Portable sequencing using nanopore technology

MinION was used to sequence microbial DNA from frozen soil in the Qilian Mountains, 3,976 meters above sea level. ‘The main task of this field investigation is to explore the changes in the function of microbial communities caused by the degradation of glaciers and frozen soils in Qilian Mountains under a global warming environment.’ — Xia, Y. et al.

'Using Oxford Nanopore Technologies sequencing systems, WGS serotyping provides for a faster, portable (with a MinION sequencer), and potentially high-throughput (with a GridION sequencer) alternative to conventional serotyping.' — Xu, F. et al.

In East Africa, the affordable, real-time, portable MinION device is being utilised to build viral outbreak surveillance capacity, in low-resource settings.

MinION has been used for low-cost, high-throughput phylogenetic analysis of rabies virus in countries where sequencing has previously not been possible. Valuable insights into rabies virus diversity were generated, plus a new rabies virus lineage and evidence of rabies spread across international borders were demonstrated.

Real-time nanopore sequencing at the epicentre of an outbreak of Lassa fever virus (LASV) in Nigeria revealed extensive LASV diversity, established the dynamics of virus transmission, and disproved concerns of an emergent strain. These findings were communicated immediately to authorities and the World Health Organisation (WHO) to inform the public health response.

Phylogenetic analysis using MinION has indicated the recent Ebola outbreak (March 2021) is a result of human transmission of the virus from a survivor of the 2013-2016 outbreak. Previously the longest known virus latency period was 500 days. It’s great to see the MinION Mk1C supporting the community here in Guinea, just as the original MinION did back in 2015.

The goal of the project was to train Malagasy scientists to rapidly detect tuberculosis (TB) and drug-resistance using nanopore sequencing to improve pathogen identification and provide insights on disease transmission — ultimately supporting better public health outcomes for the people of Madagascar.

Twelve undergraduate students used MinION to perform DNA analysis of seawater aboard the Sikuliaq research vessel in order to understand the biology of the Alaskan ocean, identify the microorganisms that live there, and the threats posed by climate change.

MinION has been used to sequence antimalarial resistance genes in mosquitos in Zambia, and whole mosquito genomes in Kenya. The project’s aim was to teach mobile genetic sequencing in low-resource settings, with local project co-leads, and 'promote the feasibility of a decentralised approach to pathogen and vector sequencing' — Jason Hendry, Mobile Malaria Project.

'Using Nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hr sample-to-answer turnaround time, and in a timeframe amenable to actionable clinical and public health diagnostics'. — Greninger, A.L. et al.

'A mobile genetics lab can provide expeditious results, and allow scientists to conduct genetic analyses, potentially allowing for rapid interventions under emergency conditions in situ.' — Blanco, M.B. et al.

Photograph: Blanco, M.B. et al.?

’Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.’ — Pomerantz, A. et al.

Photograph: Aaron Pomerantz ?

'Ultimately, in-field sequencing potentiated by nanopore devices raises the prospect of enhanced agility in exploring Earth’s most remote microbiomes.' – Arwyn Edwards et al.

Photograph: Joseph Cook?

MinION is being used to compare the genomes of blacktip reef sharks afflicted with leucism at a beach research station on Kihaadhuffaru Island in the Maldives.

The largest epidemic of yellow fever virus (YFV) in Brazil, in decades, began in December 2016, highlighting the urgent need to monitor risk of YFV establishment and transmission in the Americas. Using MinION, Nuno Faria and colleagues established 'a framework for monitoring YFV transmission in real-time, contributing to the global strategy of eliminating future yellow fever epidemics' — Faria, N. et al.

'Our work highlights the potential for nanopore sequencing on Earth and beyond in mobile and dynamic environments such as on passenger aircraft, drones, wheeled vehicles, ships, buoys, underwater vehicles, or other platforms.' — Carr, C.E. et al.

MinION can 'open new perspectives for real-time-on-site DNA sequencing, thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.' — Menegon, M. et al.

'Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica' – Sarah S.Johnson et al.

Photograph: Sarah S. Johnson et al ?

'Widespread success of the MinION nanopore sequencing technology in providing accurate, rapid, and convenient gene sequencing suggests a promising future within research laboratories and to improve care for neurosurgical patients. — Patel, A. et al.

Copy number variations (CNVs) are clinically important in cancer, and technologies that can identify them offer the potential for genomics-based precision oncology. Researchers have shown that the high sequencing yields offered by nanopore technology are amenable to high-resolution CNV detection in acute myeloid leukaemia (AML) offering ‘the potential for broader clinical utility, for example in smaller hospitals, due to lower instrument cost, higher portability, and ease of use.' - Michael Schatz et al.

Cancer cell detection using conventional methods, including traditional short-read sequencing, where samples are sent to external laboratories, can take weeks — a delay that can drastically increase the risk of tumour re-establishment. Researchers are investigating the future potential of portable, low-cost, real-time, nanopore sequencing to identify residual cancer cells immediately following tumour surgery, with results provided within just a few hours.

Illegal fishing is a global ecological problem. Currently it is very easy to misreport and mislabel the origins and species of catches. In contrast, the 'genetic signatures of marine animals are tamper proof' and can be used to identify the species and where it has come from. Shaili Johri and co-workers at San Diego State University, USA, used nanopore sequencing to help identify illegally caught marine species. The portable MinION device enables real-time sequencing to be conducted at sample source (e.g. boats) supporting rapid species identification and enabling law enforcement to act before it is too late.

Multiple researchers have demonstrated the potential benefits of real-time, portable, long-read sequencing for improving HLA typing for transplantation and reducing risk of antibody mediated rejection The Genome Canada Transplant Consortium has shown how accurate typing can be achieved within just 1 hour of sequencing, significantly reducing time to result, while the long nanopore sequencing reads ‘make HLA assignment and phasing much easier'. Their rapid workflow further enables the application of high-resolution sequence-based typing to transplant tissues from deceased donors, which have a very narrow time window for transplantation.

Identification of plant pathogens is crucial for sustainable agricultural management and strategic deployment of virus-resistant crop varieties globally. Current methods to identify plant pathogens require a lab, are costly and time consuming, thus less accessible in low resource settings. Smallholder farmers in sub-Saharan Africa used MinION to identify the begomoviruses ravaging their crops and have 'taken immediate restorative action, based on information about the health of their plants, generated using the portable, real-time DNA sequencing device.'

In 2016, MinION was used to conduct the first ever DNA sequencing in space. MinION performance was unaffected by the flight to the International Space Station (ISS) or microgravity conditions. The team stated that 'these findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.' Further to this, in 2020, an end-to-end sample-to-sequencer workflow conducted entirely aboard the ISS resulted in off-Earth identification of microbes for the first time.

Photograph: NASA ?

In 2019, Gowers et al. used MinION to demonstrate 'the ability to conduct DNA sequencing in remote locations, far from civilised resources (mechanised transport, external power supply, internet connection, etc.), whilst greatly reducing the time from sample collection to data acquisition'. The team transported their portable lab for 11 days using only skis and sledges across Europe’s largest ice cap (Vatnaj?kull, Iceland), before carrying out a tent-based study, resulting in 24 hours of sequencing data using solar power alone.

The origin and epidemic history of Zika virus (ZIKV) in Brazil and the Americas remained poorly understood despite observed trends in reported microcephaly. Using a mobile genomics lab to conduct genomic surveillance of ZIKV, the team identified the earliest confirmed ZIKV infection in Brazil. Analysis of these genomes estimated that ZIKV is likely to have disseminated from north-east Brazil in 2014, before the first detection in 2015, indicating a period of pre-detection cryptic transmission that would not have been identified without genomic sequencing.