The Limpopo province of South Africa is not where one would expect to find cutting-edge genomics technology. Known for vast open spaces, abundant wildlife, and large-scale farming, Limpopo is a beautiful place that is often short on resources for its nearly six million people. Normally, NGS technology is found in well-staffed and well-resourced labs in academic centers, where most genomics research takes place. Thermo Fisher Scientific’s Genexus Integrated Sequencer is easy enough to set up that it turns this pattern on its head, expanding Africa’s genomic surveillance network with fast, powerful sequencing technology to discover new SARS-CoV-2 variants and help drive the development of public health strategies that may save lives.
South Africa is buffeted with some of the world’s highest levels of hepatitis, HIV, and other infectious diseases, and rural areas tend to be short on testing facilities. A recent news story highlighted an advanced genomic testing facility at Limpopo’s Ndlovu Care Group, which was founded in 1994 by Dutch researcher Dr. Hugo Tempelman. The laboratory performs upward of 2,000 PCR tests per day for Limpopo and its neighboring provinces, and it became central to the region’s strategy during the emergence of SARS-CoV-2 as the world’s preeminent infectious-disease concern.
Ndlovu partnered with local industries to perform SARS-CoV-2 testing to help keep rural South Africa’s workforce safe through viral surveillance. The local mining industry is invested in PCR testing and sequencing to help prevent outbreaks and has donated resources and even equipment to facilitate it. This testing has allowed Ndlovu to build up a database of 20,000 positive SARS-CoV-2 samples collected from miners throughout the region, which are now used for genomic research with their Genexus sequencer. Genexus provides sequencing results in 24 hours, far faster than the three to four days required for some other devices. It also requires fewer operators and resources to run and maintain, compared to otherwise similar tools currently available, and it is compatible with several forms of automation to speed up sample processing even more.
These advantages made Ndlovu and its Genexus sequencer a crucial pillar of South Africa’s SARS-CoV-2 containment strategy and a key member of Dr. Tulio de Oliveira’s Network for Genomic Surveillance in South Africa (NGS-SA), which monitors the genomes of SARS-CoV-2 in South Africa. By providing data on South Africa’s northern provinces, Ndlovu makes the overall sample set more representative and gives a more complete picture of SARS-CoV-2 in South Africa. Ndlovu was therefore one of the first labs to report the emergence of the now world-spanning Omicron variant and to further report that this variant is rapidly displacing the previous variant of concern, Delta.
Labs like Ndlovu provide a wealth of knowledge for understanding infectious diseases in general and SARS-CoV-2 in particular, a veritable gold mine of data that benefits not only the people it immediately serves, but the entire world. Thanks to these world-class efforts, South Africa has been at the forefront of detecting new SARS-CoV-2 variants of concern, including Omicron, and will likely remain so for the foreseeable future. Bringing NGS to rural areas not only helps improve the quality of care at the local level but can also have a global impact on SARS-CoV-2 surveillance, and it has never been more possible.
Read the news story here: Why South Africa has discovered so many virus variants | Faithful (trouw.nl)
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