Covid-19: Traces of Omicron variant detected in Cape Town's wastewater

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  • Wastewater samples show that the Omicron variant was already in Cape Town before it was announced in November. 
  • These tests are conducted as part of early warning systems monitoring possible resurgence of the virus and outbreak hotspots. 
  • The SA Medical Research Council said three-quarters of the sites tested in Nelson Mandela Bay also showed signs of Omicron overtaking the Delta variant. 

The recently identified Omicron variant of the coronavirus was found in Cape Town International Airport wastewater as far back as 23 November, the SA Medical Research Council (SAMRC) said on Friday. 

This was the first detection of the variant in the city's wastewater system and came a day before the announcement of the identification of the variant, which inadvertently set off a travel lockdown to some countries. 

By then it had already been spotted by a laboratory scientist on 4 November, whose curiosity was piqued by a slightly different positive test result. 

READ | Inside SA leg of Omicron variant discovery: A single test result, a missing gene, and an email 

Wastewater treatment plant sampling is found to be a reliable indicator of where new outbreaks of the coronavirus associated with Covid-19 could occur. 

The SAMRC said it was first detected on 23 November from a Cape Town International Airport wastewater system sample. By 30 November, it was seen in 11 of 12 samples of wastewater collected from the city's treatment plants. 

Professor Rabia Johnson, deputy director of the SAMRC's Biomedical Research and Innovation Platform, said in a statement that this coincided with an increase of Covid-19 cases in the city. 

Gauteng had been hardest hit in the latest surge in cases, with KwaZulu-Natal and the Western Cape following with a sudden increase in cases.

READ | SA scientist to lead WHO research into Covid-19 origins

Dr Mongezi Mdhluli, leader of the SAMRC Wastewater Surveillance and Research Programme (SAMRC-WSARP), said this was the first report of the Omicron variant being detected in the City of Cape Town's wastewater system. 

Since July 2020, scientists had monitored the concentration of fragments of the SARS-CoV-2 virus RNA in wastewater in Limpopo, Eastern Cape, Western Cape and Gauteng. 

These tests were being conducted in countries across the world as scientists get to grips with the latest variant of infectious disease.  

Professor Craig Kinnear, Director of the SAMRC Genomics Centre, said that although viral remains were shed in the faeces of individuals with Covid-19, the fragments found at wastewater treatment plants were not infectious. 

The extent to which the Omicron variant had spread to rural areas outside the City of Cape Town was not known, with the Delta variant still appearing to be dominant at the Rawsonville site in the Breede Valley. 

READ | Sanlam paid more than R14bn in death claim over 10 months, mostly due to Covid-19 third wave

In addition, in partnership with Nelson Mandela University, preliminary results showed that three out of four wastewater treatment plants in Nelson Mandela Bay in the Eastern Cape tested positive for Omicron.

SAMRC-WSARP results generated this week showed that concentrations of SARS-CoV-2 fragments were now increasing in virtually all of Cape Town's wastewater treatment plants, as well as in other parts of the country. 

SAMRC President and CEO Professor Glenda Gray, said these findings illustrated how crucial it was to get vaccinated and to stick to the non-pharmaceutical interventions of masks, hand washing, social distancing and avoiding crowds. 

"Essential gatherings should preferably be held outdoors, or in very well-ventilated indoor spaces, as this is one of the ways to curb the transmission of Covid-19 during the coming festive season. We, therefore, advocate for fellow South Africans to vaccinate before vacation."

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