Director of CERI (Centre for Epidemic Response & innovation) @StellenboschUni and KRISP (KZN Research Innovation & Sequencing Platform) @UKZN
5 added to My Authors
May 19 • 11 tweets • 4 min read
As scientists working in infectious diseases, the first thing that we do when a virus reemerges is to read the scientific literature. Ten MonkeyPox scientific publications that I read yesterday, thanks @rjlessells for the list!
BA.4 & BA.5 Recent Developments:
- Wave of infections in SA has peaked with, so far, low hospitalizations & deaths
- Rapid increase of infections in Portugal, with older & highly vaccinated population
- Resurgence in both countries without BA.2 wave
- ECDC listed as VOCs
In the last weeks, we exchanged information with Portuguese colleagues, specially @borges__vitor who is doing a great job at Genomics Surveillance. Here, comparisons between South Africa & Portugal may help the world to understand more about the early spread of BA.4 & BA.5
May 8 • 11 tweets • 6 min read
Summary of BA.4 & BA.5 in South Africa
- 100% of infections
- Fuelling 5th wave
- Low testing & high positivity ratio
- Increasing number of hospitalizations, however still much lower than in previous waves
- SA may guide the world on the future of the pandemic
South Africa had multiple waves of infections, the first dominated by multiple lineages (> 50 614G lineages), the second by Beta, them Delta, Omicron BA.1, BA.2 and Omicron BA.4 and BA.5.
Apr 29 • 7 tweets • 4 min read
Summary of what we know about Omicron BA.4 & BA.5:
- Suggesting a discrete reservoir, such as chronic human infections and/or animal reservoirs
- BA.4 and BA.5 have a growth advantage over BA.2
- Escape BA.1 infection & potential new wave
The emergence of BA.2 and BA.4 was highlighted in our pre-print (krisp.org.za/manuscripts/ME…), a previous Twitter thread (
Pre-print Out - Continued Emergence and Evolution of Omicron in South Africa: New BA.4 & BA.5 lineages - ceri.org.za/publication/?t… - In this thread, we explain the origin, evolution, and epidemiology of the new Omicron lineages causing the increase of infections in SA.
Omicron BA.4 & BA.5 were recently designated lineages of Omicron. Bayesian phylogenetic methods
revealed that BA.4 and BA.5 are distinct from other Omicron lineages. BA.4 and BA.5 are
estimated to have originated in mid-December 2021 and early January 2022, respectively.
Apr 24 • 5 tweets • 4 min read
Very honored to announce the best training program in the world. An act of love to give back to public health & scientific response to epidemics & pandemics, 26th edition of the virus evolution and molecular epidemiology (VEME) at Panama City, 21-26 Aug - veme-fiocruzbr.ceri.africa
Four modules, “Phylogenetic Inference”, “Evolutionary Hypothesis Testing”, “Next Generation Sequencing Analysis”, and “From Trees to Public Health Policy”. 26 years committed to training the next generation of scientists in the world.
Apr 11 • 12 tweets • 4 min read
New Omicron BA.4 & BA.5 detected in South Africa, Botswana, Belgium, Germany, Denmark, and U.K. Early indications that these new sublineages are increasing as a share of genomically confirmed cases in SA. No cause for alarm as no major spike in cases, admissions or deaths in SA
The good news is that BA.4 and BA.5 (like BA.1) can be identified by proxy marker of SGTF using the Thermo Fisher qPCR assay. These sublineages are responsible for an increasing share of sequenced cases in SA from early March and are well tracked by the NHLS and NGS-SA.
Apr 8 • 4 tweets • 2 min read
Let me try again with corrections from followers: #Omicon BA.2 in the U.K. Household surveillance with almost 1 in 13 people infected in recent weeks. Daily deaths were 350 and 100s flights canceled. Please living with the virus is not letting the virus spread without control.
Sources: 1 in 13 people infected per week theguardian.com/world/2022/apr…
Mar 5 • 5 tweets • 2 min read
Amazing how our very early analysis in Nov 2021 showed that Omicron was the most transmissible variant. We also estimated that would take over everywhere in the world and that is true now. Today >99% of infections in the world are Omicron. 1/
It is also impressive how Africa is now doing real-time genomics surveillance at similar levels to other continents.
Feb 20 • 5 tweets • 1 min read
I tried to promise to family and friends to stop attacking ‘some developed countries’, but can not help to say that the USA is really screwing the pandemic response and cause unnecessary panic in the world. A small thread
One of the main reasons why the USA is, on my opinion, one of the only countries to have a higher death from Omicron than Delta are due to:
1 - Poor vaccination
2 - Lack of preparation to a more transmissible variant
3 - Lack of consistency of public health messages
Feb 9 • 8 tweets • 4 min read
As expected, Omicron BA.2 takes over in South Africa, close to 100% of the new genomes. What does it mean?
First, this comes on a background of decreasing infections. South Africa takes an approach of random and proportional surveillance. Below is a number of high-quality genomes per week which matches cases per week.
Jan 26 • 9 tweets • 5 min read
A thread on #Omicron sub-lineages BA.1, BA.1.1, BA.2, and BA.3. Here, we go back to original papers and highlight what we currently know about them in the geographic location where Omicron emerged and caused the first large wave of infections in the world.
The BA.1, BA.2, and BA.3 were originally identified in southern Africa - the BA.2 and BA.3 share many not all of the characteristic mutations of BA.1/Omicron and both having many unique mutations of their own nature.com/articles/s4158…
Dec 31, 2021 • 9 tweets • 5 min read
South Africa decreases restrictions in spite of #Omicron dominating all of the infections. This action is puzzling to the world. Here are a few thoughts on why the government in SA may be correct by acting in this way... Tweets 1/8
1 - #Omicron emerged on Nov 21, when infections were at a record low (for example 200-300 a day in SA vs 40,000-50,000 a day in the UK). In addition, at present, the Reproductive number is < 1, which suggests that the epidemic is not expanding very fast.
Dec 21, 2021 • 7 tweets • 3 min read
Today at BBC some coverage of our work. In this thread, I highlight what we know about the plausible hypothesis of variants to emerge from immunosuppressed individuals. bbc.com/news/world-afr…
The emergence, for instance, of the Alpha variant has been linked to a patient receiving treatment for cancer in the UK. A good review of this and other events @NEJM - nejm.org/doi/full/10.10…
Dec 18, 2021 • 25 tweets • 16 min read
Finally out! Our article on the rapid epidemic expansion of #Omicron in southern Africa. Here, we describe the discovery of #Omicron, its origins, evolutionary history, and growth advantage. Article available at: ceri.africa/publication/?t…
In Nov 2021, genomic surveillance teams in South Africa & Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections. Within 3 days, it was designated a variant of concern (Omicron) by @WHO and, within 3 weeks, had been identified in 87 countries.
Dec 8, 2021 • 10 tweets • 5 min read
The #omicron has been detected in 60 countries in the world. Many of the countries show higher daily cases than South Africa and many show signs of increasing infections (e.g. U.K. estimates that #omicron cases are doubling every 2-3 days). Thread on the over 1000 genomes @GISAID
In South Africa, and expected in many countries in the world, Omicron has grown very fast in prevalence. In
Dec 6, 2021 • 4 tweets • 2 min read
If the world keeps punishing Africa for the discovery of #Omicron and 'Global Health Scientists' keep taking the data, who will share early data again? Just saying thanks and keep hoarding of vaccine, antiviral, diagnostics, PPEs, funding, etc - Thread on unfair practices 1/4
Countries had blocked Africa and caused massive economic costs. Instead of helping, they are now hoarding more vaccines for boosters, antivirals for the prevention of diseases, reagents for genotyping their samples. 2/4
Nov 25, 2021 • 8 tweets • 5 min read
Busy day on B.1.1.529 - a variant of great concern - The world should provide support to South Africa and Africa and not discriminate or isolate it! By protecting and supporting it, we will protect the world! A plea for billionaires and financial institutions. 1/8 tweets
We have been very transparent with scientific information. We identified, made data public, and raised the alarm as the infections are just increasing. We did this to protect our country and the world in spite of potentially suffering massive discrimination.
Oct 21, 2021 • 6 tweets • 2 min read
A thread on the Delta AY.4.2 in South Africa. AY.4.2 has been detected in very small numbers in SA. No current cause for alarm – continued surveillance and monitoring important. Tweet 1/6
In total 6 of 9,017, Delta genomes in SA are the sub-lineage AY.4.2 (PANGO analysis as of today). No sign of growth and the current COVID-19 cases in SA. On the opposite, infections in SA are current low, and the positivity rate is also very low. Tweet 2/6
Sep 23, 2021 • 14 tweets • 8 min read
Publication online - Rapid replacement of the SARS-CoV-2 Beta variant by the Delta variant in South Africa - ceri.africa/publication/?t…
The Delta variant was imported to South Africa primarily from India, spread rapidly in all provinces, and became dominant within 3 months of introduction. Associated with a resurgence in community transmission and a 3rd wave which was associated with a high number of deaths
Sep 9, 2021 • 5 tweets • 3 min read
Because the pandemic is very fast-moving, we are updating every week the results of our pan-African collaboration published in Science today at: genomics.africa/sars-cov-2-das…
SARS-CoV-2 variants in lineages in African countries