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Tulio de Oliveira

13 May, 9 tweets, 2 min read

Confirmed Detection of eight (8) more genomes B.1.617.2 and two (2) community transmission of B.1.1.7 in South Africa, By Network for Genomic Surveillance in South Africa (NGS-SA), 13 May 2021

The eight new cases of B.1.617.2 variant have been detected from KwaZulu-Natal province. More specifically, these were cases in crew members of a commercial vessel that arrived in Durban Port from India.

The cases were isolated on the vessel, and other crew members have been quarantined according to national COVID-19 case management guidelines. The individuals who tested positive for COVID-19 did not disembark in South Africa, with exception of one that was admitted to hospital

@WHO

The B.1.617.2 is spreading widely around the world, and this week was listed as a variant of concern (VOC) by @WHO . The reason for the increase of classification, form variant of interest (VOI) to VOC was due to evidence of rapid spread of B.1.617.2 in different countries.

Genomic surveillance in South Africa has also this week identified another two new cases of the B.1.1.7. In total, we have detected 13 confirmed cases of the B.1.1.7 in South Africa. The two new cases of B.1.1.7 were identified in Gauteng – there was no recent travel history

At present, we have identified three of the four main variants of concern in South Africa (B.1.351/501Y.V2, B.1.1.7/501Y.V2 and the B.1.617.2).

New results from the start of the third wave in the Northern Cape show that this was dominated by the B.1.351/501Y.V2 . At present, we are working to classify variants in the the Free State and Gauteng, which were provinces that are seeing a surge of infections.

NGS-SA is a consortium of scientists funded by the Department of Science and Innovation (DSI) and the South Africa Medical Research Council (SAMRC).

@GISAID

All new sequences are available @GISAID ! More info: krisp.org.za/ngs-sa/ngs-sa_…

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Tulio de Oliveira

@Tuliodna

14 May

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa medrxiv.org/content/10.110…

By 5 May 2021, 14,504 SARS-CoV-2 genomes had been submitted to the GISAID database from 38 African countries and two overseas territories (Mayotte and Réunion) (Fig. 1A). Overall, this corresponds to approximately one sequence per ~300 reported cases.

Overall, the number of sequences correlates closely with the number of reported cases per country. lmost half of the sequences were from South Africa, consistent with it being responsible for almost half of the reported cases in Africa.

Read 21 tweets

Tulio de Oliveira

@Tuliodna

9 May

@DrZweliMkhize

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.

Read 17 tweets

Tulio de Oliveira

@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.

@trvrb

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

Tulio de Oliveira

@Tuliodna

29 Mar

@nature

Today paper on neutralization of 501Y.V2 (B.1.351) - Show effective neutralization of other SARS-CoV-2 lineages by 501Y.V2 @nature

nature.com/articles/s4158…

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

Tulio de Oliveira

@Tuliodna

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

@jbloom_lab

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.

Read 8 tweets

Tulio de Oliveira

@Tuliodna

9 Mar

@rjlessells

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.

Read 10 tweets

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