COVID-19 UPDATE: DELTA VARIANT IN SOUTH AFRICA

29 June , 2021

The National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, has been performing genomic surveillance for SARS-CoV-2 and can confirm that the Delta variant is becoming more dominant in Gauteng, South Africa.

Genomic data, generated by the Network for Genomic Surveillance in South Africa (NGS-SA : sequencing teams at the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal (UKZN); the Division of Medical Virology at NHLS Tygerberg Hospital, Stellenbosch University (SU); the Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town (UCT); the Division of Virology at NHLS Universitas Academic Laboratories, University of the Free State (UFS) The Division of Virology at NHLS Inkosi Albert Luthuli Central Hospital (IALCH), University of KwaZuluNatal (UKZN), the Zoonotic Arbo and Respiratory Virus Program at the University of Pretoria (UP) and the Department of Virology at NHLS, University of the Witwatersrand (WITS)), from sequenced COVID-19 specimens during May 2021, shows that 70% of 680 genomes were the Beta variant.

However, in June 2021 genomes (n=541) sequenced from samples revealed a 31% drop in the Beta variant to 39%, with the Delta variant increasing and accounting for 45%.

Gauteng, undoubtedly the epicentre of the resurgence, presently accounts for an average of 65% of daily new cases. In Gauteng, 64% of 244 genomes sequenced from May 2021 are attributed to the Beta variant, while in June 2021 this dropped to 37%. In contrast, during June, 53% of genomes (n=341) from Gauteng were the Delta variant.

Data from the UK shows that the Delta variant (first detected in India) is 97% more transmissible than the original lineage. COVID-19 vaccines remain highly effective in preventing severe disease after Delta variant infection, with the Pfizer-BioNTech vaccine showing 96% efficacy after two doses.

“It is important to be mindful that reinfection with the Delta variant is possible following a Beta infection, due to waning of immunity,” comments Prof Adrian Puren, the NICD’s Acting Executive Director. Limited data are available on whether different symptoms result following Delta infection, and preliminary data from the UK suggests that the Delta variant can potentially cause more severe disease.

Given the current COVID-19 resurgence, other variants of concern (VOC), including Alpha, and Eta variants, were also detected in May and respectively accounts for 6% and 1% of the samples collected over the same period. No Eta variant detections have been recorded in samples collected in June and the Alpha variant accounts for 7% of infections sequenced in June. These and other VOC are also being monitored globally because of concerns about possible increased transmissibility and immune evasion.

Genomic data is available from South AfrIca on the GISAID database, a system that enables rapid and open access to epidemic and pandemic virus data. As of 29 June 2021, the Network for Genomics Surveillance (NGS-SA) reports that 10,200 SARS-CoV-2 genomes from South Africa have been generated of which 97% has been deposited on GISAID.

“It is not surprising that new variants have been detected in South Africa”, adds Adrian Puren. “We would like to assure the public that the institute is focusing their resources and research efforts towards understanding the variants and we would like to salute all healthcare workers who continue to fight bravely against COVID-19.”

Minimising the spread of the disease and flattening the curve through compliance with non-pharmaceutical interventions cannot be emphasised enough. “We understand that many are suffering from COVID-19 fatigue and becoming relaxed in exercising preventative measures. But for the sake of yourselves and your loved ones, wash or sanitise your hands, wear your masks and maintain physical distance of 1.5 m from others. Remember to avoid gatherings and to roll up your sleeve once the COVID-19 vaccine becomes available to you,” Puren concludes.

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NGS-SA worked hard to increase sequencing in South Africa. We know now that the explosive #COVID19 third wave is dominatedd by the Delta variant.

In this tweet thread, we present recent data (sampled up to 24 June in many provinces in SA, including Gauteng) - Tweet 1/8 pic.twitter.com/BHUbSSSZpC

— Tulio de Oliveira (@Tuliodna) June 30, 2021

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LATEST CONFIRMED CASES OF COVID-19 IN SOUTH AFRICA (29 JUNE 2021)

• 29 June , 2021

The National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, continues the monitoring and surveillance of COVID-19 in order to inform the public health response.

Today the institute reports 13,347 new COVID-19 cases that have been identified in South Africa, which brings the total number of laboratory-confirmed cases to 1,954,466.  This increase represents a 26.2 % positivity rate.  A further 226 COVID-19 related deaths have been reported, bringing total fatalities to 60,264 to date. For more detailed information, visit the GIS Dashboard.

 13,062,835 tests have been conducted in both public and private sectors as per the table below.

PROVINCIAL BREAKDOWN
The Gauteng province accounts for the majority of new cases (67%), followed by the Western Cape and KwaZulu-Natal provinces (7% each). The following table shows the total number of cases per province:

THE 7-DAY MOVING AVERAGE NUMBER OF NEW CASES BY PROVINCE

HOSPITAL ADMISSIONS
An increase of 711 hospital admissions have been reported in the past 24 hours. The following is a list of COVID-19 hospital admissions that have been reported:

VACCINE UPDATE
For updates on the national vaccine programme, click here.

Thank you for your interest and remember that adhering to preventative measures limits your risk of contracting and spreading COVID-19. For more information on COVID-19, click here.

Issued by NICD, 29 June 2021