The document describes using nanopore sequencing to characterize foot-and-mouth disease virus (FMDV) in clinical samples. It details the experimental workflow involving ligation, PCR barcoding, and reference sequencing. The MinION sequencer was able to characterize FMDV down to the strain level across different serotypes and sample types. Real-time sequencing could inform decisions on vaccine use to control potential FMD outbreaks.

1. Pirbright receives strategic funding from BBSRC UKRI
Characterising foot-and-mouth
disease virus in clinical
samples using nanopore
sequencing
Emma Brown
Research Assistant, Transmission Biology

2. MinION sequencing workflows
Experimental workflow:
 The ligation (SQK-LSK109) and PCR barcoding kit (EXP-PBC001) (Oxford Nanopore
Technologies).
 Reference sequences generated on the MiSeq (Nextera XT kit from Illumina).
Data analysis:
 Assembled reference genomes
(Canu v. 2.0).
 Polished consensus sequences
(Medaka v. 0.11.5)
 Coverage profiles (BEDTools
v.2.26.0)

3. MinION sequencing results
Serotype
Percentageofmappedreads(%)
A) Coverage over time
B) Coverage across amplicon
C) Mapped reads

4. Conclusions
 The MinION sequencer can characterise FMDV down to strain level in a
variety of different sample matrices and across different serotypes.
 Real-time sequencing could be a useful tool for providing information on
circulating strains of FMDV, which could inform critical decision making
on appropriate use of vaccines to control or prevent an outbreak of
FMD.
Acknowledgements
The Pirbright Institute
Dr David King
Dr Graham Freimanis
Dr Andrew Shaw
Dr Simon Gubbins Defra project SE2816
University of Surrey
Dr Dan Horton
Dr Arnoud van Vliet