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Tulio de Oliveira

25 Mar, 8 tweets, 3 min read

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

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.

When compared with other variants of concern and variants of interest, this is the most divergent one.

Manuscript has been deposited at medRxiv and until online is freely accessible at: krisp.org.za/publications.p…

Sequences are available in GISAID with accessions: EPI_ISL_1347940, EPI_ISL_1347941, EPI_ISL_1347942

We decided to report this as a new VOI given the constellation of mutations with known or suspected biological significance, specifically resistance to neutralizing antibodies and potentially increased transmissibility.

Whilst we have only detected three cases with this new VOI, this warrants urgent investigation as the source country, Tanzania, has a largely undocumented epidemic and few public health measures in place to prevent spread within and out of the country.

Thanks @AfricaCDC, Minister of Health of Angola, @rjlessells @houzhou @Mittenavoig and many other colleagues from Angola and Africa to help on the analysis of the data.

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More from @Tuliodna

Tulio de Oliveira

@Tuliodna

9 Mar

Finally out! Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein disq.us/t/3vewz4s

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.

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Tulio de Oliveira

@Tuliodna

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.

medrxiv.org/content/10.110…

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...

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.

Read 6 tweets

Tulio de Oliveira

@Tuliodna

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 biorxiv.org/content/10.110…

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.