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Tulio de Oliveira

@Tuliodna

9 Sep

'Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants'. science.org/doi/10.1126/sc…

@RockefellerFdn

So many people to thank! 100s of authors from Africa and funders to believe that we can do high-level science that influences public health response - Thanks, @RockefellerFdn @RickABright @fdesouza @illumina @thermofisher @stevensonmarkp @WHOAFRO @AfricaCDC @dsigovza

@christian_happi

The most rewarding part of this collaboration was the holistic approach of trust and capacity building! What to say! African dream team working together @christian_happi @houzhou @Mittenavoig @EduanWilkinson @rjlessells

Read 4 tweets

Tulio de Oliveira

@Tuliodna

27 Aug

Evolution of the C.1 lineage in South Africa with multiple Spike mutations - pre-print at: medrxiv.org/content/10.110… - In this tweet thread, I highlight this lineage (assigned as C.1.2), the potential impact of the mutations, and the likelihood that this become a variant of concern

The C.1.2 has 14 mutations in Spike, including three mutations at the Receptor Binding Motif, the Y449H, E484K, and N501Y - two of the mutations have been found in three of the four variants of concern (Alpha, Beta, and Gamma).

In relationship to decrease neutralization, in addition to the E484K, there are also deletions at position 144 and positions 242-243, the 144 deletions are also seen in the Alpha and the 242-243 in the Beta, which associates with a decrease neutralization of antibodies

Read 13 tweets

Tulio de Oliveira

@Tuliodna

23 Jul

Seems that the level4 restrictions in South Africa helped to control the third wave of #COVID19 - Reproductive number < 1 in the whole country and in most provinces.

The Western Cape and Eastern Cape seem to have peaked now, R =1

Gauteng #COVID19 cases are really in the downward path, R = 0.6

Read 5 tweets

Tulio de Oliveira

@Tuliodna

30 Jun

NGS-SA worked hard to increase sequencing in South Africa. We know now that the explosive #COVID19 third wave is dominatedd by the Delta variant.

In this tweet thread, we present recent data (sampled up to 24 June in many provinces in SA, including Gauteng) - Tweet 1/8

This graph shows the distribution of the variants over time in the different provinces. 2/8

@nicd_sa

The third wave in Gauteng was caused by the Delta variant, thanks to @nicd_sa and @krisp_news who worked day and night on the weekend to increase genomics surveillance in Gauteng.
Graph shows Black line = Daily cases (7-day average), Yellow = Beta, Green = Delta. Tweet 3/8

Read 8 tweets

Tulio de Oliveira

@Tuliodna

17 Jun

A Novel and Expanding SARS-CoV-2 Variant, B.1.1.318, dominates infections in Mauritius medrxiv.org/content/10.110…

Mauritius is an example of controlling #COVID19 in Africa, with 1,700 infections and only 18 deaths. However, one variant seems to have caused the great majority of all of the infections

Mauritius has stopped dozens of introductions of the Beta (501Y.V2/B.1.351) and Alpha (B.1.1.7) but the B.1.1.318, which has the 484K mutation (common to Beta) and the 681H mutation (common to Alpha) has caused all local transmitted cases.

Read 14 tweets

Tulio de Oliveira

@Tuliodna

3 Jun

@sigallab

In this online pre-print, we present a case of persistent SARS-CoV-2 infection with accelerated intra-host evolution in a patient with advanced HIV and antiretroviral treatment failure in South Africa.

Paper deposited at medRxiv &available at: krisp.org.za/publications.p… @sigallab

SARS-CoV-2 RT-PCR was positive for 216 days (27 weeks). At all time-points between day 0 and day 216 there was a mean Ct ranging from 16.4 to 31.6. The patient had HIV drug resistance and was not responding to therapy.

Over 30 mutations accumulated over time, many of them changing aminoacids that are common of variants of concern.

Read 15 tweets

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