“We want our technology to be accessible so that it can bring the widest benefits to society. This is especially necessary as we face increasing inequality in healthcare in society, as global challenges in food productivity and security mount, and as the consequences of climate change reach beyond the environment to include human health.”
Gordon Sanghera, CEO, Oxford Nanopore Technologies
Supporting efforts to combat the coronavirus pandemic
Since the initial outbreak of COVID-19, teams in more than 85 countries around the world have used nanopore technology to track SARS-CoV-2 — the virus that causes COVID-19.
The information gained by these scientists has informed public health decision making and enabled new variants to be detected very quickly for a rapid response.
We’ve seen nanopore sequencing technology being used to scale up sequencing in central laboratories but also to help establish more decentralised networks, in locations that had not previously been able to access sequencing technology.
As a result, there are now pockets of localised sequencing expertise in many more locations around the world, enabling tailored responses to local challenges arising throughout the pandemic, and beyond.
Nurturing bioinformatics expertise in Africa
In 2021 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 14 scientists selected by application from institutes across the African continent undertook advanced training in all aspect of the genomics workflow from sample selection, DNA extraction, nanopore sequencing and bioinformatics. The students emerged 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.
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:
In 2018 we initiated a pilot programme to support the use of MinION 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
Establishing a distributed sequencing network in Sri Lanka
In 2021, we supported teams as they established sequencing laboratories across Sri Lanka. These teams wanted to rapidly increase the sequencing capacity of Sri Lanka, in order to improve genomic surveillance of SAR-CoV-2 genomes, at a time when Sri Lanka needed it most.
The teams were able to identify different circulating variants of SARS-CoV-2, as well as those entering the country, enabling public health officials and the government to make informed decisions on how to contain the spread of the virus.
Whole-genome sequencing of SARS-CoV-2 is just the start. This new network of sequencing expertise will enable new insights to be gained across a range of applications, from cancer research to identifying emerging pathogens. Sri Lanka is also a country rich in biodiversity and agriculture is central to its economy. Genomic insights gained from these sequencing hubs could help to improve crop yields and manage conservation efforts of Sri Lanka’s unique wildlife.
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.
Tackling drug-resistant TB in Madagascar
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.