Faster, more convenient and more broadly available technology has the potential to bring many benefits to many communities – our vision of the future is to enable analyses in a variety of healthcare settings from operating theatre to pharmacies, on farms or food production supply chains, even in the classroom or at home. In short, to enable the analysis of anything, by anyone, anywhere.
Genomic insight has historically been inaccessible to most of the world, with only developed nations and advanced institutions able to utilise the technology due to the prohibitive costs of sequencing devices, expert knowledge required to operate sequencing technology, and the relatively large device size.
Traditionally, sequencing technologies have been expensive, complicated, and sold primarily to large, centralised laboratories, resulting in a lack of access to the broad communities who may benefit. At Oxford Nanopore, we aim to drive change to a new paradigm of broader access to biological information – from centralised labs to point-of-sample / in-field use, and for that biological information to be richer and deeper than with traditional technologies. As a result, we have brought solutions to the market that are affordable, simple to use, and portable, to foster a new generation of biological science researchers and device users who are making positive impacts that can be felt on a global scale.
"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."
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 (the virus that causes COVID-19) genomes, at a time when Sri Lanka needed it most. The country also wanted to establish distributed DNA analysis infrastructure, so that as it recovered from COVID, it was able to support its other needs from health to agriculture.
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 was just the start. This new network of sequencing technology and expertise will enable new insights to be gained across a range of applications, from cancer research to identifying emerging pathogens.
African Orphan Crops Consortium
Orphan crops are crop types that are of local importance but are not traded internationally. This can mean that their abundance is diminished in favour of more lucrative cash crops. The African Orphan Crops Consortium (AOCC) partnership, of which Oxford Nanopore is a founding partner, works to ensure the availability of nutritious orphan crops to consumers in Africa by promoting their production, through the adoption of modern breeding methods for crop improvement purposes.
To aid the development of genomics in Africa, Oxford Nanopore sponsored advanced training for 14 African scientists in the '3rd Generation Genomics and Bioinformatics in Africa' course held on in Nairobi, Kenya. This gender balanced program had participants from 8 different African countries and consisted of a 4-month residential course during which time the students learned experimental design, DNA/RNA extraction methods, nanopore library preparation and sequencing, and crucial data handling and bioinformatics.
Sequencing African Swine Fever to prevent outbreaks
African Swine Fever (ASF) is a highly contagious viral disease in swine that causes extremely high mortality in domesticated pigs. The 2018 outbreak in China killed more than 50% of farmed pigs (25% of the total global population) and caused an estimated $14bn of harm to the Chinese economy. In 2021 there were outbreaks in Germany (the second largest exporter of pork globally), the Dominican Republic, and Haiti, bringing the virus to the 'doorstep’ of the United States.
The United States is on high alert and implementing measures to stop ASF reaching its shores including using Oxford Nanopore sequencing to detect and characterise the virus. Researchers at the University of Tennessee, using virus samples provided by the USDA, used MinIONs coupled with their novel companion software script to perform analysis in real time, detecting ASF in pig samples within 6 minutes after initiation of sequencing.
They disclosed "one of the greatest advantages of the Oxford Nanopore MinION platform is the ability to generate data in real time, thus facilitating the rapid analysis that is critical during an investigation of high-consequence pathogens such as ASF”, adding "this work demonstrates the utility of this technology for sequence-based diagnostics, supporting effective emergency management in the event of an outbreak of the disease".
Animal and plant breeding related data can be used to produce livestock and crop varieties that produce more abundant and nutritious food with reduced input and environmental impact. The ability to sequence longer DNA fragments - as is possible with Oxford Nanopore - has enabled the discovery and characterisation of additional types of genome variants, which in some agriculturally important species can represent greater than 50% of all genomic variation. This all helps to better select individuals for breeding and make other more informed farm management decisions.
Both livestock and crops are effected by pests and pathogens that negatively impact agricultural yields. The sequencing of pathogens provides deep insights which can be used to track their spread and help farmers mitigate against them.
More than 200 diseases are spread through unsafe food and water; these food safety problems persist in both developing and developed countries. Nanopore technology has strengthened the food supply chain by proliferating genomic technologies in environments across food supply chains, between farms and consumers, that would not previously have benefited from genomic insight.