This document summarizes research using nanopore sequencing to generate complete genomes of foot-and-mouth disease virus (FMDV). The researchers developed a tiling strategy using RT-PCR and nanopore sequencing to amplify and sequence entire FMDV genomes. They were able to generate over 50 complete genome sequences of the virus spreading in Zambia from 2019 to 2021 to allow for fine-scale mapping of outbreaks. Complete genome sequencing provides information beyond the 1D region typically used and is important for understanding certain phenotypic traits and antigenic sites.

1. EuFMD
OS22
Andrew Shaw, Antonello Di Nardo, Ugo Ihearahu,
Kebaneilwe Lebani, Nick Knowles, Jemma Wadsworth,
Natasha Edwards, Donald King
Complete genome sequencing
of FMDV using Nanopore
sequencing

2. #OS22
Digitalization and innovation applied to the prevention and control of
foot-and-mouth and similar transboundary animal diseases (FAST) OS22 2
Introduction
Why generate complete FMDV genomes?
FMDV phylogenies are classically based upon the 1D region encoding VP1 due to its
information dense nature and lack of recombination
However…
● Complete genomes are required for fine-scale mapping of outbreaks
● Certain phenotypic traits are encoded outside of 1D, e.g. antigenic sites
Andrew Shaw
Nanopore sequencing of FMDV

3. #OS22
Digitalization and innovation applied to the prevention and control of
foot-and-mouth and similar transboundary animal diseases (FAST) OS22 3
Genome tiling strategy
Andrew Shaw
Nanopore sequencing of FMDV
Adapted from Grubman and Baxt 2004
RT-PCR amplification of genomes followed by
nanopore sequencing

4. #OS22
Digitalization and innovation applied to the prevention and control of
foot-and-mouth and similar transboundary animal diseases (FAST) OS22 4
Outcome
Pan-FMDV oligo pools amplify entire genomes
Andrew Shaw
Nanopore sequencing of FMDV
O/ZAM/8/2019 (MZ486070)
O/ZAM/57/2019 (OM259994)
O/ZAM/18/2019 (OM259984)
O/ZAM/3/2019 (MZ486067)
O/ZAM/7/2019 (MZ486069)
O/ZAM/24/2019 (OM259987)
O/ZAM/55/2019 (OM259992)
O/ZAM/2/2019 (MZ486066)
O/ZAM/4/2019 (MZ486068)
O/ZAM/56/2019 (OM259993)
O/ZAM/2/2020 (OM259999)
O/ZAM/1/2020 (OM259998)
O/ZAM/21/2019 (OM259986)
O/ZAM/20/2019 (OM259985)
O/ZAM/27/2019 (OM259989)
O/ZAM/26/2019 (OM259988)
O/ZAM06/2019* (MZ486071)
O/ZAM07/2019* (MZ486072)
O/ZAM/58/2019 (OM259995)
O/ZAM/28/2019 (OM259990)
O/ZAM/16/2019 (OM259983)
O/ZAM/15/2019 (OM259982)
O/ZAM/62/2019 (OM259997)
O/ZAM/6/2020 (OM260002)
O/ZAM/7/2020 (OM260003)
O/ZAM/4/2020 (OM260001)
O/ZAM/11/2020 (OM260007)
O/ZAM/12/2020 (OM260008)
O/ZAM/3/2020 (OM260000)
O/ZAM/8/2020 (OM260004)
O/ZAM/9/2020 (OM260005)
O/ZAM/10/2020 (OM260006)
O/ZAM/7/2021 (OM260012)
O/ZAM/11/2021 nanopore
O/ZAM/11/2021 (OM260014)
O/ZAM/9/2021 (OM260013)
O/NMB/1/2021
O/UGA/3/2002 (DQ165077)
O/KEN/5/2002 (DQ165073)
O/TAN/2/2004 (KF561679)
O/MAL/1/98 (DQ165074)
EA-2
EA-1
O/K40/84* (KY091280)

5. Thank you !..
www. https://www.pirbright.ac.uk/
andrew.shaw@pirbright.ac.uk
@VirusMuser