This study evaluated using sampling of asymptomatic livestock at slaughterhouses in Vietnam for molecular surveillance of foot-and-mouth disease virus (FMDV). Samples collected from cattle and buffalo at two slaughterhouses showed viral diversity reflecting strains circulating in the source population. Phylogenetic analysis found that for some FMDV serotype O clades, slaughterhouse sequences pre-dated later outbreak sequences by 4-6 months, suggesting slaughterhouse sampling could provide early detection of emerging strains. Additionally, some farm sequences clustered with older outbreak sequences, indicating subclinical circulation may occur up to 18 months after observed outbreaks. The study concludes routine slaughterhouse sampling provides a cost-effective means for molecular surveillance to identify circulating and emerging FMDV strains in

1. Molecular Surveillance of Foot and Mouth
Disease Virus through Slaughterhouses in
Vietnam
Umanga Gunasekera1, M.R.Bertram2, Le T. Vu3, Do H. Dung3, Bui H. Hoang3, Nguyen T.
Phuong3, Vo V. Hung3 ,Long Nguyen3, A. Perez1, J. Arzt2, K. VanderWaal1
1Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA,
2 Foreign Animal Disease Research Unit, USDA-ARS, Plum Island Animal Disease Center,
Greenport, NY, USA,
3Department of Animal Health, Vietnam.

2. Introduction and Methods
• Introduction
• The genetic and antigenic diversity of foot-and-mouth disease virus (FMDV) poses a
significant challenge to successful control in endemic countries.
• The objective of this study was to evaluate sampling of asymptomatic livestock at
slaughterhouses as a strategy for molecular surveillance of FMDV in Vietnam.
• We investigated the extent to which viruses recovered from slaughterhouses reflect the
diversity found in the source population, and whether they can serve as sentinels for the early
detection of emerging outbreak strains.
• Materials and Methods
• Oropharyngeal fluid (OPF) samples collected from 944 asymptomatic cattle and buffalo in two
slaughterhouses, to characterize viral diversity in the source population, sequences obtained
from longitudinal sampling of OPF from farms (2015-2017) from eight provinces, outbreak
sequences from clinical cases(2009 to 2019) from passive surveillance were used in this
study.
• Discriminant Principal Component Analysis (DPCA) was performed on 193 VP1 region of
Serotype O to identify clusters of closely related sequences
• A time-scaled phylogenetic tree was created for serotypes O using Bayesian evolutionary
sampling tree (BEAST).

3. Results
• Within a given serotype, time-scaled trees
showed that a series of viral clades emerged,
spread, and subsequently declined over time.
• Each viral clade was representative of
circulating strains in different parts of the
country.
• For several serotype O clades that included
outbreak, slaughterhouse, and farm
sequences, subclinical slaughterhouse
sequences pre-dated the outbreak sequences
by 4-6 months.
• For other clades, sequences isolated from
animals without clinical signs from farms
clustered with older outbreak sequences,
suggesting the sub-clinical circulation of the
viral strain may occur up to 18 months after
the observed outbreak. Sequencenumber

4. Discussion
In endemic regions, routine sampling at slaughterhouses may provide a cost-effective means
for molecular surveillance to identify circulating and emerging FMDV strains. Within this study,
virus sequences obtained in this manner provided a subset of the diversity present in other
regional viral populations
Reported outbreaks
Population level virus circulation
Active surveillance
Farms and Slaughterhouses