Home Phylodynamics Data Links

Foot and Mouth Disease Virus

Genome

The Foot and Mouth Disease Virus (FMDV) is an Picornavirus with an single stranded RNA genome, encoding for one polyprotein. The polyprotein is post-translationally processed into individual proteins, including the surface protein VP1.
See http://viralzone.expasy.org/viralzone/all_by_species/98.html

There are seven main serotypes of FMDV; the Eurasian serotypes are A, C, O and Asia1, and the South African Territories serotypes are SAT1, SAT2, SAT3.

FMDV Database

There is a sequence database at Pirbright (last updated 2010) http://www.wrlfmd.org/fmdv_seqs/fmdv_seq.htm
this has details of individual serotypes, complete genomes and VP1 sequences

Complete Genome Sequences

Global

Carrillo et al performed a study of whole genome FMDV sequences:
Carrillo et al (2005) "Comparative Genomics of Foot-and-Mouth Disease Virus" J. Virol.May 2005 79(10):6487-6504 doi: 10.1128/JVI.79.10.6487-6504.2005
Phylogenetic trees for different regions of the genome, in Figure 4
The published genome set is on GenBank (see table 1): PopSet: 46810758

Table 1: Carrillo 2005 - 103 Genome Set, renamed in the format Accession|Serotype|Country|Year|Strain

Serotype	Length	Num.Seqs.	FASTA
All	8162	103	Full Genomes

Complete Genomes in the UK 2001

Cottam et al sequenced 23 UK FMDV complete genome sequences from the 2001 epidemic, and table 1 in the paper gives the locations of the sequences.
Cottam et al (2006) "Molecular Epidemiology of the Foot-and-Mouth Disease Virus Outbreak in the United Kingdom in 2001" J. Virol. November 2006 80(22):11274-11282 doi: 10.1128/JVI.01236-06

Table 2: Cottam 2006 - 23 UK Genome Sequences, renamed in the format Accession|Host|Place|Farm|Strain|Date|DecimalDate

Serotype	Length	Num.Seqs.	FASTA	NJ Tree	ML Tree
O	8196	23	Full Genomes	TN93 NJ Tree	GTR ML Tree

In Cottam et al 2008, the authors extended the analysis the 2001 FMDV UK outbreak.
Cottam et al (2008) "Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus" Proc. R. Soc. B 22 April 2008 275(1637):887-895 doi:10.1098/rspb.2007.1442 - Figure 1 showing inferred transmission pattern

Table 3: Cottam 2008 - 22 UK Genome Sequences, renamed in the format Accession|Host|Country|Sample|Strain|Date|DecimalDate
Note that these are mostly the same as in Cottam 2006, but the names correspond to the locations in Cottam 2008 Figure 1

Serotype	Length	Num.Seqs.	FASTA	NJ Tree	ML Tree
O	8195	22	Full Genomes	TN93 NJ Tree	GTR ML Tree

Konig et al 2009
Konig et al (2009) "Sequence data and evidence of possible airborne spread in the 2001 foot-and-mouth disease epidemic in the UK" Veterinary Record 2009;165:410-412 doi:10.1136/vr.165.14.410

Complete Genomes in the UK 2007

11 FMDV whole genomes were sequenced by Cottam et al 2008(b) in the UK FMDV 2007 outbreak
Cottam et al (2008) "Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007" PLoS Pathog. 2008 Apr 18;4(4):e1000050. doi: 10.1371/journal.ppat.1000050

Serotype	Length	Num.Seqs.	FASTA	NJ Tree	ML Tree
O	8176	11	Full Genomes	TN93 NJ Tree	GTR ML Tree

Sequences

VP1

FMDV sequences from were downloaded from GenBank on 28th May 2014. Initial processing to extract the VP1 sequences was performed using a custom R script epic_process_background_seqs_fmdv.R, sequences shorter than 500 nucleotides were excluded, followed by some manual editting of the sequence files.

Nucleotide sequences (fasta format) were translated to amino acids for alignment using MUSCLE in MEGA 5.

Neighbour joining trees (newick format) were created in MEGA with the TN93 model, pairwise deletetion, and heterogenous rates between sites and lineages.

Table 4: VP1 with GenBank accession numbers as names - VP1 Sequence information all serotypes

Serotype	Length	Num.Seqs.	FASTA
A	686	677	A seqs
Asia1	633	226	Asia1 seqs
C	636	29	A seqs
O	642	1203	O seqs
SAT1	663	38	SAT1 seqs
SAT2	648	225	SAT2 seqs
SAT3	654	4	SAT3 seqs

Table 5: Individual serotpyes with names in format Host|Country|Year|Strain|Date|DecimalDate for sequences with complete details
Note the smaller number of sequences than above due to the incomplete annotation in GenBank.

Segment	Length	Num.Seqs.	FASTA	NJ Tree	Strain Information
A	686	494	A seqs	TN93 NJ Tree	Info table
Asia1	633	166	Asia1 seqs	TN93 NJ Tree	Info table
C	636	2	A seqs	-	Info table
O	642	779	O seqs	TN93 NJ Tree	Info table
SAT1	663	38	SAT1 seqs	TN93 NJ Tree	Info table
SAT2	648	167	SAT2 seqs	TN93 NJ Tree	Info table
SAT3	654	4	SAT3 seqs	-	Info table

---