Two genomics powerhouses team up to expand infectious disease surveillance

LONDON — Two research centers that have been at the forefront of following the evolution of the SARS-CoV-2 coronavirus — one in the U.K. and one in South Africa — have teamed up on a partnership that they say will expand their efforts to track emerging disease threats around the world.

The collaboration between the U.K.’s Wellcome Sanger Institute and South Africa’s Centre for Epidemic Response and Innovation, announced Thursday, comes as much of the infrastructure built up during the pandemic to sequence SARS-2 has dwindled. Global health officials have decried the lack of ongoing surveillance of the virus.

“There are many blind spots,” said Tulio de Oliveira, who leads CERI at South Africa’s Stellenbosch University. “That’s one of the big motivations for this partnership.”

De Olivera’s research group was the first to identify the Beta and Omicron variants of the coronavirus; the team’s quick warning about the latter put the world on alert for what became a massive wave. The Sanger Institute at the height of the pandemic was sequencing more Covid-19 samples than any other research site in the world. The new collaboration between the institutions will allow them to pool resources and coordinate on research and responses to outbreaks, instead of duplicating efforts, de Oliveira said.

Both institutions have strong international ties, with CERI sequencing coronavirus samples from more than two dozen African countries during the pandemic. One idea is to design sequencing tools and tests that can be rapidly deployed to just about anywhere in the world during an emerging outbreak, to find out whether it’s caused by a known pathogen, a new strain of a bug, or something new entirely.

“You need speed to find epidemics,” de Oliveira said.

His team, for example, recently sent fellows and supplies to Malawi during an outbreak of cholera there, which, through sequencing, they learned spread out of Pakistan’s record cholera outbreaks tied to massive flooding in the country.

The idea of sequencing different pathogens — viruses, bacteria, and parasites, as well as the animals that spread some of them, like mosquitoes — is not just to track transmission routes of different diseases, work that itself can inform public health responses. Such surveillance allows researchers to get warning signs that viruses like HIV are becoming resistant to treatment, or that diagnostic tests that sniff out the genetic information of a bug might need to be tweaked, or that vaccines need to be updated.

Donors to the two institutes include the European Commission, the National Institutes of Health, the World Bank, the Gates Foundation, and the Rockefeller Foundation. De Oliveira said part of his job now will be to attract additional funding. Though he’s taking on the role of deputy director of the Sanger’s Genomic Surveillance Unit, de Oliveira is remaining based at CERI.

De Oliveira has been a major proponent for building up sequencing capacity and knowledge at African institutions and among African scientists. While CERI offers a training program for African researchers in sequencing pathogens, an added benefit of the partnership is that those fellows will now also receive training at the Sanger, he said.