FMD prototype strains

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.

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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).

These sequences are available in FASTA format


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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).

These sequences are available in FASTA format


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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 three topotypes: EUROPE-SOUTH AMERICA (EURO-SA), ASIA and AFRICA.

These sequences are available in FASTA format


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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.

These sequences are available in FASTA format


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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.

These sequences are available in FASTA format


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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.

These sequences are available in FASTA format


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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 five topotypes: I to V.

These sequences are available in FASTA format


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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)

Lineage Sub-lineage Isolate name Accession no. Reference
- - SAT3/UGA BUFF/27/70
(aka UGA/92/70)
KF219685 Stirling and Knowles, unpub.
- - SAT3/UGA/2/97/3* DQ009742 Maree et al., unpub.

 

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