Research day recap: responding to COVID in South Africa and Senegal

An EPI affiliate presents her research to three people who view her poster.

The Emerging Pathogens Institute’s annual research day event celebrates pathogens research and the people who work in this critical academic space. After three years of meeting virtually, the event was held in person at the Reitz Union on Feb. 16, 2023 on the University of Florida’s campus. Researchers and students exhibited 123 abstracts and posters that probed pathogens and infectious diseases topics spanning from lab research to field investigations and bioinformatic analyses.

“While that is not the peak number of posters we have had—prior to the pandemic we were up in the 160s—we still had some outstanding science presented today and my thanks to everyone who contributed,” said EPI Director J. Glenn Morris, M.D., and M.P.H. & T.M. in welcoming remarks before the event’s two keynote speeches.

Genomic surveillance uncovers viral variants

Dr. Tulio de Oliveira poses with his arms crossed.
Dr. Tulio de Oliveira joins virtually for his presentation to discuss the impact of important viral detection work in South Africa, where he and collaborators discovered the omicron variant.

Keynote speaker Tulio de Oliveira, Ph.D., was a key figure in the South African response to the COVID-19 pandemic. He spoke at Research Day about his role in efforts by researchers with the University of KwaZulu-Natal, where he is a professor of bioinformatics, to quickly convert findings about emerging coronavirus viral variants of concern into public health messaging that reverberated around the world early in the pandemic.

De Oliveira discussed organizational challenges in developing pandemic preparedness, responses, communication, and training of medical staff and scientists to quell COVID outbreaks. He recounted his team’s involvement in initial efforts to trace the origins of a large hospital-based outbreak in Netcare St Augustine’s Hospital in Durban, South Africa which ultimately yielded bioinfection control measures adopted around the world.

“This was basic detective work on how this virus could have entered South Africa and entered the hospital and caused a large outbreak,” De Oliveira said. “And we linked everything to three possible sources of infection.” Ultimately, of the 119 known infections at the hospital, 80 were medical staff of whom 15 died.

The report they produced from this investigation was used to train healthcare workers globally. It has been downloaded more than 10,000 times in more than 120 countries, he said.

His team continued COVID viral surveillance by conducting genomic analyses on countrywide samples and looking for new mutations. By April 2020, they were just the second country in the world to be doing this, he said.

A large room filled with rows of poster boards in which people walk around and look at research posters.
Attendees network and look at research posters at the EPI Research Day 2023 in the Reitz Grand Ballroom.

By October 2020, they had evidence that a new variant was taking over infections in South Africa. “It became known as beta variant,” De Oliveira said. “It had multiple mutations where you do not want this virus to have them, like the spike receptor binding domain and N-terminal domain.” The discovery spurred a meeting of the World Health Organization.

His team excelled at communicating findings in near real-time with governmental agencies within hours. This allowed the South African president to discuss national-level responses in almost real time.

De Oliveira and his team continued their genomic surveillance work and were the first to discover what became known as the Omicron variant. They also conducted research on how viral variants affected immunity conferred by the AstraZeneca vaccine used in South Africa.

In 2022, he was listed as one of TIME’S 100 most influential people, along with his former Ph.D. student, Sikhulie Moyo, a lab director in Botswana.

De Oliveira closed his comments with a nod to climate change. He estimates that 65% of future epidemics will be affected by climate change in what he termed climate amplified diseases and epidemics. His new research venture, a consortium named CLIMADE, focuses on these interactions to help society prepare for new and possibly more frequent novel epidemics and pandemics.

Curbing emerging pathogens in Africa

Dr. J. Gleen Morris, Jr., Dr. Derek Cummings and Dr. Amadou Sall stand side by side for a picture.
Dr. Amadou A. Sall travels from Dakar, Senegal to present at the EPI Research Day 2023. (photographed from left to right: Dr. J. Gleen Morris, Jr., Dr. Derek Cummings and Dr. Amadou Sall).

Surveying for viruses in Africa was a common thread in the keynote given by virologist Amadou Alpha Sall, Ph.D., director of the Institute Pasteur de Dakar in Senegal, and director of the World Health Organization collaborating center for arboviruses and viral hemorrhagic fever. Sall spoke about the organizational challenges in responding to epidemics in his home country of Senegal.

Before COVID-19, his country’s greatest challenges derived from mosquito-borne diseases such as malaria, and viral hemorrhagic fevers such as yellow fever, Zika, and Ebola. With more than 140 infectious outbreaks annually in Africa, Sall said: “We obsess about how to detect them and set a response.”

Sall described his institute’s involvement in sentinel viral surveillance work using monkeys and mosquitos to search for known viral threats. This is combined with a symptom-based surveillance program that tracks reports of fever syndromes in local care facilities. This was network was adapted to incorporate COVID surveillance after the pandemic reached Senegal.

For example, they recently evaluated more than 200,000 cases annually, and within these found 27,000 fever syndromes. This further broke down to 10,400 cases of COVID and 1,700 arboviruses.

His teams have also been involved in analyzing seropositivity to COVID in communities to estimate population-level exposure and immune responses during times of viral surges.

Dr. Amadou A. Sall speaks at a podium on stage during his presentation. Behind him a screen projects his slides.
Dr. Amadou A. Sall gives a presentation about the emerging pathogens in Africa. His team in Senegal are currently working on various innovations for tracking pathogens across the continent and fighting infections.

The aim is to use data-driven public health decision-making to control outbreaks, Sall said. But controlling outbreaks includes not just seeing what’s coming and what has passed through, but also having the tools to curb viral threats.

To this end, his institute has been involved in vaccine production for more than 80 years and they are working with others to create diagnostics with price points of around $1 that can be used at the point of care in a clinic, without having to rely on a laboratory or expensive equipment.

They are aiming for a model of demand-driven test production for diagnostics. Sall said the institute is working with Diatropix to ramp up COVID-19 vaccine production so that by 2040, 60% of what is used in continental Africa will be produced domestically, compared to the current 1%. They are also targeting the production of 30 million doses of yellow fever vaccine, and 300 million doses of other essential vaccines, he said.

Africa’s future, Sall said, lies in biomanufacturing for health equity.

By: DeLene Beeland