1.
Next Generation Sequencing Reveals New
Southern African Territories Genotypes Bringing Us
Closer to Understanding the History of
Foot-and-Mouth Disease Virus in Africa
Lidia Lasecka-Dykes, Nick J. Knowles, Caroline F. Wright,
Grace Logan, Toby Tuthill, Terry Jackson and Donald P. King

2.
Foot-and-mouth disease virus (FMDV)
• Genus Aphthovirus , family Picornaviridae;
• Causes highly contagious disease of cloven-hoofed animals;
• 7 serotypes: O, A, Asia1, C, SAT1-3;
• African buffalo (Syncerus caffer) as ancestral reservoir of FMDV;
• Biased sampling of true sequence diversity.
VP1
O (58%)
C (4%)
A (20%)
Asia1 (10%)
SAT2 (3%)
SAT1 (3%)
SAT3 (1%)

3.
SAT viruses with ‘non-SAT’ S-fragment
ORF
Mason et al. (2003) Virus Res; 91 [modified]
What is the genetic basis of these unusual S-fragments?

4.
SAT1,2,3 – ‘common’ SAT S-fragment
SAT,1,2,3 – QEP (Queen Elizabeth Park)
SAT1,2 – East Africa
Serotype A
Serotype O
Serotype Asia 1
Serotype C
5’UTR of SAT viruses
from Queen Elizabeth
Park and East Africa
show a distinct
phylogenies
S-fragment
S-fragment
Restof5’UTR
VP1
SAT1
SAT2
SAT3
A
Asia1
C
O

5.
SAT1,2,3 – ‘common’ SAT S-fragment
SAT,1,2,3 – QEP (Queen Elizabeth Park)
SAT1,2 – East Africa
Serotype A
Serotype O
Serotype Asia 1
Serotype C
Non-structural proteins of
SAT viruses from Queen
Elizabeth Park and East
Africa also show distinct
phylogenies
Maximum likelihood
trees suggest distinct
evolutionary pathway
of these viruses
S-fragment
2B 2C 3C 3D

6.
[Phylogenetic Signal Scan (SSE) - Toy Example]
1 10 20 30 40
Sgr A
Sgr B
Sgr C
Sgr D
Simmonds (2006) J Virol; 80 [modified]
Method for identifying recombination

7.
5’UTR
L
VP4
VP2 VP3 VP1
2A
2B 2C 3A
3B1-3
3C 3D 3’UTR
Genome positionTreeposition
O
C
A
Asia1
SAT2
SAT1
SAT3
Phylogenetic Signal Scan
(SSE)
(Bootstrap ≥ 70%) for 100
sequences and using 300
nts sliding window
SSE: Simmonds (2012) BMC
Research Notes; 20
Evidence of
frequent
recombination
events in 5’UTR
and NS region but
not capsid

8.
Genome positionTreeposition
5’UTR
L
VP4
VP2 VP3 VP1
2A
2B 2C 3A
3B1-3
3C 3D 3’UTR
O
C
A
Asia1
SAT2
SAT1
SAT3
East Africa
QEP
SEE: Simmonds (2012) BMC
Research Notes; 20
Lack of recombination SAT viruses from East Africa and Queen Elizabeth Park
suggests that these viruses evolved separately (e.g. parallel evolution?)
Phylogenetic Signal Scan
(SSE)
(Bootstrap ≥ 70%) for 100
sequences and using 300
nts sliding window

9.
“Common” SAT1/2/3
East Africa (SAT1/2)
QEP (SAT1/2/3)
Bayesian maximum clade credibility tree of 3C
Cattle plague (Rinderpest) epidemic has influenced the genetic
variability of SAT viruses currently found in Africa
1887
1889
1890
1892
Rinderpest spread
according to Hutcheon (1897)
Cattle distribution (present)
Buffalo distribution (past)
1890
1890-92
1892
1893
Mar. 1896
Apr. 1896
Oct. 1896
1897
Feb. 1896
African Rinderpest
Pandemic
of 1887-1897

10.
Historical Records: QENP

11.
Acknowledgements
The Pirbright Institute:
Valerie Mioulet (samples)
Graham Freimanis (“bioinformatics chat”)
David King (“bioinformatics chat”)
Nicolas
strategic longer and larger grant
Nic Stonehouse
Dave Rowlands
Sam Stephen
Eleni-Anna Loundras
Joseph Ward
Martin Ryan
Fiona Tulloch
Garry Luke
John Nicholson
Angus Lamond
Armel Nicolas
Jürgen Haas
Samantha Griffiths