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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.

There are currently 50 FMDV topotypes distributed thus: O (11); A (3); C (3), Asia 1 (1); SAT 1 (13); SAT 2 (14); and SAT 3 (5).

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

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...) (to be updated)

Download MEGA format text files of VP1 sequences: All types (to be updated)

Download the table as a Microsoft Excel file: FMDV Reference Virus Table (to be updated)

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.

Updated - 02 Mar 2017

  Topotype Lineage Sub-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) KY091280 Knowles et al., 2016
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 KF561679 Kasanga et al., 2015
EA-3 -   O/SUD/2/86 DQ165075 Knowles et al., 2005
EA-3 -   O/ETH/3/2004 FJ798109 Ayelet et al., 2009
EA-3 -   O/ETH/2/2006 FJ798127 Ayelet et al., 2009
EA-3 -   O/ETH/1/2007 FJ798137 Ayelet et al., 2009
EA-4 -   O/UGA/17/98 HM211075 Ayelet et al., 2009
EA-4 -   O/ETH/58/2005 FJ798141 Ayelet et al., 2009
EURO-SA O1   O1/BFS 1860/UK/67 AY593815 Carrillo et al., 200
EURO-SA O2   O2/Brescia/ITL/47 M55287 Krebs et al., 1991
EURO-SA O3   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 -   O/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   O/LAO/2/2006 (2003) EU667451 Khounsy et al., 2009
ME-SA PanAsia-2   O/IRN/8/2005 KY091281 Knowles et al., 2016
ME-SA PanAsia-2 TER-08 O/TUR/257/2008* n/a Parlak, unpubished
ME-SA PanAsia-2 FAR-09 O/IRN/31/2009 KY091284 Knowles et al., 2016
ME-SA PanAsia-2 BAL-09 O/IRN/18/2010 KY091283 Knowles et al., 2016
ME-SA PanAsia-2 SAN-09 O/TUR/264/2009* n/a Parlak, unpubished
ME-SA PanAsia-2 ANT-10 O/IRN/88/2009 KY091282 Knowles et al., 2016
ME-SA PanAsia-2 PUN-10 O/PAK/16/2010 KY091285 Knowles et al., 2016
ME-SA PanAsia-2 QOM-15 O/IRN/6/2015 n/a Knowles et al., unpub.
ME-SA PanAsia-2 KAT-15 O/NEP/1/2015 n/a Knowles et al., unpub.
ME-SA Ind-2001a   O/KUW/3/97 DQ164904 Knowles et al., 2005
ME-SA Ind-2001b   O/OMN/7/2001 DQ164941 Knowles et al., 2005
ME-SA Ind-2001c   O/UAE/4/2008 KM921876 Knowles et al., 2016
ME-SA Ind-2001d   O/BHU/3/2009 KM921814 Knowles et al., 2016
SEA - O/TAI/189/87* KY091288 Knowles et al., 2016
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 KF561699 Kasanga et al., 2013
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 GU566064 Habiela et al., 2010
AFRICA G-V   A/NGR/2/73 KF561704 Kasanga et al., 2013
AFRICA G-VI   A/GHA/16/73 KF561698 Kasanga et al., 2013
AFRICA G-VII   A/UGA/13/66 KF561705 Kasanga et al., 2013
? 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 Iran-87   A/IRN/2/87 EF208770 Knowles et al., 2007
ASIA Iran-96   A/IRN/1/96 EF208771 Knowles et al., 2007
ASIA Iran-99   A/IRN/22/99 EF208772 Knowles et al., 2007
ASIA Iran-05   A/IRN/1/2005 EF208769 Knowles et al., 2007
ASIA Iran-05 AFG-07 A/AFG/6/2007 FJ755007 Knowles et al., 2009
ASIA Iran-05 ARD-07 A/TUR/1/2008 FJ755133 Knowles et al., 2009
ASIA Iran-05 EZM-07 A/TUR/33/2008 FJ755155 Knowles et al., 2009
ASIA Iran-05 BAR-08 A/BAR/6/2008 FJ755010 Knowles et al., 2009
ASIA Iran-05 FAR-09 A/IRN/78/2009 KY091291 Knowles et al., 2016
ASIA Iran-05 KSS-09 A/TUR/3/2010 KY091294 Knowles et al., 2016
ASIA Iran-05 ESF-10 A/IRN/9/2010 KY091290 Knowles et al., 2016
ASIA Iran-05 HER-10 A/AFG/10/2010 KY091293 Knowles et al., 2016
ASIA Iran-05 SIS-10 A/IRN/125/2010 KY091296 Knowles et al., 2016
ASIA Iran-05 QAZ-11 A/IRN/9/2011 KY091295 Knowles et al., 2016
ASIA Iran-05 SIS-12 A/IRN/15/2012 KY091297 Knowles et al., 2016
ASIA A15   A15/Bangkok/TAI/60 AY593755 Carrillo et al., 2005
ASIA Thai-87   A/TAI/118/87* EF208777 Knowles et al., 2007
ASIA Sea-97   A/TAI/2/97 EF208778 Knowles et al., 2007
ASIA Sea-97   A/TAI/7/2003 HQ116312 Abdul-Hamid et al., 2010
ASIA G-VII   A/IND/40/2000* (1999) AF390646 Tosh et al., 2002
EURO-SA A12   A12/119/Kent/UK/32 M10975 Robertson et al., 1985
EURO-SA A5   A5/Allier/FRA/60 AY593780 Carrillo et al., 2005
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) KY091300 Knowles et al., 2016
AFRICA     C/ETH/1/71 FJ798151 Ayelet et al., 2009
ASIA     C/N65/Tadjikistan/USSR/67 KY091302 Knowles et al., 2016
ASIA     C/IND/51/79 (1977) KY091301 Knowles et al., 2016
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 KY091303 Knowles et al., 2016
?     C/Germany/c.26 (CGC) EU553893 Valarcher et al., 2005
?     C/UK/149/34 AY593810 Carrillo et al., 2005
A
S
I
A

1
ASIA     Asia1/PAK/1/54 AY593795 Carrillo et al., 2005
ASIA G-I   Asia1/AFG/1/2001 DQ121109 Valarcher et al., 2005
ASIA G-II   Asia1/IRN/10/2004 DQ121119 Valarcher et al., 2005
ASIA G-III   Asia1/IND/762/2003* DQ101240 Valarcher et al., 2005
ASIA G-IV   Asia1/HKN/19/74 FJ785230 Valarcher et al., submitted
ASIA G-V   Asia1/IND/18/80 DQ121116 Valarcher et al., 2005
ASIA G-VI?   Asia1/IND/14/95 AF390678 Gurumurthy et al., unpub.
ASIA G-VIII   Asia1/BAR/8/2009 n/a Knowles et al., unpublished
ASIA Sindh-08   Asia1/PAK/8/2008 KY091304 Knowles et al., 2016
ASIA     Asia1/Shamir/ISR/89 JF739177 Lee et al., unpublished
ASIA     Asia1/IND/63/72* AY304994 Saravanan et al., unpub.
ASIA     Asia1/YNBS/China/58 AY390432 Chang et al., unpub.
S
A
T

1
I (NWZ)     SAT1/T155/71* KF561706 Kasanga et al., 2013
I (NWZ)     SAT1/ZIM/23/2003 KF219690 Knowles et al., unpub.
II (SEZ)     SAT1/RV/11/37 AY593839 Carrillo et al., 2005
II (SEZ)     SAT1/RHO/5/66 AY593846 Carrillo et al., 2005
III (WZ)     SAT1/BEC/1/48 AY593838 Carrillo et al., 2005
III (WZ)     SAT1/BOT/1/68 AY593845 Carrillo et al., 2005
IV (EA-1)     SAT1/UGA BUFF/21/70 KF219682 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 DQ009725 Maree et al., unpub.
VII (EA-2)     SAT1/UGA/13/74 AY442010 Sahle et al., 2007
VIII (EA-3)     SAT1/UGA/1/97* AY442012 Sahle et al., 2007
IX     SAT1/ETH/3/2007 FJ798154 Ayelet et al., 2009
X     SAT1/NIG/1/2015 KX822796 Ehizibolo et al., 2017
XI     SAT1/TCH/1/72 n/a Knowles et al., unpub.
XII     SAT1/ANG/9/74 n/a Knowles et al., unpub.
XIII     SAT1/MOZ/1/75 n/a Knowles et al., unpub.
XIII     SAT1/MOZ/P13/2010_BUF_B16 KF219691 Kasanga et al., unpub.
S
A
T

2
I     SAT2/SA/106/59 AY593848 Carrillo et al., 2005
I     SAT2/ZIM/14/2002 KF219689 Knowles et al., unpub.
II     SAT2/ZIM/7/83* AF136607 van Rensburg and Nel, 1999
II     SAT2/ZIM/5/81 EF134951 Brocchi et al., unpub.
III     SAT2/RHO/1/48 AY593847 Carrillo et al., 2005
III     SAT2/BOT/P3/98 (buff 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 JX570616 Ahmed et al., 2012
VIII     SAT2/ZAI/1/74 DQ009737 Maree et al., unpub.
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., 2009
XIV     SAT2/ETH/2/91 AY343938 Sahle et al., 2007
S
A
T

3
I (SEZ)     SAT3/SA/57/59 AY593850 Carrillo et al., 2005
I (SEZ)     SAT3/KNP/10/90/3* AF286347 van Rensburg et al., 2002
II (WZ)     SAT3/BEC/1/65 AY593853 Carrillo et al., 2005
II (WZ)     SAT3/BEC/20/61 AY593851 Carrillo et al., 2005
III (NWZ)     SAT3/ZIM/P25/91 (UR-7) KY091306 Knowles et al., 2016
IV     SAT3/ZAM/P2/96 (MUL-4) DQ009741 Maree et al., unpub.
V (EA)     SAT3/UGA BUFF/27/70
  (aka UGA/92/70)
KF219685 Stirling and Knowles, unpub.
V (EA)     SAT3/UGA/2/97/3* DQ009742 Maree et al., unpub.

*, not a WRLFMD Ref. No.


 

   
 

 
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