The National Institute for Communicable Diseases (NICD) has released genomic surveillance data for the coronavirus (SARS-CoV-2) which shows that the Delta variant is becoming more dominant in Gauteng.
Data sequenced from Covid-19 specimens during May 2021 shows that 70% of 680 genomes were the Beta variant. However, in June the genomes sequenced from samples revealed a 31% drop in the Beta variant to 39%, with the Delta variant increasing and accounting for 45%.
Gauteng, which the NICD said is 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 the 341 genomes sequenced from Gauteng were the Delta variant.
|Variant||May 2021||June 2021|
|Beta — discovered in South Africa||70%||39%|
|Delta — discovered in India||—||45%|
|Beta — discovered in South Africa||64%||37%|
|Delta — discovered in India||—||53%|
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,” said Professor Adrian Puren, the NICD’s Acting Executive Director.
Limited data is 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, including Alpha, and Eta variants, were also detected in May and respectively accounted for 6% and 1% of the samples collected over that period 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 variants of concern are 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,” Puren stated.
“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.”
The NICD said that minimising the spread of the disease and flattening the curve through compliance with non-pharmaceutical interventions such as wearing a mask, physical distancing, and avoiding gatherings cannot be emphasised enough.
“We understand that many are suffering from COVID-19 fatigue and becoming relaxed in exercising preventative measures,” said Puren.
“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.”