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

Sep 15
The African Scientific Dream Team strikes again! Today a scientific report in Science, revealed that a large consortium of over 300 African scientists and public health institutions illustrated how the SARS-CoV-2 variants reached and spread across Africa. science.org/doi/10.1126/sc…
The study shows that most of the introductions of variants in Africa were from abroad and not from Africa. The consortium found that the initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe).
The ironical part of these results is that most of the introductions of variants in Africa were from abroad, but Africa was the most discriminated and penalized continent in the world with travel bans.
Read 8 tweets
Aug 23
Most important sentences of our most recent peer-reviewed publication :

Every case of monkeypox infection should be treated with the same attention and sense of urgency as the ones now in European countries and North America.
The entire epidemic of hMPXV regardless of the location needs to be halted, not just this Northern hemisphere outbreak.

We hope that the world provides the funding and focus for effective regional and global public health surveillance for emerging and re-emerging threats.
By supporting a non-discriminatory and non-stigmatizing classification, we can encourage African and other researchers in low- and middle-income countries (LMICs) to advance genomic surveillance, share sequence data, and minimize negative impacts.
Read 7 tweets
Jul 30
Omicron BA.5 went to dominate most of the recent COVID infections in the world. This lineage was first identified in April 2022 in South Africa. The paper that describes the emergence of the BA.4 & BA.5 is now final and OPEN at Nature Medicine -
As the previous Omicron lineages BA.1, BA.2, BA.3, the BA.4 and BA.5 was identified close to the largest airport and main economic hub of South Africa, in Gauteng. Interesting, BA.5 went a large application event in Durban, the capital of KwaZulu-Natal and SA biggest harbour.
KwaZulu-Natal, home of Durban, was the province that BA.5 (in orange) went to dominate infections quicker. It is still not clear why BA.5 has an advantage over BA.4 as they have identical Spike proteins.
Read 5 tweets
Jul 7
Thread for our latest publication on the intrahost evolution of SARS-CoV-2 virus in an immunocompromised individual with HIV in South Africa for at least 270 days with consistently replicating viruses at a high viral load. 1/n
The patient was a 22-year-old female with uncontrolled advanced HIV infection who was persistently infected with the SARS-CoV-2 Beta variant for 9 months. Phylogenetic analysis confirmed the infecting virus from three swabs clustered together on a background of 7977 sequences.
> 270 days, the virus acquired at least 10 mutations in the spike glycoprotein and 11 mutations outside spike. The additional spike mutations included six in RBD (S371F, N450D, A475V, F490Y, S494P and Q498R); a deletion at 141-143 NTD which leads to neutralizing antibody escape.
Read 6 tweets
Jun 27
Finally out after peer-review @NatureMedicine:
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. In this publication, we describe the origins, evolution and impact of BA.4 & BA.5, which emerged in SA and now dominate most of the global COVID infections. 1/x
BA.4 & BA.5 emerged between Johannesburg & Tshwane. This region is in close proximity to the largest airport in Africa. The lineages could come from anywhere and quickly spread in SA. BA.5 went through amplification in Durban. BA.5 is starting to dominate most global infections. Image
There is much recent discussion on the origin of BA.4 and BA.5. Bayesian phylogenetic methods revealed that BA.4 and BA.5 are distinct from the other Omicron lineages (Molecular clock signal: correlation coefficient = 0.6, R2 = 0.4). Image
Read 14 tweets
Jun 10
We propose a novel non-discriminatory & non-stigmatizing classification of monkeypox aligned with best practices in the naming infectious diseases to minimize negative impacts on nations, economies & people and consider the evolution & spread of the virus
Why we did do this? In the current classification of monkeypox genetic diversity, only two clades are recognized – referred to as West African & the Central African or Congo Basin clades. However, these historic names are counter to the best practices and generate discrimination
In the context of the current global outbreak, continued reference to this virus being African is not only inaccurate but also discriminatory & stigmatizing. The most obvious manifestation is the use of photos of African patients to depict the pox lesions.
Read 19 tweets

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