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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Senior Communications Manager
National Institute for Communicable Diseases