Confirmed Detection of B.1.617.2 and B.1.1.7 in South Africa by NGS-SA

This report was sent to our Health Minister @DrZweliMkhize yesterday.

In this Twitter thread, we highlight the details and repercussion of the discovery to South Africa

In response to the continued emergence and spread of new variants around the world, the Network for Genomic Surveillance in South Africa (NGS-SA) recently intensified the monitoring of confirmed COVID-19 cases in recent arrivals to the country.

We can now confirm that today we detected four cases of the B.1.617.2 variant. The four cases have been detected from Gauteng (n=2) and KwaZulu-Natal (n=2) provinces and all have a history of recent arrivals from India.

All cases have been isolated and managed according to national COVID-19 case management guidelines and contact tracing has been performed in order to limit the spread of this variant.

The B.1.617.2 is listed as a variant of interest by the @WHO and is spreading rapidly in India. On 7 May 2021, B.1.617.2 was classified as a variant of concern (VOC) by Public Health England ( @PHE_uk ) based on evidence of a rapid increase in cases in England.

There is some preliminary evidence to suggest that B.1.617.2 may be associated with increased transmissibility. There is also some evidence to suggest some degree of immune evasion, but that may be modest and lower than what has been observed with 501Y.V2 (B.1.351).

The available evidence suggests that the B.1.617.2 may not have a major effect on vaccine efficacy. At present, the scientific community has no reliable data on disease severity with this variant.

“We reiterate that there is no need for panic as the fundamentals of the public health response (testing, contact tracing, isolation, and quarantine) have not changed.” Commented. Prof. Koleka Mlisana, co-chair of the Ministerial Advisory Committee on COVID

“We all have a responsibility to adhere to prevention measures (avoiding large gatherings, physical distancing, mask-wearing, ventilation, and hand sanitation) in order to limit the spread of SARS-CoV-2 in South Africa.”

In addition, genomic surveillance in South Africa has also this week identified 2 new cases of the B.1.1.7. In total, we have detected 11 confirmed cases of the B.1.1.7. The B.1.1.7 is highly transmissible, and this variant is dominating infections in Europe and North America.

However, the B.1.1.7 is not associated with significant immune evasion and does not seem to affect vaccine efficacy.

As the epidemic progresses, the detection of new variants is inevitable and the movement of people around the world means that these variants will continue to spread. NGS-SA remains vigilant and is supporting the Department of Health.

There are a number of other samples from cases with recent travel into South Africa that are currently being sequenced with results expected over the next few days.

NGS-SA is a consortium of scientists funded by the Department of Science and Innovation (DSI) and the South Africa Medical Research Council (SAMRC).

The sequencing for these recently confirmed cases was performed by the National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS) and the University of KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP).

Furthermore, a recent case of 501Y.V2 imported into South Africa from Bangladesh has sequenced the University of Stellenbosch. The other labs in the network, the University of Cape Town and at the University of the Free State have also intensified surveillance of imported cases.

More information on the Network for Genomic Surveillance in South Africa (NGS-SA) activities at: https://www.krisp.org.za/ngs-sa/