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.
At present, we believe that the 501Y.V2 (B.1.351) antibody response may be strong enough to neutralize the B.1.617 as the 501Y.V2 can neutralize other lineages and variants with many mutations, such as P1 - see some of SA papers at:…
Another important paper showing the neutralization breath of the 501Y.V2 on the paper at:…
The identification of the first genome from a traveller from India in South Africa was due to very diligent and fantastic work of Prof Susan Engelbrecht, who is a member from the Network for Genomic Surveillance in South Africa (NGS-SA) from @StellenboschUni
We are strengthening genomic surveillance in South Africa. So far, the dominant variant is the 501Y.V2 (around 99%), we have also detected multiple introductions of B.1.1.7 and the A.23.1. We will keep reporting on results and keep an eye for new variants.
The very important take home message is that the known public health interventions (testing, contact tracing and isolation) together with non-pharmaceutical interventions (social distance, washing hands and wearing masks) are extremely important as we scale vaccination.

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More from @Tuliodna

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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