Portable Sequencer Provides Real-Time Outbreak Surveillance

By Lori Solomon, Editor, Diagnostic Testing & Emerging Technologies

Real-time genomic surveillance is possible in resource-limited settings to monitor infectious disease outbreaks, according to a study published Feb. 11 in Nature. A novel, portable nanopore DNA sequencing instrument (MinION; Oxford Nanopore Technologies, United Kingdom) was able to identify single nucleotide polymorphisms at whole genome resolution to inform surveillance efforts and guide control measures during the 2014-2016 West African Ebola outbreak. The MinION had been previously used to investigate a bacterial outbreak, but not a viral outbreak.

“Real-time genomic surveillance is a new tool in our arsenal to assist difficult epidemiological investigations, and to provide an international and environmental context to emerging infectious diseases,” writes Joshua Quick, from University of Birmingham (United Kingdom) and his international team. “This may improve the efficiency of resource allocation and the timeliness of epidemiological investigations through genomically informed investigations of transmission chains. Real-time genomic surveillance also increases the possibility of identifying previously unknown chains of transmission.”

Genome sequencing of infectious agents provides a lot of useful information including: identification of signatures of host adaptation, monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. Additionally, sequencing can characterize the evolutionary rate of viral agents. But, genomic surveillance during the Ebola epidemic was sporadic due to a lack of local sequencing capacity and logistical challenges—transportation infrastructure deficiencies, interruptions in power, and lack of laboratory space and trained personnel.

The MinION, based on nanopore technology, weighs less than 100 g and sequencing data are read off the MinION from a laptop via a USB port, from which the instrument also draws power. The genome surveillance system transported to West Africa (April 2015) consisted of three MinION instruments, four laptops, a thermocycler, a heat block, pipettes, and sufficient reagents and consumables. The system fit in standard airline luggage for transport to Guinea.

The laboratory protocol the researchers established used a targeted reverse transcriptase polymerase chain reaction to isolate sufficient DNA for sequencing and a panel of 38 primer pairs that could span the Ebola virus genome. The consensus sequences were compared to those generated using Illumina sequencing with a high degree of concordance and no false positive variant calls.

The genome sequencing workflow, including amplification, sequence library preparation, and sequencing could be accomplished within a working day. The fastest time from patient sample to answer was achieved in less than 24 hours, including remote bioinformatics analysis. In half of cases, the researchers were able to generate sufficient reads on the MinION (between around 5,000 and 10,000) in less than an hour. In total, 142 samples were sequenced over 148 MinION runs during a 6-month period.

“Genome sequencing information is valuable for researchers and epidemiologists during an epidemic, yet, generating such information is a laborious process typically performed in well-equipped laboratories using large, delicate and expensive hardware,” co-author Nick Loman, said in a statement. “Having a portable DNA sequencing system opens up the possibility to do outbreak genome sequencing in real-time, which can directly impact on the response on the ground, as well as providing a wealth of information about pathogen evolution.”