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.
Sequences are organised by serotype and (within each serotype) topotype. Prototype strains for each topotype (and sometime lineage) are shown in bold case.
(Note for tables: *, not a WRLFMD Reference Number)
The O serotype is divided into eleven topotypes: EAST AFRICA 1 to 4 (EA-1 to -4), SOUTHEAST ASIA (SEA), EUROPE-SOUTH AMERICA (EURO-SA), INDONESIA-1 and -2 (ISA-1 and -2), CATHAY, MIDDLE EAST-SOUTH ASIA (ME-SA) and WEST AFRICA (WA).
CATHAY
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/HKN/21/70 | AJ294911 | Knowles et al., 2001 |
- | - | O/HKN/6/83 | AJ294919 | Knowles et al., 2001 |
- | - | O/PHI/7/96 | AJ294926 | Knowles et al., 2001 |
- | - | O/Yunlin/Taiwan/97 | AF308157 | Beard and Mason, 2000 |
INDONESIA-1 (ISA-1)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O11/ISA/1/62 | AJ303500 | Samuel and Knowles, 2001 |
- | - | O/ISA/9/74 | AJ303502 | Samuel and Knowles, 2001 |
- | - | O/ISA/8/83 | AJ303503 | Samuel and Knowles, 2001 |
INDONESIA-2 (ISA-2)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/JAV/5/72 | AJ303509 | Samuel and Knowles, 2001 |
- | - | O/ISA/1/74 | AJ303501 | Samuel and Knowles, 2001 |
EUROPE-SOUTH AMERICA (EURO-SA)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
O1 | - | O1/BFS 1860/UK/67 | AY593815 | Carrillo et al., 2005 |
O2 | - | O2/Brescia/ITL/47 | M55287 | Krebs et al., 1991 |
O3 | - | O3/Venezuela/51 | AJ004645 | Leister et al., 1993 |
- | - | O/Corrientes/ARG/06 | DQ834727 | Malirat et al., 2007 |
EAST AFRICA 1 (EA-1)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/K83/79* (Kenya) | AJ303511 | Samuel and Knowles, 2001 |
- | - | O/K40/84* (Kenya) | KY091280 | Knowles et al., 2016a |
- | - | O/UGA/5/96 | AJ296327 | Samuel and Knowles, 2001 |
EAST AFRICA 2 (EA-2)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/MAL/1/98 | DQ165074 | Knowles et al., 2005a |
- | - | O/UGA/3/2002 | DQ165077 | Knowles et al., unpub. |
- | - | O/KEN/5/2002 | DQ165073 | Knowles et al., unpub. |
- | - | O/TAN/2/2004 | KF561679 | Kasanga et al., 2015 |
EAST AFRICA 3 (EA-3)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/SUD/2/86 | DQ165075 | Knowles et al., 2005a |
- | - | O/ETH/3/2004 | FJ798109 | Ayelet et al., 2009 |
- | - | O/ETH/2/2006 | FJ798127 | Ayelet et al., 2009 |
- | - | O/ETH/1/2007 | FJ798137 | Ayelet et al., 2009 |
EAST AFRICA 4 (EA-4)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/UGA/17/98 | HM211075 | Ayelet et al., 2009 |
- | - | O/ETH/58/2005 | FJ798141 | Ayelet et al., 2009 |
WEST AFRICA (WA)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/GHA/5/93 | AJ303488 | Samuel and Knowles, 2001 |
- | - | O/CIV/8/99 | AJ303485 | Samuel and Knowles, 2001 |
MIDDLE EAST-SOUTH ASIA (ME-SA)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/Manisa/TUR/69 | AY593823 | Carrillo et al., 2005 |
- | - | O/R2/75* (India) | AF204276 | Hemadri et al., unpublished |
- | - | O/IND/53/79 | AF292107 | Hemadri et al., unpublished |
PanAsia | - | O/UKG/35/2001 | AJ539141 | Mason et al., 2003 |
PanAsia | - | O/LAO/2/2006 (2003) | EU667451 | Khounsy et al., 2009 |
PanAsia-2 | - | O/IRN/8/2005 | KY091281 | Knowles et al., 2016a |
PanAsia-2 | TER-08 | O/TUR/257/2008* | n/a | Parlak, unpubished |
PanAsia-2 | FAR-09 | O/IRN/31/2009 | KY091284 | Knowles et al., 2016a |
PanAsia-2 | BAL-09 | O/IRN/18/2010 | KY091283 | Knowles et al., 2016a |
PanAsia-2 | SAN-09 | O/TUR/264/2009* | n/a | Parlak, unpubished |
PanAsia-2 | ANT-10 | O/IRN/88/2009 | KY091282 | Knowles et al., 2016a |
PanAsia-2 | PUN-10 | O/PAK/16/2010 | KY091285 | Knowles et al., 2016a |
PanAsia-2 | QOM-15 | O/IRN/6/2015 | n/a | Knowles et al., unpub. |
PanAsia-2 | KAT-15 | O/NEP/1/2015 | n/a | Knowles et al., unpub. |
Ind-2001a | - | O/KUW/3/97 | DQ164904 | Knowles et al., 2005b |
Ind-2001b | - | O/OMN/7/2001 | DQ164941 | Knowles et al., 2005b |
Ind-2001c | - | O/UAE/4/2008 | KM921876 | Knowles et al., 2016b |
Ind-2001d | - | O/BHU/3/2009 | KM921814 | Knowles et al., 2016b |
SOUTHEAST ASIA (SEA)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | O/TAI/189/87* | KY091288 | Knowles et al., 2016a |
Cam-94 | - | O/CAM/3/98 | AJ294910 | Knowles et al., 2001 |
Mya-98 | - | O/MYA/7/98 | DQ164925 | Knowles et al., 2005b |
The A serotype is divided into three topotypes: AFRICA, ASIA and EUROPE-SOUTH AMERICA (EURO-SA).
ASIA
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
A22 | - | A22/IRQ/24/64 | AY593763 | Carrillo et al., 2005 |
Iran-87 | - | A/IRN/2/87 | EF208770 | Knowles et al., 2007 |
Iran-96 | - | A/IRN/1/96 | EF208771 | Knowles et al., 2007 |
Iran-99 | - | A/IRN/22/99 | EF208772 | Knowles et al., 2007 |
Iran-05 | - | A/IRN/1/2005 | EF208769 | Knowles et al., 2007 |
Iran-05 | AFG-07 | A/AFG/6/2007 | FJ755007 | Knowles et al., 2009 |
Iran-05 | ARD-07 | A/TUR/1/2008 | FJ755133 | Knowles et al., 2009 |
Iran-05 | EZM-07 | A/TUR/33/2008 | FJ755155 | Knowles et al., 2009 |
Iran-05 | BAR-08 | A/BAR/6/2008 | FJ755010 | Knowles et al., 2009 |
Iran-05 | FAR-09 | A/IRN/78/2009 | KY091291 | Knowles et al., 2016a |
Iran-05 | KSS-09 | A/TUR/3/2010 | KY091294 | Knowles et al., 2016a |
Iran-05 | ESF-10 | A/IRN/9/2010 | KY091290 | Knowles et al., 2016a |
Iran-05 | HER-10 | A/AFG/10/2010 | KY091293 | Knowles et al., 2016a |
Iran-05 | SIS-10 | A/IRN/125/2010 | KY091296 | Knowles et al., 2016a |
Iran-05 | QAZ-11 | A/IRN/9/2011 | KY091295 | Knowles et al., 2016a |
Iran-05 | SIS-12 | A/IRN/15/2012 | KY091297 | Knowles et al., 2016a |
A15 | - | A15/Bangkok/TAI/60 | AY593755 | Carrillo et al., 2005 |
Thai-87 | - | A/TAI/118/87* | EF208777 | Knowles et al., 2007 |
Sea-97 | - | A/TAI/2/97 | EF208778 | Knowles et al., 2007 |
Sea-97 | - | A/TAI/7/2003 | HQ116312 | Abdul-Hamid et al., 2010 |
G-VII | - | A/IND/40/2000* (1999) | AF390646 | Tosh et al., 2002 |
AFRICA
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
G-I | - | A/KEN/42/66 | KF561699 | Kasanga et al., 2013 |
G-II | - | A/EGY/1/72 | EF208756 | Knowles et al., 2007 |
G-III | - | A21/Lumbwa/KEN/3/64 | AY593761 | Carrillo et al., 2005 |
G-IV | - | A/SUD/3/77 | GU566064 | Habiela et al., 2010 |
G-V | - | A/NGR/2/73 | KF561704 | Kasanga et al., 2013 |
G-VI | - | A/GHA/16/73 | KF561698 | Kasanga et al., 2013 |
G-VII | - | A/UGA/13/66 | KF561705 | Kasanga et al., 2013 |
EUROPE-SOUTH AMERICA (EURO-SA)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
A12 | - | A12/119/Kent/UK/32 | M10975 | Robertson et al., 1985 |
A5 | - | A5/Allier/FRA/60 | AY593780 | Carrillo et al., 2005 |
A24 | - | A24/Cruzeiro/BRA/55 | AY593768 | Carrillo et al., 2005 |
A-81 | - | A/Alem/ARG/81 | AJ306219 | König et al., 2001 |
?
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
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 |
The C serotype is divided into threetopotypes: EUROPE-SOUTH AMERICA (EURO-SA), ASIAand AFRICA.
AFRICA
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | C/K267/67* (KEN/32/70) | KY091300 | Knowles et al., 2016a |
- | - | C/ETH/1/71 | FJ798151 | Ayelet et al., 2009 |
ASIA
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | C/N65/Tadjikistan/USSR/67 | KY091302 | Knowles et al., 2016a |
- | - | C/IND/51/79 (1977) | KY091301 | Knowles et al., 2016a |
EUROPE-SOUTH AMERICA (EURO-SA)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | C3/Resende/BRA/55 | M90381 | Martínez et al., 1992 |
- | - | C1/Santa Pau/Spain/70 (C-S8c1) |
AJ133357 | Toja et al., 1999 |
- | - | C3/Indaial/BRA/71 | M90376 | Martínez et al., 1992 |
- | - | C/PHI/7/84 | KY091303 | Knowles et al., 2016a |
?
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | C/Germany/c.26 (CGC) | EU553893 | Valarcher et al., 2005a |
- | - | C/UK/149/34 | AY593810 | Carrillo et al., 2005 |
The Asia 1 serotype is divided into one topotype: ASIA.
ASIA
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | Asia1/PAK/1/54 | AY593795 | Carrillo et al., 2005 |
G-I | - | Asia1/AFG/1/2001 | DQ121109 | Valarcher et al., 2005b |
G-II | - | Asia1/IRN/10/2004 | DQ121119 | Valarcher et al., 2005b |
G-III | - | Asia1/IND/762/2003* | DQ101240 | Valarcher et al., 2005b |
G-IV | - | Asia1/HKN/19/74 | FJ785230 | Valarcher et al., submitted |
G-V | - | Asia1/IND/18/80 | DQ121116 | Valarcher et al., 2005b |
G-VI? | - | Asia1/IND/14/95 | AF390678 | Gurumurthy et al., unpub. |
G-VIII | - | Asia1/BAR/8/2009 | n/a | Knowles et al., unpub. |
Sindh-08 | - | Asia1/PAK/8/2008 | KY091304 | Knowles et al., 2016a |
- | - | Asia1/Shamir/ISR/89 | JF739177 | Lee et al., unpub. |
- | - | Asia1/IND/63/72* | AY304994 | Saravanan et al., unpub. |
- | - | Asia1/YNBS/China/58 | AY390432 | Chang et al., unpub. |
The SAT 1 serotype is divided into thirteen topotypes: I to XIII.
I (NORTHWEST ZIMBABWE, NWZ)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/T155/71* | KF561706 | Kasanga et al., 2013 |
- | - | SAT1/ZIM/23/2003 | KF219690 | Knowles et al., unpub. |
II (SOUTHEAST ZIMBABWE, SEZ)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/RV/11/37 | AY593839 | Carrillo et al., 2005 |
- | - | SAT1/RHO/5/66 | AY593846 | Carrillo et al., 2005 |
III (WESTERN ZIMBABWE, WZ)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/BEC/1/48 | AY593838 | Carrillo et al., 2005 |
- | - | SAT1/BOT/1/68 | AY593845 | Carrillo et al., 2005 |
IV (EAST AFRICA1, EA-1)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/UGA BUFF/21/70 | KF219682 | Knowles et al., unpub. |
V
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/NIG/11/75 | AF431711 | Sangare et al., 2003 |
VI
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/ISR/4/62 | AY593844 | Carrillo et al., 2005 |
- | - | SAT1/SUD/3/76 | DQ009725 | Maree et al., unpub. |
VII (EAST AFRICA 2, EA-2)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/UGA/13/74 | AY442010 | Sahle et al., 2007 |
VIII (EAST AFRICA 3, EA-3)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/UGA/1/97* | AY442012 | Sahle et al., 2007 |
IX
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/ETH/3/2007 | FJ798154 | Ayelet et al., 2009 |
X
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/NIG/1/2015 | KX822796 | Ehizibolo et al., 2017 |
XI
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/TCH/1/72 | n/a | Knowles et al., unpub. |
XII
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/ANG/9/74 | n/a | Knowles et al., unpub. |
XIII
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT1/MOZ/1/75 | n/a | Knowles et al., unpub. |
- | - | SAT1/MOZ/P13/2010_BUF_B16 | KF219691 | Kasanga et al., unpub. |
The SAT 2 serotype is divided into fourteen topotypes: I to XIV.
I
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/SA/106/59 | AY593848 | Carrillo et al., 2005 |
- | - | SAT2/ZIM/14/2002 | KF219689 | Knowles et al., unpub. |
II
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/ZIM/7/83* | AF136607 | van Rensburg and Nel, 1999 |
- | - | SAT2/ZIM/5/81 | EF134951 | Brocchi et al., unpub. |
III
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/RHO/1/48 | AY593847 | Carrillo et al., 2005 |
- | - | SAT2/BOT/P3/98 (buff 29) | AF367124 | Bastos et al., 2003 |
IV
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/KEN/1/84 | AY344505 | Sahle et al., 2007 |
- | - | SAT2/ETH/1/90 | AY343935 | Sahle et al., 2007 |
V
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/NIG/2/75 | AF367139 | Bastos et al., 2003 |
- | - | SAT2/GHA/2/90 | AF479415 | Bastos et al., 2003 |
VI
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/GAM/8/79 | AF479410 | Bastos et al., 2003 |
VII
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/SAU/6/2000 | AF367135 | Bastos et al., 2003 |
- | - | SAT2/CAR/8/2005 | JX570616 | Ahmed et al., 2012 |
VIII
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/ZAI/1/74 | DQ009737 | Maree et al., unpub. |
- | - | SAT2/RWA/1/00* | AF367134 | Bastos et al., 2003 |
IX
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/KEN/3/57 | AJ251473 | Newman et al., unpub. |
- | - | SAT2/KEN/2/84 | AY343941 | Sahle et al., 2007 |
X
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/ZAI/1/82 | AF367100 | Bastos et al., 2003 |
- | - | SAT2/UGA/19/98 | AY343969 | Sahle et al., 2007 |
XI
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/ANG/4/74 | AF479417 | Bastos et al., 2003 |
XII
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/UGA/51/75 | AY343963 | Sahle et al., 2007 |
XIII
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/SUD/6/77 | AY343939 | Sahle et al., 2007 |
- | - | SAT2/ETH/2/2007 | FJ798161 | Ayelet et al., 2009 |
XIV
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT2/ETH/2/91 | AY343938 | Sahle et al., 2007 |
The SAT 3 serotype is divided into fivetopotypes: I to V.
I (SOUTHEAST ZIMBABWE, SEZ)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT3/SA/57/59 | AY593850 | Carrillo et al., 2005 |
- | - | SAT3/KNP/10/90/3* | AF286347 | van Rensburg et al., 2002 |
II (WESTERN ZIMBABWE, WZ)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT3/BEC/1/65 | AY593853 | Carrillo et al., 2005 |
- | - | SAT3/BEC/20/61 | AY593851 | Carrillo et al., 2005 |
III (NORTHWEST ZIMBABWE, NWZ)
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT3/ZIM/P25/91 (UR-7) | KY091306 | Knowles et al., 2016a |
IV
Lineage | Sub-lineage | Isolate name | Accession no. | Reference |
---|---|---|---|---|
- | - | SAT3/ZAM/P2/96 (MUL-4) | DQ009741 | Maree et al., unpub. |
V (East Africa, EA)