A new seminar series covering a wide range of topics related to epidemics and genomics was launched at the Tygerberg campus during the first week of February 2022.
World-renowned bioinformatician Prof Tulio de Oliveira, who was involved in identifying the Beta variant of SARS-CoV-2 in South Africa and heads CERI (an SU based consortium focussed on epidemic response and innovation that will be launched later this year), presented the first seminar.
This series is a joint initiative between the Faculty of Medicine and Health Sciences (FMHS), the Faculty of Science, the School of Data Science and Computational Thinking and CERI. It is intended to encourage collaboration between the different departments within the university and beyond and to expose young investigators to high-level science.
De Oliveira was also one of the key players in the establishment of the Network for Genomics Surveillance in South Africa (NGS-SA). Since March 2020, the NGS-SA has been monitoring changes in SARS-CoV-2, the virus that causes Covid-19. It is a collaboration between hundreds of scientists, universities, laboratories, the National Health Laboratory Service (NHLS), the National Institute of Communicable Diseases (NICD), CERI and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). It is supported by the Department of Science and Innovation and the SA Medical Research Council.
In his presentation, “Collaboration in SA to lead the world on the discovery and characterisation of SARS-CoV-2 variants", De Oliveira described how this close collaboration enabled the identification and classification of the Omicron variant of the virus within three critical days in November last year and elaborated on the lessons South Africa's experience can offer the rest of world about future variants.
De Oliveira recalled how scientists thought South Africa was “out of the woods" during the end phases of the Delta wave when there was increased vaccination, “but then everything changed very quickly".
“There were only a couple of hundred infections per day. However, on 23 November 2021, the data of a small cluster of eight samples from Gauteng showed a high number of mutations, much higher than that of the other known variants. The number of infections also suddenly increased dramatically.
“The NGS-SA immediately swung into action. We contacted laboratories in Johannesburg and we received hundreds of samples in less than six hours. Thanks to rapid genome sequencing by our labs, we knew within 24 hours the infections were all due to the same new variant and that they were widespread.
“Dr Nicholas Crisp, acting director-general of the Department of Health, gave us 36 hours to confirm that we had found a new variant and we worked like mad. By 24 November we had close to 100 genome sequences that showed the variant was spreading very fast."
The NGS-SA then presented the findings to the Minister of Health, Dr Joe Phaahla, and the Minister of Science and Innovation, Dr Blade Nzimande, who both “understood the repercussions right away".
“They helped us to contact Pres Cyril Ramaphosa and on 25 November we had a press conference with Phaahla. On 26 November we had a very urgent meeting with the World Health Organisation, who identified the new variant as a variant of concern and named it Omicron."
De Oliveira described the period during which they received the first samples until the identification and validation of the new variant as “three very, very busy days".
He emphasised that South Africa managed to ride the fourth wave quite well thanks to the outstanding collaboration between scientists and excellent communication with government and public health. “We have a very effective system from which the rest of the world can learn."
Prof Nico Gey van Pittius, FMHS Vice-Dean: Research, remarked that one of science's mantras is “collaborate or die". “This pandemic has shown us how something that is local can spread very quickly. You have shown us that collaboration is key to address crises such as these and that it is very important to ensure that we take collaboration in the institution, in the country, on the continent and in rest of world very seriously," he concluded.
*The bimonthly seminars will be held at the Tygerberg campus and at STIAS (the Stellenbosch Institute for Advanced Study) in Stellenbosch.
Caption: Prof Tulio de Oliveira