New coronavirus infections in Gauteng are now dominated by the more easily transmitted Delta variant first identified in India, according to analysis released by the National Institute of Communicable Diseases (NICD) on Tuesday.
Data provided to Business Day by the NICD shows how Delta has rapidly displaced other variants, including Beta, which was first detected in SA late in 2020 and quickly came to dominate local transmission. The data comes from genomic sequencing of SARS-CoV-2 samples.
In Gauteng, the proportion of Delta rose from 15% in May to 53% in June. Over the same period, the proportion of Beta dropped from 64% to 37%, and the proportion of Alpha, which was first detected in the UK, fell from 13% to 9%, said Jinal Bhiman, principal medical scientist at the NICD.
Nationally, the proportion of Delta rose from 14% in May to 43% in June. The proportion of Beta fell from 70% to 37%, and the proportion of Alpha rose slightly from 6% to 8%, over the same period, said Bhiman. A small proportion of Eta and other variants of concern were detected, she said.
The data was generated by the Network for Genomic Surveillance in South Africa (NGS-SA), which includes researchers from the KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp), several universities and the National Health Laboratory Service. The data is publicly available on the international Gisaid database. The NGS-SA has to date sequenced 10,200 Sars-CoV-2 genomes from SA, 97% of which have been deposited on Gisaid, said the NICD.
The NICD said the Delta variant was 97% more transmissible than the original SARS-CoV-2 lineage detected in China in late 2019, but vaccines were highly effective at preventing severe disease caused by infection with this strain.
“It is important to be mindful that reinfection with the Delta variant is possible following a Beta infection, due to waning of immunity,” said NICD acting executive director Adrian Puren.
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