Abstract

Genomic surveillance is a technique that is becoming increasingly important for detecting and responding to viral outbreaks. It requires the sequencing of many viral isolates allowing the use of phylogenetics to provide a high-resolution view of the outbreak. The technique is particularly powerful if it can provide feedback in real-time which is best achieved by deploying a mobile lab equipped with real-time sequencing technology into an ongoing outbreak. The MinION (Oxford Nanopore Technology) is the currently the only such real-time sequencer portable enough to be used in the field. The sequencing equipment and all required consumables can fit in bags that can be transported in standard airline luggage.
To obtain sufficient material for sequencing we have developed a multiplex PCR method known as PrimalSeq which given a set a reference genomes, will design a set of primers optimised for amplification of low viral titre samples. Multiple samples can be barcoded and run on a single MinION flowcell reducing the labour and sample cost to under $10 a sample in materials[1]. We have validated SOPs for building a mobile lab, sequencing protocols, nanopore bioinformatics and phylogenetic analysis which can be adapted for other viruses (http://artic.network/resources.html).
We have demonstrated that a mobile laboratory can be flown into an ongoing outbreak and provide rapid, actionable results from the field and avoiding the delays associated with shipping samples. We have deployed mobile labs to Guinea during the 2014 West African Ebola outbreak[2], to Brazil during the 2015 Zika outbreak[3], to DRC during the Kivu Ebola outbreak and are on standby to provide support in any future outbreaks as part of the Wellcome Trust funded ARTIC network project. Further work could improve the primer design and sequencing methods for faster answers and to enable untargeted sequencing for unknown viruses.

[1] Tyson J et al. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. https://doi.org/10.1101/2020.09.04.283077
[2] Quick J et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016 Feb 11;530(7589):228-32.
[3] Faria NR, Quick J et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. Nature. 2017 Jun 15;546(7658):406-410.