South Africa’s weapon for the early detection of Covid-19

Professor Tulio de Oliveira keeps an eye on new pathogens and variants in the fight against Covid-19. l FILE

Professor Tulio de Oliveira keeps an eye on new pathogens and variants in the fight against Covid-19. l FILE

Published Jan 28, 2023


Surveillance and early detection of new pathogens and variants is the weapon our scientists are using to keep their finger on the pulse.

Professor Tulio de Oliveira, of the Centre for Epidemic Response & Innovation confirmed that just weeks ago, health authorities instructed that each positive case undergoes PCR tests. These must be made available for genomic surveillance and to have a short turnaround time.

“The minister of health has asked that every positive case to be confirmed by PCR, be made available for genomic surveillance in a short turnaround time,” De Oliveira said during the World Health Organization's first media webinar held this week. They were discussing the impact of Covid-19, new variants and Africa’s health systems.

“So we are continuing to see that genomic sequencing is happening. At the moment, we are alert for new variants.”

While hospitalisation and mass infection has slowed down dramatically, De Oliveira said Africa’s best defence to fight a new wave driven by a variant was keeping their eyes open by continuous surveillance.

He added the emergence of a sub lineage, XBB.15, just a few weeks ago, was a typical example of the work done in early detection.

They have noted that this sub lineage has had a low infection rate, hospitalisation and death. “In the last two years, Africa has increased its genomic surveillance, so we have data from all parts of Africa,” he stated.

“It is important that genomic sequencing is started at a lower level and that everyone is doing the work over a short period of time. For example, this week Africa passed 150 000 genomes. That gives (us) a public database.

“With our last genome coming from January 18, especially from the southern end of the country, running a very short turnaround time.”

He added that from all the data from Africa, the variants that are circulating are dominated by Omicron.

“At the moment we have 23 genomes of this variant (which) we detected in southern Africa, four in Botswana and 19 South Africa, with the last data coming from last week.

“But despite the discovery of this new sub lineage, XBB1.5, which is at 10% of the genomes in South Africa, we didn’t see exactly an increase in infection or hospitalisation in the past two weeks.

“We see this new variant, XBB1.5, couldn’t drive a new wave of infection, of hospitalisation and death.

“What helped here in South Africa is the early detection of the variant. If you can do good surveillance, with early pathogens and variants, you can help to prepare your health system .

“Early detection is something we did very well. We can also improve but it was something that we were focused on and we saw the results in the two Omicron waves.”

Dr Matshidiso Moeti, WHO regional director for Africa, said the pandemic had not only put a strain on the public health sector, it also taught them many lessons on immunisations which were disrupted, leaving millions of adults and children vulnerable.

“Children under the age of five, who receive immunisation to protect them against diseases such as yellow fever and measles.

“Other routine services for adults, such as family planning, safe deliveries for pregnant women, access to antiviral retrieval services, which is a very important part of healthcare on the African region; all of these were disrupted significantly by the lockdowns and people who were afraid to come to health facilities.

“We have seen an increase in diseases, millions of children have been at risk of measles, yellow fever and we have seen measles outbreaks in 20 African countries and that is quite unprecedented.”

Weekend Argus