The Data for Research Award for an outstanding contribution to science, engineering and technology (SET) is given to an individual or team that advanced the availability, management and re-use of research data. At the 2022 NSTF-South32 Awards, the Network for Genomics Surveillance in South Africa (NGS-SA) was awarded for bringing together virologists, scientists, bioinformaticians and clinicians in an engagement that resulted in one of the most successful genomic surveillance networks globally. The Network detected two SARS-CoV-2 variants of concern. 

Dr Jinal Bhiman, one of the eight co-founders of NGS-SA, explains: “A lot of people were involved in this consortium and contributed to the data that was generated. We’ve been looking at how SARS-CoV-2 has been evolving over the course of the last few years. We started at the National Institute for Communicable Diseases (NICD) as this was the sole testing lab for the country, and this is where we sequenced the first cases we received.”

Soon after that, the team connected with other laboratories and universities in South Africa alongside clinicians and virologists to create an active team. Initially the testing generated very similar sequences which was, as Bhiman pointed out, pretty boring, but then things got interesting in December 2020.

“This was when we first detected the Beta variant and it had a concentration of mutations within one part — the spike — of the SARS-CoV-2 genome. This is also the part of the virus that antibodies target so we thought either the virus will enter our cells more easily or it’s escaping immune responses,” she explains. “Then we were able to show that a large number of these mutations were escaping the immune response. As a result, many people were interested in continuing genomic surveillance, not just in South Africa but globally.”

The team also works closely with the Africa Pathogen Genomics Initiative (Africa PGI) that has extensive infrastructure and human resources dedicated to the work. NGS-SA kept sequencing and looking for anything odd or unusual and then picked up the Omicron variant which made Beta, says Bhiman, look timid by comparison.

“Omicron had between 30 and 50 mutations in the spike region and we were worried as this was a huge collection of mutations, but thankfully because of wide-scale vaccination programmes globally and because many people were previously infected, the background immunity was in place so that people handled this variant relatively well.”

The NGS-SA is an impressive network that not only came together at speed but is one of the most successful genomic surveillance networks in the world. In addition to discovering two variants of concern, the team has established sequencing pipelines at five laboratories, increased infrastructure and developed strong communication with the government to relay insights in real-time. 
— Tamsin Oxford

 Read the special Mail & Guardian supplement about all the NSTF-South32 Award winners.