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:

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More from @Tuliodna

4 May
First genomic surveillance results from a traveler to India in South Africa. A patient at Tygerberg Hospital who tested positive for SARS-CoV-2 about 3 days after traveling to SA from India. This first genome is a 501Y.V2 (B.1.351) and not the B.1.617 described in India.
The 501Y.V2 (B.1.351) is the 3rd most common variant in India after the B.1.617 and the B.1.1.7. Below a graph from @trvrb showing the spread of the variants in India.
The 501Y.V2 (B.1.351) was firstly identified in South Africa by the network for genomic surveillance in South Africa (NGS-SA). It shows how variants can be introduced back and forth between countries.
Read 8 tweets
29 Mar
Today paper on neutralization of 501Y.V2 (B.1.351) - Show effective neutralization of other SARS-CoV-2 lineages by 501Y.V2 @nature…

All start with a good cohort... We obtained convalescent plasma & sequenced the matching infecting virus of 1st & 2nd wave
A first wave variant lacking the 501Y.V2 RBD and NTD mutations (B.1.1.177) was outgrown from one participant infected in the first South African infection wave, and 501Y.V2 was outgrown from a participant at the beginning of the second wave.
A focus forming live virus neutralization assay (LVNA) was used to quantify neutralization.
Read 14 tweets
25 Mar
We just submitted a pre-print 'A novel variant of interest (VOI) of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.'

This VOI has 31 amino acids mutations. In Spike has 11 mutations and three deletions in the N-terminal domain Image
It has some key mutations, including the E484K, R346K and P681H. The R346K is the associated with resistance to class 3 RBD NAbs recently described by @jbloom_lab
There are also 5 substitutions and 3 deletions in the NTD antigenic supersite (Y144Δ, R246M, SYL247-249Δ and W258L)
It the most diverse A lineage sequencers ever described. It also worry us as it was found in three travelers from Tanzania in Angola. There is almost no data from COVID-19 in Tanzania. Image
Read 8 tweets
9 Mar
Finally out! Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

So many people to thank, thank you and thank you! @rjlessells @houzhou @Mittenavoig @MRCza @dsigovza

Great to see South African science advancing fast!
The paper starts by showing how the second wave in South Africa arise so quickly, which was completely unexpected as we were in the start of our summer.
It show how a new and unusual cluster emerged among the dozens of different lineages already circulating in South Africa.
Read 10 tweets
7 Mar
A truly global collaboration between groups in South Africa, U.K., Belgium, Sweeden, USA to understand convergent evolution of the variants of concern.…
ARS-CoV-2 genome map indicating the locations and encoded amino acid changes of what we considered here to be signature mutations of 501Y.V1 (B.1.1.7), 501Y.V2 (B.1.251) and 501Y.V3 (p1) sequences. Amazing how different and similar the variants are... Image
Signals of positive selection detected at 37 signature mutation sites in the VOCs between March 2020 and January 2021. In short, must of the sites in Spike are in convergent evolution, including 501, 484, 417, 18, etc. Image
Read 6 tweets
7 Mar
Another knock down paper from South Africa! This time 501Y.V2 (B.1.351) is giving again good news with confirming that neutralise other lineages but also another VOC, the P1.

SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies…
We observed no significant difference in the magnitude of binding (Figure 1A) or neutralizing (Figure 1B) responses between the 501Y.V2 cohort and the wave 1 (i.e. B.1 original lineages) admission samples.
Plasma binding antibodies in 501Y.V2 infected individuals are cross-reactive.
Read 5 tweets

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