Supporting efforts to combat the coronavirus pandemic
Since the COVID-19 outbreak began, we have been working with labs around the world to help combat the spread of the virus. At the end of January, we shipped 200 MinION sequencers and related consumables to China, the worst affected region at the time. Since then, thousands of genomes rapidly sequenced using nanopore technology have been made available in public databases — all contributing to the epidemiological surveillance of the virus.
From the start of the pandemic, our aim was to support wide efforts to identify, track, trace, and isolate cases. By mid-May, development of our LamPORE assay, for rapid, highly scalable, low-cost COVID-19 detection, was well underway. LamPORE is designed to detect the presence of SARS-CoV-2 in a saliva swab or environmental sample. LamPORE is currently being rolled out in multiple countries.
Find out more about how we’ve been supporting the global effort on our Covid-19 information pages.
Through ensuring our sequencing technology is as accessible as possible, we are putting biological analysis tools in the hands of those who could not previously afford it – contributing to the democratisation of science:
We had designed an accessible sequencer, and in 2018 we initiated a pilot programme to support its use in communities that traditionally had less access to the benefits of sequencing insights. This started an educational program named Pore Safari.
Focusing on broad skills, a series of workshops were delivered in Kenya, Tanzania, and Zambia as a blend of classroom-based learning and hands on laboratory work. As a result, more than 100 African scientists gained practical experience of generating and analysing sequencing data.
Pore Safari continued in 2019 with missions to the Democratic Republic of Congo and Sierra Leone, reaching a further 120 scientists in severely resource limited environments. The benefits of this capacity building activity have begun to emerge in 2019 in the form of peer review publications in internationally recognised journals emanating from institutes with no prior access to genomic technologies.
On farm sequencing in DR Congo. The entire village came to watch. Molecular biology is not normally considered a great spectator sport. But little Harris watched every move with such intense fascination for 4 solid hours. He’s on the team ❤️ #poresafari @laura_boykin @REXCHAS pic.twitter.com/Q07jwcF1vg— Iain Maclaren-lee (@MaclarenLee) September 10, 2019
Nurturing bioinformatics expertise in Africa
In 2020 Oxford Nanopore partnered with the Nairobi-based BecA Hub at the International Livestock Research Institute to deliver an in-depth training programme, Third-generation genomics and bioinformatics for agribiosciences in Africa. In this programme 12 scientists selected by application from institutes across the African continent will undertake advanced training in all aspect of the genomics workflow from sample selection, DNA extraction, nanopore sequencing and bioinformatics. Students will emerge from this programme as true experts in nanopore sequencing and will go on to disseminate their knowledge in their home institutes with ongoing support from Oxford Nanopore.
Fighting Cassava Viruses With Nanopore Sequencing
Around 800 million people worldwide rely on the cassava plant for their daily calorie intake. However, this crucial food source is under attack from various viruses. These pathogens could wipe out an entire crop, resulting in farmers with very little to no yield at all – leaving the farmer hungry and without income that season.
Starting in 2017, a collaboration of scientists in Kenya, Uganda and Australia formed the Cassava Virus Action Project to explore ways of bringing technologies to the people who needed it most to fight these viruses. With the help of Oxford Nanopore’s MinION, the team were able to sequence the virus in real time and suggest a more appropriate, resistant version of cassava that the farmer could grow instead. The workflow took three hours and was performed onsite; typically smallholder farmers would not have access to such technology, and any analysis would take months in any case.
In this pilot, the farmer regained her crop and her livelihood, bringing positive benefits to a community. Work continues to deliver these benefits to broader communities.
Fighting TB in Madagascar - with real time portable DNA sequencing
Drug resistant tuberculosis (TB) is a major threat around the world and presents a public health threat to the people of Madagascar.
Starting in 2018, scientists from the Madagascar National TB Program, Institute Pasteur Madagascar, University of Oxford, European Bioinformatics Institute (EMBL-EBI) and Stony Brook University collaborated to train Malagasy scientists to rapidly detect TB and drug-resistance using DNA sequencing.
The goal of the project was to improve diagnosis and treatment, and provide insights on disease transmission, with the objective of improving public health outcomes for the people of Madagascar, and eventually other countries too.
African Orphan Crop Consortia
Oxford Nanopore is proud to be a partner of the African Orphan Crop Consortia which seeks to alleviate malnutrition in Africa by creating genomic resources for breeding of African crops. Our immediate activities within the consortia have focused on the generation of high-quality reference genomes for African crops that have enormous potential for improvement through breeding programmes and to explore the genomic variations that underly desired breeding traits in these crops.
The unique accessibility of nanopore sequencing represents a paradigm shift for genomics in Africa. A new generation of scientist will gain direct access to genomic technology, retaining ownership of data and exploiting their discoveries to improve ecosystem management, agricultural productivity and human health across Africa.