Tulio de Oliveira Profile picture
Mar 25, 2021 8 tweets 3 min read Twitter logo Read on Twitter
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
When compared with other variants of concern and variants of interest, this is the most divergent one. Image
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

Aug 31
South Africa has today detected a 3rd case of BA.2.86. In total, 3 genomes, 2 from Gauteng & 1 from Mapumalanga. Since the discovery of the first case, scientists advising the government have been alerted, here, I summarise SA advisory to this new lineage of COVID-19 🧵
South Africa is one of few countries of the world that still have an active genomics surveillance program and a scientific advisory board for the COVID-19 pandemic, which is called the Ministerial Advisory Board (MAC) that advise the ministers.
As the new Omicron BA.2.86 lineage has over 30 extra mutations was spotted in Denmark and Israel, SA increase genomics surveillance and inform the ministers. We also had special seating of the Ministerial Advisory Board (MAC) to discuss the implications of BA.2.86 2 weeks ago.
Read 16 tweets
Jan 3
A small thread on COVID recombinants:
- Omicron XBB.1.5 in U.S.A. with key Spike F486P mutation
- Omicron/Delta XAY in SA also with F486P.

The XBB.1.5 seems to be fast increasing prevalence, whereas XAY faded. Will XBB.1.5 spread further? What is the role of the F486P mutation?
A new recombinant lineage of Omicron XBB.1.5 seems to be emerging in the U.S.A. Very early data puts to an evolution of XBB.1.5 lineage to get a 'key mutation' F486P (Purple collar on graph, high prevalence in the East Coast). Image
A detailed analysis of this new XBB.1.5 Omicron recombinant has been covered by many of my US scientific colleagues. For good source of analysis see @EricTopol @ScottGottliebMD @jbloom_lab - erictopol.substack.com/p/a-new-varian…
Read 7 tweets
Dec 30, 2022
A small thread on:
1) Why we are alerted but not too concerned of the global effects of the massive wave of COVID-19 in China,
2) Why the proposed restrictions from Italy & USA are not likely to be effective.
3) Some simple global interventions for 2023.
China decided to stop its Zero-COVID intervention. The intervention worked well in the past two years and allowed time for the world and China to develop vaccines, diagnostics and therapeutics. Now, there is fear that the COVID-19 tsunami in China will detail the global efforts.
The wave of COVID-19 infections in China seems to be enormous, some of the epidemiological modelling and news point to millions of daily infections and up to 9,000 daily deaths. A really sad statistic to end 2022 and we feel for the Chinese families and communities.
Read 14 tweets
Dec 4, 2022
Like many scientists, I am also not convinced that Omicron evolved stepwise in Africa and was undetected for months. In the next tweets, I highlight some of my thoughts on this report and highlight some of the weaknesses. 1/x
First, the 'fishing' of intermediates in Africa should also have been performed in Europe and the USA, which were the regions of the world that introduced the majority of Omicron lineages to Africa - medrxiv.org/content/10.110…
Second, the quality of the sequences seems problematic. Their produced sequences could be contaminated and the date of public sequences from GISAID from Africa predating Omicron was not confirmed (P.S. they exclude all non-African sequences with dubious dates).
Read 12 tweets
Oct 23, 2022
Update of COVID-19 variants in South Africa. A new Omicron lineage (BQ.1/BQ.1.1) has been recently detected in South Africa. It is still at small prevalence (5-10%). Infectious numbers are low as well positivity rate, number of hospitalisation and deaths. A small thread 1/x
The Network for Genomics Surveillance in South Africa (NGS-SA) is alerted and has increased genomics surveillance. Our last genomes are less than 1 week old and show some increase of BQ.1 & BQ.1.1. We are current not concerned due to high population immunity and low infections.
BQ.1 and BQ.1.1 seems to also be increasing prevalence in Europe. In South Africa is mostly prevalent at the Western Cape, which is our most touristic province, highlighting that it is likely that these are introductions from Europe.
Read 7 tweets
Oct 21, 2022
In order to develop our shared vision of Global Science that values, respect & build on expertise in the Global South, we embark in an exciting & collaborative journey around the world & bring many scientific activities to Africa. This week, starts the 1st #NobelAfrica symposia
The #NobelAfrica Symposia provide a unique opportunity to support and showcase advanced research and scholarship on the African continent, and to promote research excellence and collaborative scholarship in Africa in conversation with the rest of the world. Image
The 1st #NobelAfrica Symposia is happening a few steps from my office at @Stias @StellenboschUni. A good friend & quantum physicist, Prof Francesco Pettrucione @petruccione is a main organiser. Curiously, when the pandemic started, Francesco & his team helped us to trace it!
Read 9 tweets

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