta variant in many of the Western Cape plants tested. As new data emerges, we will endeavour to share this with the public. We want to assure through the process a strong behaviour acumen by the public on continuing with the safety measures of social distancing, wearing a mask and washing hands. More so, we also want to ensure that in the wastewater and water environments the virus is not infectious. What we find is remnants of the virus in the form of a protein, which we call the RNA.

This progress has demonstrated the importance and effectiveness of WBE surveillance and why it needs to be escalated at a national level in the fight against this pandemic. Authorities have been too slow in harnessing this opportunity. From all indications and experiences globally the fight against this virus is not over and we are in for a long haul and WBE surveillance must form part of the national and local arsenal in managing the spread of infection — but also in the future be used to determine the effectiveness of the large roll-out of vaccinations in the country.

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Jay Bhagwan
Jay Bhagwan is the executive manager of the Water Use, Wastewater Resources and Sanitation Futures Key Strategic Area at the Water Research Commission and leads the WRC/SALGA/NICD/SACCESS National Wastewater Based Surveillance programme of COV-2 virus.

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