University of the Western Cape: South African universities aim to strengthen their genomic sequencing capacities
Just because pathogen genomic sequencing has become the global norm for unpacking the genetic material of a pathogen, doesn’t mean everyone gets to do it.
In many ways, there is a sequencing divide between countries and regions. In Africa, for instance, it is not uncommon for pathogen samples to be flown beyond country or even continental borders for sequencing to be done elsewhere.
As a result, it is equally routine for vital information to be ‘owned’ and published by researchers and companies in countries other than where the samples originated.
More concerning is how a lack of sequencing capacity compromises countries’ ability to respond to the outbreak of a disease, be it a global pandemic like COVID-19, or a more localised outbreak like measles or Ebola.
Often, explains Dr Lonnie van Zyl, chief officer at the Institute of Microbial Biotechnology and Metagenomics (IMBM) at UWC, it comes down to a matter of cost. For too long, sequencing capacity has been beyond the means of most labs in Africa.
IMBM has two Oxford Nanopore Technologies sequencers
But new sequencing devices – such as those produced by Oxford Nanopore Technologies (ONT), a UK-based company – are maturing fast, becoming more portable (to such a degree that a sequencing ‘lab’ can be set up in a small car), and offering more value for a scarce buck, says Van Zyl.
This offers the opportunity to expand not only access to these technologies, but also roll out training to more students and technicians. Based on their own experiences of buying a few new devices, the IMBM has even been able to offer advice and guidance to DIPLOMICS on the right technology for their objectives.
DIPLOMICS is a South African initiative supported by the national Department of Science & Innovation (DSI) that aims to equip more labs with genomic technology and skills to improve the country’s capacity in the ‘omics’ disciplines, namely genomics, proteomics and metabolomics.
“The cost of getting a machine into your lab, and actually to start doing sequencing, and the ease of use, just compelled me to advise them on some particular new technologies,” notes Van Zyl.
Other groups at UWC have similar aspirations for the Oxford Nanopore sequencing devices. The technology will be at the heart of a project at the South African National Bioinformatics Institute (SANBI), for instance, where researcher Mr Peter van Heusden is working with collaborators in the Democratic Republic of Congo to develop genomic surveillance protocols for the containment of meningitis outbreaks in that country. These protocols lay out the processes for the handling and testing of samples, as well as for the analysis of results.
Dr Uljana Hesse explains
sequencing she and her research
group have conducted
But the application for these sequencing technologies goes beyond just diseases and pathogens. The IMBM, for instance, uses sequencing for its suite of research programmes, from scouring the oceans for medicinal and other compounds, to looking at water remediation through bacteria.
A host of other applications were on display at UWC on 18 October 2022 when the IMBM hosted a day’s showcase, not just of Oxford Nanopore’s technologies, but also of South African research. This was the first of two Oxford Nanopore Open Days hosted in South Africa over the week.
Scholars and researchers from the likes of UWC, Stellenbosch University and the University of Cape Town spoke of their research on the marine microbiome along the Benguela Current; the water-sensitivity of barley for work of interest to the wine industry; and, on the many applications of rooibos in a genomics programme led at UWC by Dr Uljana Hesse of the Department of Biotechnology.
The evolution of sequencing devices, and its cost implication “per base pair”, as Van Zyl puts it, could change the genomics game in South Africa. The IMBM had long offered sequencing services to research groups at UWC and other institutions in South Africa. But increasingly there is the option – facilitated by the likes of DIPLOMICS – for others to do their own sequencing, says IMBM director, Professor Marla Trindade.
“The technology has just become so accessible and relatively easy to learn, that everybody can have their own machines and do their own sequencing,” she notes. “The whole goal is to get everyone used to the technology, so that sequencing becomes a part of research projects right from the outset and planning.”