FAO World Reference
Laboratory for
Foot-and-Mouth Disease

 Prototypes
Navigation
Home
Up
ME Reports
FMD Maps
FMDV Seqdata
Definitions
Prototypes
Bibliography

 

 
 

Below are listed the representative strains/isolates for each FMDV topotype along with an accession number pointing to the complete genome sequence (where available) or at minimum the complete VP1 sequence. These can form the basic references points of a phylogenetic tree. Prototype strains for each topotype (and sometime lineage) are shown in bold case. The downloadable text file are only VP1 sequences.

Changes to FMDV Reference Virus Sequences (last change 12 March 2009)

Download FASTA format text files of VP1 sequences: O, A, C, Asia 1, SAT 1, SAT 2, SAT 3, All types
(right-hand mouse click and Save Target As...)

Download MEGA format text files of VP1 sequences: All types

Download the table as a Microsoft Excel file: FMDV Reference Virus Table

Please check back here from time-to-time as the reference list may be updated (changes will be listed), including new accession numbers where they are currently missing.

 
  Topotype Lineage Isolate name Accession no. Reference
O CATHAY - O/HKN/21/70 AJ294911 Knowles et al., 2001
CATHAY - O/HKN/6/83 AJ294919 Knowles et al., 2001
CATHAY - O/PHI/7/96 AJ294926 Knowles et al., 2001
CATHAY - O/Yunlin/Taiwan/97 AF308157 Beard and Mason, 2000
EA-1 - O/K83/79* (Kenya) AJ303511 Samuel and Knowles, 2001
EA-1 - O/K40/84* (Kenya) n/a Knowles et al., unpub.
EA-1 - O/UGA/5/96 AJ296327 Samuel and Knowles, 2001
EA-2 - O/MAL/1/98 DQ165074 Knowles et al., 2005
EA-2 - O/UGA/3/2002 DQ165077 Knowles et al., unpub.
EA-2 - O/KEN/5/2002 DQ165073 Knowles et al., unpub.
EA-2 - O/TAN/2/2004 n/a Knowles et al., unpub.
EA-3 - O/SUD/2/86 DQ165075 Knowles et al., 2005
EA-3 - O/ETH/3/2004 FJ798109 Ayelet et al., submitted
EA-3 - O/ETH/2/2006 FJ798127 Ayelet et al., submitted
EA-3 - O/ETH/1/2007 FJ798137 Ayelet et al., submitted
EA-4 - O/UGA/17/98 n/a Ayelet et al., submitted
EA-4 - O/ETH/58/2005 FJ798141 Ayelet et al., submitted
EURO-SA - O1/BFS 1860/UK/67 AY593815 Carrillo et al., 2005
EURO-SA - O2/Brescia/ITL/47 M55287 Krebs et al., 1991
EURO-SA - O3/Venezuela/51 AJ004645 Leister et al., 1993
EURO-SA - O/Corrientes/ARG/06 DQ834727 Malirat et al., 2007
ISA-1 - O11/ISA/1/62 AJ303500 Samuel and Knowles, 2001
ISA-1 - O/ISA/9/74 AJ303502 Samuel and Knowles, 2001
ISA-1 - O/ISA/8/83 AJ303503 Samuel and Knowles, 2001
ISA-2 - O/JAV/5/72 AJ303509 Samuel and Knowles, 2001
ISA-2 - O/ISA/1/74 AJ303501 Samuel and Knowles, 2001
ME-SA - O1/Manisa/TUR/69 AY593823 Carrillo et al., 2005
ME-SA - O/R2/75* (India) AF204276 Hemadri et al., unpublished
ME-SA - O/IND/53/79 AF292107 Hemadri et al., unpublished
ME-SA PanAsia O/UKG/35/2001 AJ539141 Mason et al., 2003
ME-SA PanAsia-2 O/IRN/8/2005 n/a Knowles et al., submitted 
SEA - O/TAI/189/87* n/a  
SEA Cam-94 O/CAM/3/98 AJ294910 Knowles et al., 2001
SEA Mya-98 O/MYA/7/98 DQ164925 Knowles et al., 2005
WA - O/GHA/5/93 AJ303488 Samuel and Knowles, 2001
WA - O/CIV/8/99 AJ303485 Samuel and Knowles, 2001
A AFRICA G-I A/KEN/42/66 n/a Knowles et al., unpub.
AFRICA G-II A/EGY/1/72 EF208756 Knowles et al., 2007
AFRICA G-III A21/Lumbwa/KEN/3/64 AY593761 Carrillo et al., 2005
AFRICA G-IV A/SUD/3/77 n/a Knowles et al., unpub.
AFRICA G-V A/NGR/2/73 n/a Knowles et al., unpub.
AFRICA G-VI A/GHA/16/73 n/a Knowles et al., unpub.
AFRICA G-VII A/UGA/13/66 n/a Knowles et al., unpub.
? G-VIII A23/Kitale/KEN/64 (KEN/46/65) AY593766 Carrillo et al., 2005
? A11 A11/Germany/c.29 (AGB) EU553852 Valarcher et al., 2008
ASIA A22 A22/IRQ/24/64 AY593763 Carrillo et al., 2005
ASIA Irn-87 A/IRN/2/87 EF208770 Knowles et al., 2007
ASIA Irn-96 A/IRN/1/96 EF208771 Knowles et al., 2007
ASIA Irn-99 A/IRN/22/99 EF208772 Knowles et al., 2007
ASIA Irn-05 A/IRN/1/2005 EF208769 Knowles et al., 2007
ASIA A15 A15/Bangkok/TAI/60 AY593755 Carrillo et al., 2005
ASIA   A/TAI/118/87 EF208777 Knowles et al., 2007
EURO-SA A12 A12/119/Kent/UK/32 M10975 Robertson et al., 1985
EURO-SA A24 A24/Cruzeiro/BRA/55 AY593768 Carrillo et al., 2005
EURO-SA A-81 A/Alem/ARG/81 AJ306219 König et al., 2001
C AFRICA C/K267/67* (KEN/32/70) n/a Ayelet et al., submitted
AFRICA   C/ETH/1/71 FJ798151 Ayelet et al., submitted
ASIA   C/N65/Tadjikistan/USSR/67 n/a Knowles et al., unpub.
ASIA   C/IND/51/79 (1977) n/a Knowles et al., unpub.
EURO-SA   C3/Resende/BRA/55 M90381 Martínez et al., 1992
EURO-SA   C1/Santa Pau/Spain/70
  (C-S8c1)		 AJ133357 Toja et al., 1999
EURO-SA   C3/Indaial/BRA/71 M90376 Martínez et al., 1992
EURO-SA   C/PHI/7/84 n/a Knowles et al., unpub.
?   C/Germany/c.26 (CGC) EU553893 Valarcher et al., 2005
?   C/UK/149/34 AY593810 Carrillo et al., 2005
A
S
I
A

1		 -   Asia1/PAK/1/54 AY593795 Carrillo et al., 2005
- G-I Asia1/AFG/1/2001 DQ121109 Valarcher et al., 2005
- G-II Asia1/IRN/10/2004 DQ121119 Valarcher et al., 2005
- G-III Asia1/IND/762/2003* DQ101240 Valarcher et al., 2005
- G-IV Asia1/HKN/19/74 FJ785230 Valarcher et al., submitted
- G-V Asia1/IND/18/80 DQ121116 Valarcher et al., 2005
- G-VI? Asia1/IND/14/95 AF390678 Gurumurthy et al., unpub.
-   Asia1/Shamir/ISR/89 n/a Marquardt et al., 2000
-   Asia1/IND/63/72* AY304994 Saravanan et al., unpub.
-   Asia1/YNBS/China/58 AY390432 Chang et al., unpub.
S
A
T

1		 NWZ (I)   SAT1/T155/71* n/a Knowles et al., unpub.
NWZ (I)   SAT1/ZIM/23/2003 n/a Knowles et al., unpub.
SEZ (II)   SAT1/RV/11/37 AY593839 Carrillo et al., 2005
SEZ (II)   SAT1/RHO/5/66 AY593846 Carrillo et al., 2005
WZ (III)   SAT1/BEC/1/48 AY593838 Carrillo et al., 2005
WZ (III)   SAT1/BOT/1/68 AY593845 Carrillo et al., 2005
EA-1 (IV)   SAT1/UGA BUFF/21/70 n/a Knowles et al., unpub.
V   SAT1/NIG/11/75 AF431711 Sangare et al., 2003
VI   SAT1/ISR/4/62 AY593844 Carrillo et al., 2005
VI   SAT1/SUD/3/76 AY441996 Sahle et al., 2007
EA-2 (VII)   SAT1/UGA/13/74 AY442010 Sahle et al., 2007
EA-3 (VIII)   SAT1/UGA/1/97* AY442012 Sahle et al., 2007
IX   SAT1/ETH/3/2007 FJ798154 Ayelet et al., submitted
S
A
T

2		 I   SAT2/SA/106/59 AY593848 Carrillo et al., 2005
I   SAT2/ZIM/14/2002 n/a Knowles et al., unpublished
II   SAT2/ZIM/7/83* AF136607 van Rensburg and Nel, 1999
II   SAT2/ZIM/5/81 EF134951 Brocchi et al., unpublished
III   SAT2/RHO/1/48 AY593847 Carrillo et al., 2005
III   SAT2/BOT/P3/98
  (buffalo 29)		 AF367124 Bastos et al., 2003
IV   SAT2/KEN/1/84 AY344505 Sahle et al., 2007
IV   SAT2/ETH/1/90 AY343935 Sahle et al., 2007
V   SAT2/NIG/2/75 AF367139 Bastos et al., 2003
V   SAT2/GHA/2/90 AF479415 Bastos et al., 2003
VI   SAT2/GAM/8/79 AF479410 Bastos et al., 2003
VII   SAT2/SAU/6/2000 AF367135 Bastos et al., 2003
VII   SAT2/CAR/8/2005 n/a Knowles et al., unpublished
VIII   SAT2/ZAI/1/74 DQ009737 Maree et al., unpublished
VIII   SAT2/RWA/1/00* AF367134 Bastos et al., 2003
IX   SAT2/KEN/3/57 AJ251473 Newman et al., unpub.
IX   SAT2/KEN/2/84 AY343941 Sahle et al., 2007
X   SAT2/ZAI/1/82 AF367100 Bastos et al., 2003
X   SAT2/UGA/19/98 AY343969 Sahle et al., 2007
XI   SAT2/ANG/4/74 AF479417 Bastos et al., 2003
XII   SAT2/UGA/51/75 AY343963 Sahle et al., 2007
XIII   SAT2/SUD/6/77 AY343939 Sahle et al., 2007
XIII   SAT2/ETH/2/2007 FJ798161 Ayelet et al., submitted
XIV   SAT2/ETH/2/91 AY343938 Sahle et al., 2007
S
A
T

3		 SEZ (I)   SAT3/SA/57/59 AY593850 Carrillo et al., 2005
SEZ (I)   SAT3/KNP/10/90/3* AF286347 van Rensburg et al., 2002
WZ (II)   SAT3/BEC/1/65 AY593853 Carrillo et al., 2005
WZ (II)   SAT3/BEC/20/61 AY593851 Carrillo et al., 2005
NWZ (III)   SAT3/ZIM/P25/91 (UR-7) n/a Wadsworth et al., unpub.
IV   SAT3/ZAM/P2/96 (MUL-4) DQ009741 Maree et al., unpub.
EA (V)   SAT3/UGA BUFF/27/70
  (aka UGA/92/70)		 AJ303480 Samuel & Knowles, 2001;
Stirling and Knowles, unpub.
EA (V)   SAT3/UGA/2/97/3* DQ009742 Maree et al., unpub.

*, not a WRLFMD Ref. No.