FAO World Reference Laboratory for Foot‐and‐Mouth Disease

FAOWorldReferenceLaboratoryfor
Foot‐and‐MouthDisease(WRLFMD)
GenotypingReport
ReportDateforthisBatch:26May2014
FMDVtypeO
Country:Tunisia
Period:2014
No.ofsequences:2(VP1)
Originator:Dr.EmilianaBrocchi,NationalReferenceCentrefor
VesicularDiseases,IstitutoZooprofilatticoSperimentaledella
Lombardiaedell’EmiliaRomagna(IZSLER),Brescia,Italy.
The contents of this report are copyright and should not be reproduced without permission © The Pirbright Institute FAO World Reference Laboratory for FMD Genotyping Report
IAH-P-EP-MEG-FOR-005-3
Page 1 of 1
Serotype: O
WRLFMD Ref No: TUN/1031/2014*
Batch No: WRLMEG/2014/00010
Sender Ref: 1031 (IZSLER 134444/1)
Location: Somaa, Tunisia
Date collected: 26/04/2014
Date received by WRLFMD: 26/05/2014
Date received for sequencing: n/a
Species: Cattle
Material used: epithelial susp
Region sequenced: VP1
RT-PCR primers: O-1C244F/EUR-2B52R
O-1C272F/EUR-2B52R
Report date: 26/05/2014
Reported by: N.J. Knowles
Checked by: D.P. King
Topotype: ME-SA
Genotype/strain: Ind-2001d
Sequence filename: TUN14-AA.SEQ
Date sequence last updated: 26/05/2014
No. of Nt determined: 639
No. of ambiguities: 0
Gene length: 639
Total no. of comparisons: 3845
Min. no. of nt for comparison: 600
Total turn-around time: 0 days
Comments:
Most Closely Related Viruses
Pos.
1
2
3
4
5
6
7
8
9
10
Virus name
O/TUN/1054/2014*
O/LIB/1/2013
O/LIB/11/2013
O/LIB/12/2013
O/LIB/4/2013
O/LIB/5/2013
O/LIB/7/2013
O/LIB/13/2013
O/LIB/16/2013
O/LIB/17/2013
Filename
No. nt
comp.
No. nt
match.
No. of
ambig.
% Id.
% Diff.
Topotype
Strain
TUN14-AB
LIB13-01
LIB13-11
LIB13-12
LIB13-04
LIB13-05
LIB13-07
LIB13-13
LIB13-16
LIB13-17
639
639
639
639
639
639
639
639
639
639
637
632
632
632
632
632
632
631
631
631
0
0
0
0
0
0
0
0
0
0
99.69
98.90
98.90
98.90
98.90
98.90
98.90
98.75
98.75
98.75
0.31
1.10
1.10
1.10
1.10
1.10
1.10
1.25
1.25
1.25
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Most Closely Related Reference Viruses
(see http://www.wrlfmd.org/fmd_genotyping/prototypes.htm)
Pos.
1
2
3
4
5
6
7
8
9
10
Virus name
O/BHU/3/2009
O/OMN/7/2001 (DQ164941)
O/KUW/3/97 (DQ164904)
O/UAE/4/2008
O/IRN/31/2009
O/TUR/257/2008* (FMDI)
O/UKG/35/2001 (AJ539141)
O/IRN/8/2005
O/PAK/16/2010
O/IRN/18/2010
nt, nucleotides
*, not a WRLFMD reference number
Filename
No. nt
comp.
No. nt
match.
No. of
ambig.
% Id.
% Diff.
Topotype
Strain
BHU09-03
OMN01-07
KUW97-03
UAE08-04
IRN09-31
TUR08-AD
UKG01-35
IRN05-08
PAK10-16
IRN10-18
639
639
639
636
639
639
639
639
639
639
608
582
579
570
570
565
565
564
563
562
0
0
0
0
0
0
0
0
0
0
95.15
91.08
90.61
89.62
89.20
88.42
88.42
88.26
88.11
87.95
4.85
8.92
9.39
10.38
10.80
11.58
11.58
11.74
11.89
12.05
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
Ind-2001d
Ind-2001b
Ind-2001a
Ind-2001c
FAR-09
PanAsia-2
TER-08
PanAsia-2
PanAsia
PanAsia-2
PUN-10
PanAsia-2
BAL-09
PanAsia-2
Assembled with Report Generator v4.2
© The Pirbright Institute (not to be reproduced without permission)
FAO World Reference Laboratory for FMD Genotyping Report
IAH-P-EP-MEG-FOR-005-3
Page 1 of 1
Serotype: O
WRLFMD Ref No: TUN/1054/2014*
Batch No: WRLMEG/2014/00010
Sender Ref: 1054 (IZSLER 134444/4)
Location: Sidi Bouzid, Tunisia
Date collected: 29/04/2014
Date received by WRLFMD: 26/05/2014
Date received for sequencing: n/a
Species: Cattle
Material used: epithelial susp
Region sequenced: VP1
RT-PCR primers: O-1C244F/EUR-2B52R
O-1C272F/EUR-2B52R
Report date: 26/05/2014
Reported by: N.J. Knowles
Checked by: D.P. King
Topotype: ME-SA
Genotype/strain: Ind-2001d
Sequence filename: TUN14-AB.SEQ
Date sequence last updated: 26/05/2014
No. of Nt determined: 639
No. of ambiguities: 0
Gene length: 639
Total no. of comparisons: 3845
Min. no. of nt for comparison: 600
Total turn-around time: 0 days
Comments:
Most Closely Related Viruses
Pos.
1
2
3
4
5
6
7
8
9
10
Virus name
O/TUN/1031/2014*
O/LIB/1/2013
O/LIB/11/2013
O/LIB/12/2013
O/LIB/4/2013
O/LIB/5/2013
O/LIB/7/2013
O/LIB/13/2013
O/LIB/16/2013
O/LIB/17/2013
Filename
No. nt
comp.
No. nt
match.
No. of
ambig.
% Id.
% Diff.
Topotype
Strain
TUN14-AA
LIB13-01
LIB13-11
LIB13-12
LIB13-04
LIB13-05
LIB13-07
LIB13-13
LIB13-16
LIB13-17
639
639
639
639
639
639
639
639
639
639
637
634
634
634
634
634
634
633
633
633
0
0
0
0
0
0
0
0
0
0
99.69
99.22
99.22
99.22
99.22
99.22
99.22
99.06
99.06
99.06
0.31
0.78
0.78
0.78
0.78
0.78
0.78
0.94
0.94
0.94
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Ind-2001d
Most Closely Related Reference Viruses
(see http://www.wrlfmd.org/fmd_genotyping/prototypes.htm)
Pos.
1
2
3
4
5
6
7
8
9
10
Virus name
O/BHU/3/2009
O/OMN/7/2001 (DQ164941)
O/KUW/3/97 (DQ164904)
O/UAE/4/2008
O/IRN/31/2009
O/TUR/257/2008* (FMDI)
O/UKG/35/2001 (AJ539141)
O/IRN/8/2005
O/PAK/16/2010
O/IRN/18/2010
nt, nucleotides
*, not a WRLFMD reference number
Filename
No. nt
comp.
No. nt
match.
No. of
ambig.
% Id.
% Diff.
Topotype
Strain
BHU09-03
OMN01-07
KUW97-03
UAE08-04
IRN09-31
TUR08-AD
UKG01-35
IRN05-08
PAK10-16
IRN10-18
639
639
639
636
639
639
639
639
639
639
610
584
581
572
572
567
567
566
565
564
0
0
0
0
0
0
0
0
0
0
95.46
91.39
90.92
89.94
89.51
88.73
88.73
88.58
88.42
88.26
4.54
8.61
9.08
10.06
10.49
11.27
11.27
11.42
11.58
11.74
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
ME-SA
Ind-2001d
Ind-2001b
Ind-2001a
Ind-2001c
FAR-09
PanAsia-2
TER-08
PanAsia-2
PanAsia
PanAsia-2
PUN-10
PanAsia-2
BAL-09
PanAsia-2
Assembled with Report Generator v4.2
© The Pirbright Institute (not to be reproduced without permission)
O/TUN/1031/2014* (IZSLER)
O/TUN/1054/2014* (IZSLER)
O/LIB/12/2013
O/LIB/11/2013
O/LIB/1/2013
O/LIB/4/2013
O/LIB/13/2013
O/LIB/5/2013
O/LIB/17/2013
O/LIB/7/2013
indicates viruses in this batch
96
O/LIB/22/2013
O/LIB/2/2013
Software: MEGA 6.06
Analysis
O/LIB/3/2013
Analysis ---------------------------- Phylogeny Reconstruction
O/LIB/6/2013
Scope ------------------------------- All Selected Taxa
O/LIB/16/2013
Statistical Method ------------------ Neighbor-joining
O/IND52/2013* (PD-FMD)
Phylogeny Test
74 O/SAU/2/2014
Test of Phylogeny ------------------- Bootstrap method
87 O/SAU/3/2014
No. of Bootstrap Replications ------- 1000
O/SAU/1/2014
Substitution Model
O/SAU/7/2013
Substitutions Type ------------------ Nucleotide
O/SAU/8/2013
95
Model/Method ------------------------ Kimura 2-parameter model
Substitutions to Include ------------ d: Transitions + Transversions 95 O/SAU/6/2013
O/IND179/2013* (PD-FMD)
Rates and Patterns
O/SAU/4/2014
Rates among Sites ------------------- Uniform rates
O/SAU/3/2013
Pattern among Lineages -------------- Same (Homogeneous)
O/SAU/1/2013
Data Subset to Use
96
O/SAU/4/2013
Gaps/Missing Data Treatment --------- Pairwise deletion
O/IND127/2013* (PD-FMD)
Codons Included --------------------- 1st+2nd+3rd+Non-Coding
No. of Sites : 642
100 O/NEP/16/2013
No Of Bootstrap Reps = 1000
O/NEP/17/2013
Only bootstrap values of 70% and above are shown
O/BHU/1/2013
99
O/NEP/16/2012
93
*, not a WRLFMD Ref. No.
O/IND50/2013* (PD-FMD)
O/NEP/10/2012
O/NEP/11/2012
99
N.J. Knowles, J. Wadsworth & K. Bachanek-Bankowska,
O/NEP/13/2012
26 May 2014
O/NEP/6/2013
O/NEP/11/2013
© The Pirbright Institute
O/NEP/12/2013
(not to be reproduced without permission)
O/UAE/1/2014
99
87 O/UAE/2/2014
100
O/NEP/18/2013
O/IND205/2013* (PD-FMD)
88 O/NEP/1/2014
O/NEP/2/2014
O/IND219/2013* (PD-FMD)
O/IND222/2013* (PD-FMD)
91
O/NEP/3/2013
O/IND189/2013* (PD-FMD)
O/NEP/6/2014
O/BHU/3/2009
85
99
O/IND/102/2010* (KC506466)
O/UAE/4/2008
O/KUW/3/97 (DQ164904)
88
87
O/OMN/7/2001 (DQ164941)
99
Report on FMDV O in
Tunisia in 2014
Batch: WRLMEG/2014/00010
PanAsia
PanAsia-2
88
89
94
O/IND/53/79 (AF292107)
O/IND/R2/75* (AF204276)
O1/Manisa/TUR/69 (AY593823)
100
99
100
98
100
100
84
76
76
0.02
SEA
EA-2
EA-3
EA-4
WA
EA-1
CATHAY
ISA-1
100
ISA-2
EURO-SA
d
Ind-2001
ME-SA
c
a
b

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