Genomics, the Fleming Fund and COVID-19

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As cases of COVID-19 surge across the globe, businesses, innovators and academics are looking at new ways to combat the virus through science and technology. The Fleming Fund has been leveraging the programme’s investments, technology and scientific skill to respond to the pandemic.

One way that’s happened is through Whole Genome Sequencing. Since 2019, the Fleming Fund has partnered with sequencing facilities in Denmark, Nigeria, Tanzania and South Africa to build technical genomics and AMR surveillance capacity in Africa. Now, scientists in South Africa are using support from the Fleming Fund to sequence samples of COVID-19.

“It’s [responding to COVID-19] been very stressful, and I wouldn’t say anything has calmed down,” said Jinal Bhiman, a Medical Scientist who works at South Africa’s National Institute for Communicable Diseases (NICD). Jinal says she and her colleagues have been working around the clock since the beginning of the pandemic, “In the first two months of the response, we were the only diagnostic laboratory in the country. Once testing was decentralised, we began acting as a reference laboratory and we are now receiving about 600 samples a day. It’s been really hectic, but very fulfilling.”

As part of the response, Fleming Fund is supporting the sequencing of additional COVID-19 isolates in South Africa and other Sub-Saharan countries. Sequencing is particularly useful to monitor the diseases’ mutations and track outbreaks. Jinal says in South Africa, sequencing has helped identify gaps in infection prevention within hospitals and identify clusters of the disease.

Rene Hendriksen, Professor and Researcher at the Technical University of Denmark (DTU), who works in partnership with the NICD, says using sequencing in “real-time” for COVID-19, rather than just interrogating historical disease patterns, demonstrates the real power of genomics. “You can see if the continent has been infected with different clones [mutations of COVID-19] or the same clone and then track those to the point of entry,” he says. Understanding the point of entry is the key to curbing the spread of disease.

Sequencing is done by extracting DNA from a cell and then identifying the unique pattern or sequence of the DNA strand’s four nucleic acids (cytosine [C], guanine [G], adenine [A] or thymine [T]); every organism’s pattern is different. The DNA sequence is then compared against a database of sequencing information, helping to determine the organism’s type, its resistance to treatments and other key characteristics.

“Sequencing is a paradigm shift in medical diagnostics and surveillance. For example, in bacteriology, tests which normally took days and weeks can now be completed in a matter of hours. Whole Genome Sequencing is the future,” says Rene.

Jinal says that support from the Fleming Fund has helped increase sequencing capacity and analysis within the NICD. “Increasing sequencing in Africa is huge. There are many countries that haven’t done this before and now we can support them,” said Jinal. The Fleming Fund is also funding a bioinformatics scientist who will be able to help other countries interpret the genomics data. “We are completely overwhelmed at the moment, so having additional staff is so helpful. We are really appreciative of DTU and of Fleming Fund for supporting us with these funds. Every little bit helps!”