What can MinION sequencing uncover about hepatitis B virus?

The development of the Oxford Nanopore (ONT) MinION sequencer has begun a small revolution in both sequencing in general, and the study of infectious diseases. Surveillance of viruses such as Ebola and Zika in parts of the world without ready access to sequencing facilities, which would previously have taken truckloads of equipment, is now possible with a couple of suitcases. In this article we will discuss how we are applying this technology in novel ways to the study of hepatitis B virus, what issues still need to be resolved and future developments.

Nanopore sequencing

The MinION sequencer consists of a base unit about the size of a stapler and the consumable flow cell, which contains the nanopores and associated sensor technology. The nanopores are E. coli CsgG pore proteins in a conducting electrolyte solution with a potential difference applied. As DNA molecules (prepared with specific sequencing adapters to attract them towards the pore) move through the pore this results in a change in current, as different nucleotide sequences result in different changes in current, this data can then be used to generate DNA sequence.

Portability aside, the important difference between this method of sequencing and existing ‘second generation’ sequencing approaches are that nanopores have no theoretical limit on read length. In practice, and with very careful DNA preparation this has allowed reads of over 1Mb [1,2].  Reads of this length allow for better assembly of large genomes compared to working with short reads and can cover previously impossible to sequence large repeat regions of the human genome.

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