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Tests and wastewater analyses signal a possible 5th wave in SA

A rise in test positivity rates and the presence of the SARS-CoV-2 virus in the country’s wastewater are sounding the alarm for the arrival of a possible fifth, winter COVID-19 wave in South Africa.

Two Omicron subvariants are rising rapidly and have increased in prevalence from 16% to 44%, according to the latest sequencing data released by the National Institute for Communicable Diseases (NICD) on Monday (25 April).

Additionally, the country’s positivity rate (the percentage of cases testing positive) jumped from 16% over the weekend to 19.3% on Monday, according to the latest statistics released by the NICD, with another 1,954 people testing positive for the virus.

Sinehlanhla Jimoh from the NICD said 10,144 people tested for the virus on Monday and that in the NICD’s daily update, the majority of new cases registered were from Gauteng (55%), followed by KwaZulu-atal (23%). Western Cape accounted for 11%; Free State for 3%; Eastern Cape, Mpumalanga and North West each accounted for 2%, and Limpopo and Northern Cape each accounted for 1% of Mondayʼs new cases.

The highest number of positive tests come from young teenagers.

There have also been 65 new hospital admissions. A total of 2,282 people are currently being treated in hospital for COVID-19 related complications.

The data in the sequencing report analyse the results of sequencing tests to identify the variant of the SARS-CoV-2 virus in samples, where patients tested positive for infection, collected up to 22 April.

According to this report, the original version of Omicron – BA.1 – dominated the January data (55%), BA.2 dominated in February, March and April, but two additional sublineages of the Omicron variant (BA.4 and BA.5), increased in prevalence during March (16%) and appear to be increasing in April (44%), although additional sequencing data is needed for this period.

Another sublineage, BA.3, continues to be detected but only at low levels. Both BA.4 and BA.5 are being tracked by the World Health Organization (WHO), as more cases of these have been found in countries other than South Africa.

In the latest sequencing report, scientists said while the mutations on these two sub-variants are not defined, it may be linked to an increased ability to escape the bodyʼs immunity against SARS-CoV-2. Data are currently being monitored for recombinants.

A recombinant of the Omicron and Delta variants was first identified and then designated as a variant of concern by the WHO in January 2022.

Last Thursday (21 April), the NICD head, Professor Adrian Puren, also warned that an early warning COVID-19 outbreak alarm system, wastewater detection surveillance, was showing a spike in cases, with scientists isolating the BA.4 variant in Gauteng’s wastewater. Wastewater levels of coronavirus were also rising in KwaZulu-Natal, the Free State and Western Cape. Most samples contained Omicron’s BA.4 sub-variant.

On Friday, reports News24, while introducing his department’s annual performance plan to the Portfolio Committee on Health, Health Minister Joe Phaahla said his department had noted the worrying increase in infections, and hoped this wouldn’t continue.

“But we are monitoring, and we will be able to report back to the committee and the public once we have seen the trend,” he said, adding that the past two years had been dominated by the pandemic.

The department’s energy, financial and human resources weighed heavily in favour of containing the pandemic, he said. “We are hopeful, as we present the annual performance plan, that the 2022-23 financial year will be different from the past two financial years. We hope that there will be more stability in the pandemic, that the pandemic will be better contained.”

This would allow the department to focus on its programmes and not be “diverted” as it had been during the past two years, he added.


News24 article – Phaahla warns of 'worrying signs' after increase in Covid-19 infections (Open access)


Daily Maverick article – Expert sounds alarm on fifth wave after Covid-19 curve turns upwards in SA (Open access)


See more from MedicalBrief archives:


Why Omicron doesnʼt need its own custom COVID vaccine


South African government has ‘quietly de-prioritised vaccinations’


Omicron sub-variant BA.2 warning for US as European cases surge


SAMRC: Rising levels of SARS-CoV-2 RNA fragments in Tshwane and NMB wastewater


SAMRC's wastewater tracking of Covid-19 signals KZN third wave



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