WRLFMD Quarterly Report October-December 2014 Reference Laboratory Contract Report Foot-and-Mouth Disease

Summary of samples tested and reported FMD outbreaks

ASIA Bahrain Three samples were received by the WRLFMD from the Northern Governorate of Bahrain, collected from cattle during October 2014. Viruses isolated from all three samples were identified as FMD type O virus. Genotyping showed them to belong to the ME-SA topotype, ANT-10 PanAsia-2 lineage (see below).

Hong Kong SAR, P.R. China Two samples submitted to the WRLFMD from Sheung Shui, New Territories, collected from th pigs on 25 November 2014. One was found to contain FMD type O virus but only FMDV genome could be detected in the other. Genotyping showed the former to belong to the CATHAY topotype and to be closely related to viruses present in Hong Kong SAR since 2010 (see below). People’s Republic of China Two outbreaks due to FMD type A were reported on 08/10/2014 and 15/12/2014 at Shannan, Tibet and Lasa, Tibet, respectively, both in cattle. On 18/11/2014 a single outbreak of FMD type O was reported in pigs in Dongdai, JiangSu Province. No genotyping has been reported for any of these outbreaks.

Republic of Korea (South Korea) In December three outbreaks of FMD type O were reported in pigs in Chungcheongbuk-do (two outbreaks) and Chungcheongnam-do (one outbreak). VP1 sequencing at the Animal and Plant Quarantine Agency (ROK) showed that the virus from the first outbreak belonged to the SEA topotype, Mya-98 lineage (see below). The results of 10 samples received by the nd WRLFMD on 22 December 2014 are pending.

Vietnam Thirty two samples were submitted to the WRLFMD. These had been collected from cattle, water buffalo and pigs between December 2013 and July 2014. FMD type O virus was isolated from 12 samples, type A from 13 samples and FMDV genome was detected by realtime RT-PCR in the remaining seven samples. VP1 genotyping revealed seven of the type O viruses belonged to the ME-SA topotype, PanAsia lineage and five to the SEA topotype, Mya98 lineages. All the type A viruses belonged to the ASIA topotype, Sea-97 lineage (see below).

AFRICA Algeria Two outbreaks of FMD type O were reported to have occurred in cattle in late September 2014 in the M'Sila and Ain Defla provinces.

Botswana On 27/10/2014 an outbreak due to FMD type SAT 1 was reported in cattle at Tjaa crush, Tubu, Gumare, Ngamiland. No genotyping has been reported. Four samples were received

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

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from the BVI collected from cattle on 26/06/2014 at Mohembo East, Shakawe, Ngamiland. FMD type SAT 1 was identified in three samples and genotyping showed them to belong to topotype III (WZ) (see below). Six samples were received from the BVI collected from cattle between February and June 2013 in the Maun area of Ngamiland. FMD type SAT 2 was identified in two of these (from 20/02/2013). VP1 genotyping showed these to belong to topotype III (see below).

Egypt Twenty eight samples were received by the WRLFMD from cattle and water buffalo collected in various locations in the country between May 2012 and October 2014. FMD type O was isolated from nine samples collected between April and October 2014 and VP1 genotyping showed them all to belong to the EA-3 topotype (see below). FMD type A was isolated from four samples; one collected in May 2012 and two in March 2013 and one in May 2014. VP1 genotyping showed the virus from 2012 to belong to the AFRICA topotype, G-IV lineage while BAR-08 to other three viruses belonged to the ASIA topotype, Iran-05 lineage (see below). FMD type SAT 2 was isolated from two samples collected in May 2012 and April 2014. VP1 genotype showed them to belong to topotype VII, the former falling within the Ghb-12 lineage and the latter in the Alx-12 lineage (see below).

Ethiopia Sixteen samples were received by the WRLFMD. Half were sera collected from sheep and half tissue suspensions from samples collected from cattle. No virus was detected in any of the sheep sera. FMDV genome was detected in seven of the tissue suspensions, but no viruses could be typed by ELISA or isolated in cell cultures. RT-PCR amplification of the VP1coding region was successful in two samples (ETH/6/2014 and ETH/10/2014), although only a faint band was present in the latter sample. Both samples were identified as FMD type O. Phylogenetic analysis of ETH/6/2014 showed it to belong to the EA-3 topotype; insufficient sequence data was obtained to conclusively identify the genotype of ETH/10/2014.

Mali A partial VP1 sequence was received to WRLFMD from RRLSSA - BVI (Botswana) for a virus collected during 2014. Phylogenetic analysis showed that this sequence was derived from a SAT 2 serotype FMD virus (within topotype VII) most closely related to FMD viruses previously recovered from Nigeria in 2012.

Mozambique Four samples were received from the BVI (Botswana) collected from outbreaks in cattle in Maputo on 24/07/2014. All were identified as FMD type SAT 2. VP1 genotyping showed them to belong to topotype I as previously described by the BVI (see below).

Namibia On 01/12/2014 an outbreak due to FMD type SAT 2 was reported at in cattle at Linyati, Caprivi. Genotyping by the BVI (two VP1 sequences were received on 11/12/2014) showed viruses from Kikiya Crush, East Caprivi to belong to topotype III (see below).

South Africa Two outbreaks of FMD type SAT 2 were reported to have occurred in June 2014 in cattle in Bushbuckridge, Mpumalanga within South Africa's FMD protection zone where routine

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

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vaccination is practised. There have been a number of outbreaks in this area since August 2013.

Tunisia Sixteen new outbreaks of FMD type O were reported to have occurred between June and September 2014 in cattle, sheep and goats in eight provinces (Ariana, Beja, Ben Arous, Jendouba, Kasserine, Mannouba, Nabeul and Zaghouan).

Zimbabwe Thirteen samples were received from the BVI which had been collected from cattle between July 2010 and September 2014 at various locations. FMD type SAT 2 was isolated from six of the samples, three from 2010 and three from 2014. VP1 genotyping showed five of these to belong to toptype I (at least two distinct unnamed lineages), but one sample from Mwenezi District, Masvingo Province (collected in May 2014) belonged to topotype II (see below).

SOUTH AMERICA No new outbreaks of FMD were reported in the region.

Uncharacterised FMD viruses A number of outbreaks have occurred where samples have not been sent to the WRLFMD. It is probable that the countries involved have performed their own genetic characterisation; however, through the OIE/FAO laboratory network we would also like to encourage the submission of samples (or complete VP1 sequences) to the WRLFMD.

An up-to-date list and reports of FMD viruses characterised by sequencing can be found at the following website: http://www.wrlfmd.org/fmd_genotyping/2014.htm.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

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Results from samples received at WRLFMD (status of samples being tested) are shown in Table 1 (below) and a complete list of clinical sample diagnostics made by the WRLFMD between October and December 2014 is shown in Table 2 (Annex 1). A record of all samples received by WRLFMD (October and December 2014) is shown in Table 3 (Annex 1). Table 1: Status of sequencing of samples received by the WRLFMD from October to December 2014. WRLFMD Batch Date No. received WRLFMD/2014/0 13-Oct-14 0031 WRLFMD/2014/0 13-Oct-14 0031 WRLFMD/2014/0 13-Oct-14 0032 WRLFMD/2014/0 13-Oct-14 0033 WRLFMD/2014/0 28-Oct-14 0035 WRLFMD/2014/0 28-Oct-14 0035 WRLFMD/2014/0 4-Nov-14 0036 WRLFMD/2014/0 4-Nov-14 0037 WRLFMD/2014/0 4-Nov-14 0037 WRLFMD/2014/0 4-Nov-14 0037 WRLFMD/2014/0 27-Nov-14 0038 WRLFMD/2014/0 11-Dec-14 0039 WRLFMD/2014/0 22-Dec-14 0040

Country

Serotype

No. of samples

No. of sequences

Sequencing status

Botswana

SAT 1

3

3

Completed

Botswana

SAT 2

2

2

Completed

Mozambique

SAT 2

4

4

Completed

Zimbabwe

SAT 2

6

6

Completed

Vietnam

A

13

13

Completed

Vietnam

O

12

12

Completed

Bahrain

O

3

3

Completed

Egypt

A

4

4

Completed

Egypt

O

9

9

Completed

Egypt

SAT 2

2

2

Completed

Ethiopia

O

2

2

Completed

Hong Kong SAR

O

1

1

Completed

South Korea

Pending

10 71

Pending 61

During this reporting period, additional sequences were received to WRLFMD via RRLSSA-BVI (Botswana) for samples collected in Namibia and Mali.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

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Detailed Analysis ASIA

Figure 1: Bahrain WRLFMD/2014/00036 Date received: 04/11/2014 No. of samples: 3 ANT-10 O (ME-SA/PanAsia-2 ): 3

O/PAK/8/2010 O/KHI/PAK/42/2011* (JX170757) O/PAK/5/2010 O/PAK/2/2010 O/PAK/1/2010 O/AFG/242/2010 O/IRN/88/2009 O/PAK/3/2010 O/IRN/4/2010 O/IRN/30/2010 O/PAK/4/2010 O/KHI/PAK/41/2011* (JX170756) O/AFG/104/2010 O/PAK/21/2010 82 O/PAK/22/2010 O/IRN/3/2010 O/IRN/64/2010 77 O/TUR/39/2010 O/IRN/139/2010 O/AFG/110/2010 O/IRN/149/2010 95 O/IRN/83/2010 O/IRN/35/2010 O/AFG/59/2010 O/AFG/61/2010 O/AFG/89/2010 O/IRN/96/2010 99 O/AFG/111/2010 O/IRN/207/2010 O/BAR/1/2014 94 O/BAR/3/2014 O/BAR/2/2014 O/PAK/11/2014 74 O/PAK/13/2014 O/PAK/15/2014 100 O/PAK/16/2014 O/PAK/4/2014 O/PAK/12/2014 O/PAK/3/2014 O/PAK/27/2013 O/PAK/21/2014 O/PAK/2/2014 O/PAK/5/2014 O/PAK/58/2012 O/PAK/23/2014 O/PAK/26/2013 O/PAK/18/2014 O/PAK/24/2014 O/PAK/14/2014 O/PAK/6/2014 93 O/PAK/7/2014 O/TUR/257/2008* (FMDI) 99 O/TUR/264/2009* (FMDI) O/IRN/8/2005 O/IRN/31/2009 O/IRN/18/2010 O/PAK/16/2010

BAR/1/2014 BAR/2/2014 BAR/3/2014

O

1. Capital Governorate 2. Central Governorate 3. Muharraq Governorate 4. Northern Governorate 5. Southern Governorate

75

80

89

99 100

100 100 100

77 77

TER-08 SAN-09 FAR-09 BAL-09 PUN-10

SEA EA-2 EA-3 EA-4

100

100

ME-SA

O/IND/53/79 (AF292107) O/IND/R2/75* (AF204276) O1/Manisa/TUR/69 (AY593823)

91 90

PanAsia-2

PanAsia Ind-2001

98

73

ANT-10

WA EA-1 CATHAY ISA-1 ISA-2 EURO-SA

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

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Figure 2: Hong Kong SAR WRLFMD/2014/00039 Date received: 11/12/2014 No. of samples: 2 O (CATHAY/unnamed): 1 FMDV-GD: 1 HKN/14/2014

O/HKN/7/2014 O/HKN/8/2014 O/HKN/13/2014 O/HKN/11/2014 97 O/HKN/15/2014 O/HKN/5/2014 98 O/HKN/4/2014 72 O/HKN/6/2014 95 O/HKN/1/2013 (KM243172) O/HKN/6/2011 (KM243168) O/HKN/4/2011 (KM243166) 74 O/HKN/3/2011 (KM243165) 100 O/HKN/5/2011 (KM243167) O/HKN/7/2011 (KM243169) O/HKN/8/2011 (KM243170) 98 71 O/HKN/9/2011 (KM243171) O/HKN/26/2010 (KM243164) O/HKN/3/2008 (KM243157) O/HKN/4/2008 (KM243158) 99 O/HKN/1/2008 (KM243155) 83 O/HKN/2/2008 (KM243156) 85 O/HKN/1/2009 (KM243159) 96 O/HKN/2/2009 (KM243160) O/HKN/3/2007 (KM243152) 100 O/HKN/4/2007 (KM243153) O/HKN/5/2006 (KM243148) O/HKN/6/2006 (KM243149) O/HKN/2/2006 (KM243145) 79 O/HKN/1/2006 (KM243144) O/HKN/4/2006 (KM243147) 75 O/HKN/24/2005 (KM243142) O/HKN/22/2005 (KM243140) 92 O/HKN/23/2005 (KM243141) O/HKN/3/2006 (KM243146) O/HKN/25/2005 (KM243143) O/HKN/18/2005 (KM243136) O/HKN/19/2005 (KM243137) 89 O/HKN/20/2005 (KM243138) O/HKN/14/2005 (KM243133) 98 O/HKN/9/2005 (KM243129) O/HKN/10/2005 (KM243130) O/HKN/12/2004 (DQ164889) 78 O/HKN/9/2004 (DQ164886) O/HKN/12/2005 (KM243132) O/HKN/6/2004 (DQ164883) 100 O/HKN/7/2004 (DQ164884) O/HKN/10/2004 (DQ164887) 70 88 O/HKN/13/2004 (KM243126) O/HKN/19/2001 (DQ164876) O/HKN/1/2002 (DQ164877) 99 99 O/HKN/2002 (AF525458) O/PHI/7/96 (AJ294926KM243058) O/Yunlin/TAW/97 (AF308157) O/HKN/6/83 (AJ294919) O/HKN/21/70 (AJ294911) 87

O FMDV-GD

8 km 4 mi

© d-maps.com

HKN/15/2014

99

98

79 71

CATHAY

EURO-SA ISA-2 ISA-1 EA-2 WA EA-1 EA-4 EA-3 SEA ME-SA 100

100 100 100

99

99

70 99 80

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

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Figure 3: Republic of Korea (South Korea) WRLMEG/2014/00038 VP1 sequence received from Animal and Plant Quarantine Agency Date received: 04/12/2014 No. of sequences: 1 O (SEA/Mya-98): 1

O/SKR/10/2010 O/SKR/12/2010 (KC438373) O/RUS/Jul 2010 (JQ070329) O/SKR/5/2010 (JQ070321) O/SKR/6/2010 94 O/Andong 1/SKR/2010 (NVRQS) O/DRK/31/2011 O/SKR/7/2010 O/SKR/13/2010 O/Paju/SKR/2010 (NVRQS) 87 O/SKR/1/2011 O/SKR/3/2011 90 O/CHA/31/2010* (JF792356) O/BY/CHA/2010 (JN998085) O/TZ/CHA/2010 (HQ652081) 93 O/JPN/MZ1/2010 (AB618503) O/Yeoncheon/SKR/2010 (NVRQS) O/Yangju/SKR/2010 (NVRQS) 7586 O/SKR/8/2011 O/HKN/7/2010 (JQ070303) O/HKN/8/2010 O/HKN/13/2010 O/HKN/14/2010 88 O/HKN/15/2010 O/HKN/9/2010 (JQ070304) O/HKN/10/2010 O/HKN/11/2010 O/HKN/12/2010 O/33-P/CHA/2010 (JQ973889) O/SKR/4/2010 (JQ070320) 77 81 O/KOR/1/2010* (HM143846) O/GZ/CHA/2010 (JN998086) O/MY/CHA/2010 (HQ652079) O/VN/LC169/2009 (HM055510) 99 O/HKN/19/2010 (JQ070305) 71 O/HKN/20/2010 (HM229661) 85 O/NC/CHA/2010 (HQ652080) O/GSLX/CHA/2010 (JQ900581) O/VN/YB10/2010 (HQ260720) O/VIT/NCVD-8/2010 (NVRQS) O/VN/YB08/2010 (HQ260718) 100 O/VIT/NCVD-9/2010 (NVRQS) O/VN/YB09/2010 (HQ260719) O/VIT/NCVD-19/2010 (NVRQS) 99 O/VIT/NCVD-20/2010 (NVRQS) O/GZ-MT/CHA/2013 (KJ646655) O/JC/CB/ROK/2014 (APQA) 97 O/Primorskiy/RUS/2014 (ARRIAH) 99 O/SKR/6/2014 81 100 O/SKR/01/2014* (APQA) O/MYA/7/98 (DQ164925) O/TAI/189/87* (TRRL) 95

Gangwon-do Incheon Seoul Gyeonggi-do JC/CB/ROK/2014

Chungcheongbuk-do (Northern Chungcheong) Chungcheongnam-do Gyeongsangbuk-do (Southern Chungcheong) Daejeon (Northern Gyeongsang)

Jeollabuk-do (Northern Jeolla)

Daegu

Gyeongsangnam-do Ulsan (Southern Gyeongsang) Busan Gwangju Jeollanam-do (Southern Jeolla)

O

50 km

Jeju-teukbyeoljachido (Jeju-do)

30 mi © Daniel Dalet / d-maps.com

98

87

82

Mya-98

SEA

Cam-94 100 78 99 99

100 86

100

100

100

WA EA-1 EA-4 EA-3 EA-2 ME-SA EURO-SA ISA-2 ISA-1 CATHAY

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

8

Figure 4: Vietnam WRLFMD/2014/00035 Date received: 28/10/2014 No. of samples: 32 O (SEA/Mya-98): 5 O (ME-SA/PanAsia): 7 A (ASIA/Sea-97): 13 FMDV-GD: 7 VIT/4/2014 VIT/5/2014

VIT/8/2014 Cao Bang

Hà Giang Lai Châu

Băc Kan

Lao Cai

Đien Biên

VIT/9/2014 VIT/11/2014 VIT/12/2014

VIT/2/2014

Thái Nguyên Bac Giang

Lang Son

Yên Bái Son La

BN : Bac Ninh H : Ha Noi HNa : Ha Nam HTa : Hà Tây HY : Hung Yen

H. BN. HTa. HY. Hoa

Binh

Phú Tho

VIT/10/2014

HNa.

Vinh Phúc Thanh Hoa

Hai Phong Hai Duong Thai Binh Nam Dinh Ninh Bình

VIT/3/2014 VIT/6/2014 VIT/7/2014

Nghe An

99

VIT/62/2013 VIT/63/2013

Hà Tinh

Quang Tri

O A FMDV-GD

VIT/26/2014 VIT/27/2014

Thua Thiên-Hue Da Nang

VIT/13/2014 VIT/21/2014

VIT/14/2014 VIT/15/2014 VIT/19/2014 VIT/20/2014

Quang Nam

VIT/64/2013

Quang Ngãi Kon Tum

VIT/18/2014

VIT/22/2014 Gia Lai

VIT/1/2014

Phú Yên Đak Lak

Đong Tháp An Giang Can Tho

VIT/16/2014 VIT/28/2014 VIT/17/2014 VIT/29/2014

Kiên Giang Hau Giang

Đak Nông

Binh Duong

Long An

Tay Ninh

Bình Phuoc

Lâm Dong

94

Ninh Thuan

Dong Nai

Bà Ria–Vung Tàu Ho Chi Minh Tien Giang Ben Tre Trà Vinh Vinh Long Cà Sóc Trang Mau Bac Liêu

A/LAO/1/2014 A/LAO/2/2014 A/LAO/3/2014 A/VIT/62/2013 88 A/VIT/63/2013 A/TAI/21/2013 A/VIT/58/2013 A/TAI/1/2014 71 A/TAI/2/2014 A/TAI/3/2014 A/TAI/17/2013 71 A/TAI/20/2013 A/MAY/17/2013 A/MAY/20/2013 71 92 A/MAY/21/2013 A/VIT/14/2014 98 A/VIT/15/2014 A/VIT/49/2013 A/VIT/1/2014 A/VIT/64/2013 A/VIT/55/2013 99 A/VIT/60/2013 A/VIT/56/2013 A/VIT/19/2014 96 A/VIT/20/2014 A/VIT/42/2013 A/VIT/53/2013 A/VIT/2/2014 A/VIT/35/2013 A/VIT/54/2013 A/VIT/3/2014 A/VIT/59/2013 100 A/VIT/6/2014 A/VIT/7/2014 A/VIT/8/2014 A/TAI/4/2014 A/TAI/16/2013 86 A/TAI/12/2013 A/TAI/14/2013 A/TAI/15/2013 A/TAI/7/2003 (HQ116312)

150 km 100 mi

99

O/IND/53/79 (AF292107) O/IND/R2/75* (AF204276) O1/Manisa/TUR/69 (AY593823) O/CAM/3/98 (AJ294910) O/TAI/189/87* (TRRL) O/MYA/7/98 (DQ164925) O/LAO/1/2013 76 O/LAO/2/2013 O/MAY/25/2012 O/MAY/1/2013 74 O/TAI/18/2012 98 O/TAI/14/2012 O/MAY/34/2012 89 O/MAY/9/2014 O/MAY/2/2014 85 O/VIT/21/2014 O/VIT/26/2014 O/VIT/27/2014 O/VIT/13/2014 84 O/VIT/18/2014 O/MAY/20/2009 (HQ116218) 99 O/VN/HB166/2009 (HM055499) O/TAI/19/2009 (HQ116266) O/VIT/2/2010 (JQ070322) O/MAY/25/2009 87 O/MAY/26/2009 O/LAO/1/2010 99 O/VN/SL02/2010 (HQ260714) O/VN/SL191/2009 (HM055507) O/VN/SL192/2009 (HM055508) O/VN/SL186/2009 (HM055505) O/TAI/12/2009 (HQ116260) O/MAY/22/2009 O/TAI/13/2009 (HQ116261) O/TAI/15/2009 (HQ116262) O/TAI/16/2009 (HQ116263) O/TAI/17/2009 (HQ116264)

71

79

90

99

90

89

76

Sea-97

ASIA

74 76 72 99

87 99

99

Sea-97

99

A22

100 87 99

A15 Iran-05

AFRICA EURO-SA

99

99

Thai-87 A/TAI/2/97 (EF208778)

PanAsia

ME-SA

Ind-2001 PanAsia-2

98

VIT/25/2014 © d-maps.com

VIT/23/2014 VIT/24/2014

O/VIT/9/2014 O/VIT/12/2014 O/VIT/11/2014 O/VIT/40/2013 O/VIT/51/2013 O/VIT/46/2013 O/VIT/47/2013 O/CAM/2/2013 89 O/CAM/3/2013 94 O/VIT/32/2013 O/VIT/33/2013 O/Zabaikalsky/RUS/2014* (ARRIAH) O/MOG/4/2014 O/MOG/2/2014 O/MOG/5/2014 O/MOG/1/2014 O/MOG/3/2014 74 O/VIT/13/2013 O/VIT/15/2013 O/VIT/38/2013 99 O/VIT/11/2013 86 O/VIT/12/2013 95 O/VIT/14/2013 O/VIT/16/2013 83 O/VIT/36/2013 O/VIT/39/2013 O/VIT/4/2010 O/CAM/4/2010 O/VIT/8/2010 97 O/VIT/7/2010 O/CAM/2/2010 O/VIT/24/2013 O/VIT/27/2013 O/VIT/28/2013 99 O/VIT/22/2013 O/VIT/23/2013 70 97 O/VIT/30/2013 O/VIT/31/2013 O/VIT/16/2014 81 90 O/VIT/28/2014 97 O/VIT/23/2014 98 O/VIT/24/2014 O/UKG/35/2001 (AJ539141)

99

ME-SA Cam-94

SEA Mya-98

EURO-SA ISA-2 ISA-1 CATHAY

EA-2 EA-3 EA-4 WA EA-1

0.02

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

9

AFRICA Figure 5: Botswana WRLFMD/2014/00031 Date received: 13/10/2014 No. of samples: 10 SAT 1 (III-WZ): 3 SAT 2 (III): 2 FMDV-GD: 3 NVD: 2

BOT/2/2014 BOT/3/2014 BOT/4/2014 BOT/1/2014

BOT/1/2013 BOT/2/2013

Ngamiland

BOT/3/2013 BOT/4/2013 BOT/5/2013 BOT/6/2013

North-East Central Ghanzi

Kweneng

Kgatleng

Kgalagadi Southern South-East © Daniel Dalet / d-maps.com

150 km 100 mi

100

SAT1/BOT/14/2006 SAT1/BOT/18/2006 70 SAT1/BOT/13/2006 SAT1/BOT/12/2006 99 SAT1/BOT/16/2006 SAT1/BOT/17/2006 100 SAT1/BOT/15/2006 SAT1/BOT/20/2006 buffalo 91 SAT1/BOT/22/2006 buffalo SAT1/BOT/P3/2000 buffalo NGO-2 90 SAT1/NMB/1/2000 SAT1/ZAM/6/2012 SAT1/ZAM/7/2012 99 100 SAT1/ZAM/8/2012 SAT1/ZAM/9/2012 SAT1/BOT/P3/2000 buffalo NGO-13 76 SAT1/ZAM/4/2000 SAT1/SWA/2/89* buffalo SAT1/BOT/3/2014 SAT1/BOT/5/2014 (BVI) SAT1/BOT/4/2014 100 SAT1/BOT/6/2014 (BVI) SAT1/BOT/2/2014 SAT1/NAM/307/98* (AY770519) 100 SAT1/NAM/307/98* (DQ009717) 83 SAT1/BOT/17/77 kudu (KF219687) 100 SAT1/BOT/24/77 (KF219688) SAT1/BOT/1/77 (KF219686) SAT1/BOT-BUFF/62/74 buffalo SAT1/BOT/1/68 (AY593845) SAT1/SWA/80/62 SAT1/SWA/40/61 100 99 SAT1/SWA/40/61 (AY593843) SAT1/SA/13/61 (AY593842) SAT1/ZIM/P1/2004 (D19) SAT1/ZIM/5/2003 100 SAT1/ZIM/2/2003 97 SAT1/ZIM/4/2003 SAT1/ZIM/13/2003 89 SAT1/ZIM/20/2003 SAT1/ZIM/21/2003 SAT1/BEC/1/48 (AY593838)

100

III (WZ)

99

99

95

95

99

II (SEZ) I (NWZ) IV (EA-1)

98

XI II

92

V

99

IX

90

VI X

97 82

V 99 98 100

III

IV I

73

VIII (EA-3)

75

SAT2/BOT/5/2007 SAT2/BOT/6/2007 SAT2/BOT/3/2007 SAT2/BOT/2/2007 SAT2/BOT/7/2008 95 SAT2/BOT/11/2008 SAT2/BOT/9/2008 SAT2/BOT/16/2008 88 SAT2/BOT/18/2008 SAT2/BOT/10/2008 SAT2/BOT/6/2008 74 SAT2/BOT/8/2008 SAT2/BOT/2/2009 SAT2/BOT/3/2009 99 SAT2/BOT/4/2009 SAT2/BOT/1/2011 SAT2/BOT/2/2011 99 SAT2/BOT 02/11* (BVI) 96 SAT2/BOT/6/2009 SAT2/BOT/7/2009 99 SAT2/BOT/8/2009 SAT2/BOT/5/2009 SAT2/BOT/9/2012 SAT2/BOT/17/2012 SAT2/BOT/16/2012 SAT2/BOT/14/2012 99 SAT2/BOT/11/2012 SAT2/BOT/8/2012 SAT2/BOT/12/2012 SAT2/BOT12/12* (BVI) SAT2/BOT/10/2012 SAT2/BOT/13/2012 SAT2/BOT/15/2012 SAT2/BOT/18/2012 SAT2/BOT14/12* (BVI) SAT2/BOT/20/2012 95 SAT2/BOT/21/2012 SAT2/BOT/19/2012 SAT2/BOT/1/2013 97 SAT2/BOT/2/2013 SAT2/BOT/4/2012 99 97 SAT2/BOT/6/2012 SAT2/BOT/3/2012 SAT2/BOT/2/2012 SAT2/BOT/1/2012 76 SAT2/BOT/5/2012 70 SAT2/BOT/7/2012 SAT2/BOT/P3/98 buffalo NXA-7 99 SAT2/BOT/P3/98 buffalo NXA-16 SAT2/BOT/P3/98 buffalo 29 (AF367124) SAT2/RHO/1/48 (AY593847)

XII

VII (EA-2) VI

IX

98 74

99

XIII

74

XIV 99

0.05

99

VII VIII

0.05

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

10

Figure 6a: Egypt WRLFMD/2014/00037 Date received: 04/11/2014 No. of samples: 28 O (EA-3): 9 A (AFRICA/G-IV): 1 BAR-08 A (Iran-05 ): 3 SAT 2 (VII/ Ghb-12): 1 SAT 2 (VII/Alx-12): 1 FMDV-GD: 3 No FMDV GD: 10

89

EGY/23/2014 EGY/43/2012 EGY/37/2014 EGY/29/2014 EGY/34/2014 EGY/27/2014 EGY/38/2014 EGY/36/2014 EGY/33/2014 EGY/32/2014 EGY/39/2014 Kafr el-Sheikh EGY/40/2014 Damietta Dakahlia EGY/41/2014 Gharbia Port Said EGY/30/2013 EGY/42/2014 Alexandria EGY/31/2013 EGY/43/2014 EGY/44/2014 Sharqia Beheira North Sinai EGY/45/2014 Ismailia Monufia EGY/28/2014 EGY/46/2014 Matrouh

Qalyubia Cairo

EGY/24/2014 Suez

Faiyum

EGY/30/2014 South Sinai

EGY/42/2012

Beni Suef

EGY/25/2014 EGY/26/2014

Giza Minya

EGY/31/2014 Asyut

EGY/35/2014 Sohag

Qena Luxor

Red Sea New Valley

O A SAT 2 FMDV-GD NVD

© Daniel Dalet / d-maps.com Aswan

200 km 100 mi

100

100 99

92

86

99

77

99 100 100

92 77

O/ERI/16/2011 O/ETH/59/2011 O/ERI/13/2011 O/ERI/12/2011 O/ERI/11/2011 O/ERI/3/2011 O/ERI/2/2011 O/ERI/1/2011 O/ERI/14/2011 O/ERI/15/2011 100 O/EGY/25/2012 88 O/LIB/54/2012 O/ETH/28/2011 100 O/SUD/5/2008 (GU566061) O/SUD/6/2008 (GU566062) O/SUD/1/2010 88 O/SUD/3/2008 (GU566059) 96 100 O/SUD/4/2008 (GU566060) O/SUD/3/99 (GU566043) 100 O/SUD/4/99 (GU566044) O/SUD/1/99 (DQ165076) O/SUD/12/2004 (GU566049) O/SUD/25/2004 (GU566053) O/SUD/30/2004 (GU566055) 99 O/SUD/9/2004 (GU566048) 74 O/SUD/4/2004 (GU566047) O/SUD/14/2004 (GU566050) O/SUD/15/2004 (GU566051) O/SUD/16/2004 (GU566052) O/SUD/3/2004 (GU566046) O/SUD/1/2004 (GU566045) O/SUD/26/2004 (GU566054) O/SUD/8/2008 (GU566063) 90 O/SUD/11/2011 O/EGY/29/2014 O/EGY/32/2014 71 O/EGY/34/2014 99 85 O/EGY/36/2014 O/EGY/27/2014 O/EGY/25/2014 O/EGY/26/2014 99 O/EGY/28/2014 O/EGY/10/2014 O/EGY/25/2013 99 O/EGY/28/2013 O/EGY/29/2013 O/EGY/6/2014 O/EGY/23/2014 O/EGY/18/2014 O/EGY/24/2013 O/EGY/1/2014 O/EGY/5/2014 O/EGY/3/2014 O/EGY/4/2014 O/SUD/2/86 (DQ165075)

EA-3

EA-2 WA EA-1 SEA ME-SA EA-4 CATHAY ISA-1 100 ISA-2 EURO-SA

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

11

Figure 6b: Egypt (continued)

97

100

92

A/PAT/11/2013 A/PAT/12/2013 A/PAT/10/2013 A/EGY/21/2013 A/EGY/31/2013 A/EGY/11/2013 A/EGY/13/2013 A/EGY/15/2013 A/EGY/19/2013 A/EGY/12/2013 A/EGY/14/2013 A/EGY/30/2013 A/EGY/3/2013 A/EGY/22/2013 78 A/EGY/5/2013 A/EGY/6/2013 100 A/EGY/17/2013 A/EGY/31/2014 A/LIB/1/2009 A/LIB/10/2009 A/ISR/1/2009 A/PAT/6/2009 A/KUW/5/2009 99 A/BAR/6/2008 (FJ755010) A/4257/IRQ/2009 (PIADC) (JN099701) A/IRN/11/2009 79 A/IRN/12/2009 A/AFG/6/2007 (FJ755007) A/IRN/125/2010 A/IRN/78/2009 A/AFG/10/2010 A/IRN/1/2011 A/IRN/15/2012 A/TUR/3/2010 A/IRN/9/2010 A/TUR/1/2008 (FJ755133) A/IRN/1/2005 (EF208769) A/TUR/33/2008 (FJ755155) A/IRN/9/2011

BAR-08

Iran-05

ASIA

100 80

AFG-07 SIS-10 FAR-09 HER-10 FAR-11 SIS-12 KSS-09 ESF-10 ARD-07 EZM-07 QAZ-11

97

Sea-97 Iran-96 Iran-99 Iran-87 A22 A15

100 95

99

G-VII G-II G-V G-VI G-III G-I

98

96

100

98

VII

Lib-03

Alx-12

VIII

98

IX XII X XI V

70 90 100

A/SUD/3/77 (GU566064) A/ERI/5/2006 89 A/ERI/16/2009 A/ERI/4/2007 74 A/ERI/1/2008 74 A/SUD/1/2006 (GU566069) A/ERI/1/2006 100 A/ERI/5/2008 A/SUD/3/2006 (GU566070) A/SUD/1/2011 A/SUD/6/2011 A/SUD/13/2011 99 A/SUD/7/2011 83 A/SUD/12/2011 91 A/EGY/18/2012 A/EGY/20/2012 84 A/EGY/1/2012 A/EGY-B-2012* A/EGY-5-2012* 99 A/EGY/30/2012 99 78 A/EGY/42/2012

Ghb-12

XIV XIII

76

EURO-SA

99

SAT2/EGY/29/2012 (KF112936) SAT2/PAT/1/2012 (JX570637) SAT2/EGY/31/2012 (KF112937) SAT2/EGY/15/2012 (JX570627) SAT2/EGY/14/2012 (JX570626) SAT2/EGY/4/2012 (JX570619) SAT2/EGY/5/2012 (JX570620) SAT2/EGY/6/2012 (JX570621) SAT2/EGY/21/2012 (KF112933) SAT2/EGY/23/2012* (JX013980) SAT2/EGY/10/2012 (JX570623) SAT2/EGY/22/2012 (KF112934) SAT2/EGY/7/2012* (JX013978) SAT2/EGY/28/2012 (KF112935) 89 SAT2/EGY/43/2012 SAT2/EGY/3/2012 (JX570618) SAT2/EGY/26/2012* (JX013979) SAT2/EGY/13/2012 (JX570625) 100 SAT2/EGY/16/2012 (KF112931) 96 SAT2/EGY/17/2012 (KF112932) SAT2/EGY/9/2012 (JX570622) SAT2/EGY/11/2012 (JX570624) 100 SAT2/LIB/1/2003 (JX570631) SAT2/LIB/7/2003 (JX570632) SAT2/CAR/8/2005 (JX570616) SAT2/CAR/29/2013 SAT2/CAR/42/2013 100 SAT2/CAR/24/2013 SAT2/CAR/6/2013 95 SAT2/CAR/43/2013 SAT2/SAU/6/2000 (AF367135) SAT2/EGY/2/2012 (JX570617) SAT2/SUD/4/2010 (KF112968) SAT2/EGY/11/2014 88 SAT2/EGY/24/2014 100 SAT2/EGY/20/2014 81 SAT2/EGY/22/2014

VI 98

II I

92 89 100

AFRICA

III IV

0.05

G-IV

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

12

Figure 7: Ethiopia WRLFMD/2014/00038 Date received: 27/11/2014 No. of samples: 16 O (genome only) (EA-3): 2 FMDV-GD: 5 NVD: 9

Tigray

Afar Amhara

BenishangulGumuz

Dire Dawa

ETH/10/2014 ETH/8/2014 ETH/9/2014

Addis Ababa

ETH/11/2014 ETH/12/2014 ETH/13/2014 ETH/14/2014 ETH/15/2014 ETH/16/2014 ETH/17/2014 ETH/18/2014

Harari

Gambela Oromia ETH/7/2014

Somali

Southern Nations

ETH/6/2014 ETH/3/2014 ETH/4/2014 ETH/5/2014

O (GD only) FMDV-GD NVD 99

100

100

88

O/ETH/18/2012 O/ETH/19/2012 O/ETH/15/2012 O/ETH/17/2012 O/ETH/9/2011 95 O/ETH/10/2011 O/ETH/16/2012 O/ETH/11/2012 O/ETH/11/2011 73 O/ETH/12/2011 O/ETH/12/2012 O/ETH/46/2011 O/ETH/3/2011 76 O/ETH/4/2011 92 O/ETH/5/2011 O/ETH/42/2011 O/ETH/45/2011 O/ETH/13/2011 O/ETH/18/2011 O/ETH/38/2011 O/ETH/24/2012 O/ETH/22/2012 100 O/ETH/25/2012 O/ETH/45/2009 77 O/ETH/7/2010 O/ETH/8/2010 O/ETH/2/2011 O/ETH/32/2011 94 O/ETH/1/2011 O/ETH/7/2011 O/ETH/29/2011 O/ETH/34/2011 97 O/ETH/48/2011 O/ETH/50/2011 O/ETH/49/2011 O/ETH/51/2011 O/ETH/6/2014 O/ETH/63/2005 (FJ798122) O/ETH/64/2005 (FJ798123) O/ETH/65/2005 (FJ798124) O/ETH/55/2005 (FJ798119) 100 O/ETH/56/2005 (FJ798120) O/ETH/54/2005 (FJ798118) O/ETH/57/2005 (FJ798121) O/ETH/66/2005 (FJ798125) O/ETH/67/2005 (FJ798126) O/ETH/3/2004 (FJ798109) O/ETH/1/2005 (FJ798106) O/ETH/1/2007 (FJ798137) O/ETH/26/2007 (FJ798138) O/ETH/27/2007 (FJ798139) 100 O/ETH/28/2007 (FJ798140) O/ETH/2/2006 (FJ798127) O/SUD/2/86 (DQ165075)

EA-1 EA-2 WA EA-4

96 100 100

100

98

EA-3

ME-SA SEA

90

100 100 100

79 87

CATHAY ISA-1 ISA-2 EURO-SA

0.02

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

13

Figure 8: Mozabique WRLFMD/2014/00032 Date received: 13/10/2014 No. of samples: 4 SAT2 (I): 4 86

91

Cabo Delgado

Niassa

Nampula

Tete

Zambezia

Sofala Manica

80

SAT 2

71

Inhambane Gaza

SAT2/KNP/17/88* (AF367105)(impala) SAT2/KNP/2/89* (AF367109)(impala) SAT2/KNP/16/88* (AF367104)(impala) SAT2/KNP/20/88* (AF367107)(impala) 100 SAT2/KNP/19/88* (AF367106)(impala) SAT2/KNP/18/88* (AF367138)(impala) SAT2/KNP/7/88* (AF367103)(buffalo) SAT2/KNP/19/89* (DQ009735) 91 SAT2/KNP/19/89* 99 97 SAT2/KNP/19/89* (AF367110)(buffalo) SAT2/KNP/18/95* (AF367118)(buffalo) 100 SAT2/KNP/31/95* (AF367119)(buffalo) SAT2/MOZ/3/2014* (BVI) SAT2/MOZ/6/2014* (BVI) 100 SAT2/MOZ/3/2014 SAT2/MOZ/4/2014 SAT2/MOZ/1/2014 SAT2/MOZ/4/2014* (BVI) SAT2/MOZ/2/2014 SAT2/MOZ/5/2014* (BVI) SAT2/SAR/8/01* (AY442910) SAT2/SAR/9/01* (AY442911) 100 88 SAT2/SAR/10/01* (AY442912) SAT2/SAR/11/01* (AY442913) SAT2/SAR/1/01* (AY442903) SAT2/SAR/4/01* (AY442906) SAT2/SAR/3/01* (AY442905) SAT2/SAR/2/01* (AY442904) SAT2/SAR/7/01* (AY442909) SAT2/SAR/5/01* (AY442907) SAT2/SAR/6/01* (AY442908) SAT2/KNP/1/92* (AF367114)(impala) SAT2/PAL/5/83* (AF367102) 99 SAT2/BOT/3/2011 SAT2/BOT/7/2011 SAT2/MOZ/1/2010 100 SAT2/MOZ/3/2010 SAT2/MOZ/4/2010 93 SAT2/MOZ/5/2010 SAT2/MOZ/7/2010 SAT2/MOZ/2/2010 SAT2/MOZ/6/2010 SAT2/KNP/32/92* (AF367115)(buffalo) SAT2/SA/106/59 (AY593848) SAT2/MOZ/1/70 (KF112959) 100 SAT2/MOZ/1/70 SAT2/ZIM/14/2002 (KF219689) SAT2/MAL/1/2003 72

87

MOZ/1/2014 MOZ/2/2014 MOZ/3/2014 MOZ/4/2014 88

Maputo Maputo City

72 98

100 km 60 mi

90

© Daniel Dalet / d-maps.com

77

I

III IV

100

XI II

80

100

V VI 100

XIII XIV 100

99 99

73 95

VII VIII IX XII X

0.05

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

14

Figure 9: Namibia

Ohangwena

Oshana

Omusati

WRLMEG/2014/00039 VP1 sequences received from the BVI, Botswana Date received: 11/12/2014 No. of sequences: 2 SAT2 (III): 2

Kunene

Oshikoto

Caprivi

Kavango

Otjozondjupa

NMB/1/2014 (BVI) NMB/2/2014 (BVI) 84

Omaheke Erongo Khomas

99

Hardap

Karas

200 km 95

100 mi © Daniel Dalet / d-maps.com

98

97

SAT2/BOT/15/2012 SAT2/BOT/18/2012 SAT2/BOT/13/2012 SAT2/BOT/17/2012 SAT2/BOT/16/2012 99 SAT2/BOT/14/2012 SAT2/BOT/12/2012 SAT2/BOT/11/2012 SAT2/BOT/10/2012 82 SAT2/BOT/8/2012 97 SAT2/BOT/1/2013 SAT2/BOT/2/2013 99 SAT2/BOT/2/2012 99 SAT2/BOT/19/2012 99 SAT2/BOT/20/2012 SAT2/BOT/P3/98 NXA-7 99 SAT2/BOT/P3/98 NXA-16 SAT2/SWA/4/89 (KF112969) SAT2/BOT/3/77 (KF112928) 99 SAT2/BOT/1/80 (BVIBOT 08/78)(KF112929) SAT2/BOT/P3/98 (buffalo 29) (AF367124) 99 SAT2/BOT/P3/98 VUM-29 SAT2/BOT/6/2005 SAT2/BOT/8/2005 SAT2/BOT/3/2005 SAT2/BOT/1/2005 99 SAT2/BOT/2/2005 SAT2/BOT/4/2005 SAT2/BOT/5/2005 70 SAT2/BOT/7/2005 SAT2/BOT/P3/2000 SAV-24 SAT2/BOT/P9/2010 (buffalo) SAT2/NMB/1/2014* (BVI) 99 SAT2/NMB/2/2014* (BVI) SAT2/BOT/24/2006 (buffalo) SAT2/ZAM/12/2009 99 SAT2/ZAM/16/2009 SAT2/ZAM/14/2009 SAT2/ZAM/13/2009 99 SAT2/BOT/14/2008 SAT2/BOT/15/2008 SAT2/ZAM/8/2008 SAT2/NMB/1/2007 83 SAT2/NMB/4/2007 SAT2/ZAM/2/2007 9993 SAT2/ZAM/3/2007 SAT2/ZAM/1/2007 SAT2/NMB/2/2008 SAT2/NMB/1/2008 93 SAT2/NMB/3/2008 SAT2/NMB/4/2008 SAT2/RHO/1/48 (AY593847)

99

III

IV I

81

XI II

92

V

99 99 70 99 78 99 99

75 97

VI XIII XIV VII VIII IX XII X

0.05

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

15

Figure 10: Zimbabwe WRLFMD/2014/00033 Date received: 13/10/2014 No. of samples: SAT 2 (I): 5 SAT 2 (II): 1

Mashonaland West

Mashonaland Central Mashonaland East

86

Harare

99

Matabeleland North Midlands

ZIM/8/2014 ZIM/7/2010

Manicaland

Matabeleland South

ZIM/3/2014 ZIM/5/2014 ZIM/2/2014 ZIM/4/2014 ZIM/6/2014 ZIM/7/2014

Bulawayo

ZIM/8/2010 ZIM/9/2010

SAT2/ZIM/17/2003 SAT2/ZIM/1/2004 (BTy plaque 5) SAT2/ZIM/15/2003 SAT2/ZIM/14/2003 89 SAT2/ZIM/12/2003 SAT2/ZIM/11/2003 70 SAT2/ZIM/8/2003 SAT2/ZIM/7/2003 SAT2/ZIM/18/2002 SAT2/ZIM/P1/2004 (B7) SAT2/ZIM/2/2003 75 SAT2/ZIM/3/2003 SAT2/ZIM/20/2003 77 SAT2/ZIM/6/2003 98 SAT2/ZIM/1/2004 SAT2/ZIM/12/2002 SAT2/ZIM/14/2002 (KF219689) 99 SAT2/ZIM/13/2002 71 SAT2/ZIM/15/2002 SAT2/ZIM/10/2010 SAT2/ZIM/5/2010 99 99 SAT2/ZIM/6/2010 SAT2/ZIM/3/2014 99 SAT2/ZIM/5/2014 SAT2/SA/106/59 (AY593848) 73 SAT2/MOZ/3/2014 SAT2/MOZ/4/2014 99 SAT2/MOZ/1/2014 SAT2/MOZ/2/2014 SAT2/BOT/6/2011 95 SAT2/BOT/7/2011 SAT2/BOT/3/2011 SAT2/ZIM/8/2010 81 99 SAT2/ZIM/9/2010 SAT2/MOZ/1/2010 SAT2/MOZ/3/2010 SAT2/MOZ/4/2010 87 SAT2/MOZ/5/2010 SAT2/MOZ/7/2010 SAT2/MOZ/2/2010 SAT2/MOZ/6/2010 SAT2/MAL/1/2003

Masvingo

ZIM/1/2014 100 km 60 mi

ZIM/1/2011

ZIM/10/2010

© Daniel Dalet / d-maps.com

91

70

94

I

I

III IV

98

SAT2/ZIM/5/81 (EF134951) SAT2/BOT/P3/98 (buffalo 1) (AF367122) 79 SAT2/BOT/P3/98 NXA-1 99 SAT2/BOT/P3/98 NXA-10 SAT2/BOT/P3/98 NXA-15 SAT2/BOT/P3/98 (buffalo 18) (AF367123) 99 SAT2/BOT/P3/98 NXA-18 99 SAT2/ZIM/2/2010 SAT2/ZIM/4/2010 SAT2/ZIM/1/2014 99 SAT2/ZIM/11/2014 (BVI) SAT2/BOT-BUFF/170/74 (buffalo) SAT2/ZIM/5/87 (KF112974) 99 SAT2/ZIM/8/89 (KF112975) SAT2/ZIM/7/83 (AF136607) SAT2/ZIM/31/89 buffalo SAT2/ZIM/23/89 buffalo 99 SAT2/ZIM/1/88 buffalo 77 SAT2/ZIM/4/89 buffalo 85

91

95

99

95 92

II

VI XI V

99 99

XIII XIV X XII

93

99 99

99

VII IX VIII

0.05

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

16

Vaccine matching For individual data see Table 4 (Annex 1).

Serotype O Two serotype O/ME-SA/Ind-2001 isolates were tested from the batch of samples received from Sri Lanka. These were both a vaccine match to O 3039 and O TAW/98. However only one strain was a vaccine match with O/TUR/5/2009 (the other was borderline) and neither of these two isolates generated a positive matching result against O BFS and O Manisa. Two further serotype isolates from Malaysia (MAY/2/2014 and MAY 3/2014) from the SEA topotype were tested and were both matched to O 3039. One isolate (MAY/3/2014) also matched O Manisa, O TAW/98 and O/TUR/5/09 antigens, while the other (MAY/2/2014) generated borderline values for O Manisa and O TAW/98 and a poor in-vitro match for O/TUR/5/2009.

Serotype A Three field viruses from Malaysia and two field viruses from Cameroon were tested by VNT against serotype A. For Malaysia the isolates gave a good vaccine match to A22 IRQ, A MAY/97 and A TUR/06; however, one isolate (MAY/23/2013) did not match against A TUR/06. For Cameroon there was a good match against A TUR/06 and there was a poor vaccine match against A22 IRQ. All five serotype O strains did not match in this in-vitro test against A IRN/05

Serotype SAT 2 One sample from Cameroon was tested against SAT 2 ERI and SAT 2 ZIM by VNT. Both of these vaccine viruses were a match against this field isolate.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

17

Annex 1 Table 2: Clinical sample diagnostics made by the WRLFMD® between October-December 2014 Country BAHRAIN

EGYPT

ETHIOPIA

WRL for FMD Sample Identification BAR 1/2014 BAR 2/2014 BAR 3/2014 EGY 42/2012 EGY 43/2012 EGY 30/2013 EGY 31/2013 EGY 23/2014 EGY 24/2014 EGY 25/2014 EGY 26/2014 EGY 27/2014 EGY 28/2014 EGY 29/2014 EGY 30/2014 EGY 31/2014 EGY 32/2014 EGY 33/2014 EGY 34/2014 EGY 35/2014 EGY 36/2014 EGY 37/2014 EGY 38/2014 EGY 39/2014 EGY 40/2014 EGY 41/2014 EGY 42/2014 EGY 43/2014 EGY 44/2014 EGY 45/2014 EGY 46/2014 ETH 3/2014 ETH 4/2014 ETH 5/2014 ETH 6/2014 ETH 7/2014 ETH 8/2014 ETH 9/2014 ETH 10/2014 ETH 11/2014 ETH 12/2014 ETH 13/2014 ETH 14/2014 ETH 15/2014 ETH 16/2014

Results

Species

Date of Collection

VI/ELISA

RT-PCR

Final report

CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE BUFFALO BUFFALO CATTLE BUFFALO CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE OVINE OVINE OVINE OVINE OVINE OVINE

16-Oct-14 16-Oct-14 27-Oct-14 20-May-12 21-May-12 20-Mar-13 20-Mar-13 07-Apr-14 17-Apr-14 22-Apr-14 22-Apr-14 05-May-14 06-May-14 09-May-14 17-May-14 28-May-14 14-Jun-14 14-Jun-14 18-Aug-14 08-Sep-14 09-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 11-Oct-14 13-Feb-14 13-Feb-14 13-Feb-14 13-Feb-14 07-Sep-14 07-Oct-14 07-Oct-14 07-Oct-14 29-Oct-14 29-Oct-14 29-Oct-14 29-Oct-14 29-Oct-14 29-Oct-14

O O O A SAT 2 NEG NEG O SAT 2 O O O O O NEG A O NEG O NEG O NT NT NT NT NT NT NT NT NT NT NEG NEG NEG NEG NEG NEG NEG NEG NEG NEG NEG NEG NEG NEG

POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS NEG NEG NEG NEG NEG NEG NEG NEG NEG NEG POS POS POS POS NEG POS POS POS NEG NEG NEG NEG NEG NEG

O O O A SAT 2 FMDV GD FMDV GD O SAT 2 O O O O O FMDV GD A O FMDV GD O FMDV GD O FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV NGD FMDV GD FMDV GD FMDV GD FMDV GD NVD FMDV GD FMDV GD FMDV GD NVD NVD NVD NVD NVD NVD

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

18

WRL for FMD Sample Identification ETH 17/2014 ETH 18/2014 HONG KONG HKN 14/2014 HKN 15/2014 SOUTH KOREA SKR 11/2014 SKR 12/2014 SKR 13/2015 SKR 14/2015 SKR 15/2016 SKR 16/2016 SKR 17/2017 SKR 18/2017 SKR 19/2017 SKR 20/2017 VIETNAM VIT 62/2013 VIT 63/2013 VIT 64/2013 VIT 1/2014 VIT 2/2014 VIT 3/2014 VIT 4/2014 VIT 5/2014 VIT 6/2014 VIT 7/2014 VIT 8/2014 VIT 9/2014 VIT 10/2014 VIT 11/2014 VIT 12/2014 VIT 13/2014 VIT 14/2014 VIT 15/2014 VIT 16/2014 VIT 17/2014 VIT 18/2014 VIT 19/2014 VIT 20/2014 VIT 21/2014 VIT 22/2014 VIT 23/2014 VIT 24/2014 VIT 25/2014 VIT 26/2014 VIT 27/2014 VIT 28/2014 VIT 29/2014 Country

TOTAL:

Results

Species

Date of Collection

VI/ELISA

RT-PCR

Final report

OVINE OVINE PIG PIG PIG PIG PIG PIG PIG PIG PIG PIG PIG PIG CATTLE CATTLE CATTLE CATTLE BUFFALO CATTLE BUFFALO BUFFALO PIG PIG CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE PIG CATTLE CATTLE CATTLE CATTLE CATTLE CATTLE PIG PIG CATTLE CATTLE CATTLE PIG PIG

29-Oct-14 29-Oct-14 25-Nov-14 25-Nov-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 03-Dec-14 17-Dec-13 17-Dec-13 21-Dec-13 20-Jan-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 24-Apr-14 26-Apr-14 26-Apr-14 26-Apr-14 30-Apr-14 19-May-14 19-May-14 05-Jun-14 05-Jun-14 20-Jun-14 09-Jul-14 10-Jul-14 10-Jul-14 16-Jul-14 17-Jul-14 17-Jul-14 24-Jul-14 24-Jul-14

NEG NEG NEG O Pending Pending Pending Pending Pending Pending Pending Pending Pending Pending A A A A A A NEG NEG A A A O NEG O O O A A O NEG O A A O NEG O O NEG O O O NEG

NEG NEG POS POS Pending Pending Pending Pending Pending Pending Pending Pending Pending Pending POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS

NVD NVD FMDV GD O Pending Pending Pending Pending Pending Pending Pending Pending Pending Pending A A A A A A FMDV GD FMDV GD A A A O FMDV GD O O O A A O FMDV GD O A A O FMDV GD O O FMDV GD O O O FMDV GD

91

Sample results pending from previous report The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

19

Country

SRI LANKA

WRL for FMD Sample Identification

Species

Date of Collection

VI/ELISA

RT-PCR

Final report

SRL 18/2014 SRL 19/2014 SRL 20/2014 SRL 21/2014 SRL 22/2014 SRL 23/2014 SRL 24/2014 SRL 25/2014 SRL 26/2014 SRL 27/2014 SRL 28/2014 SRL 29/2014 SRL 30/2014 SRL 31/2014 SRL 32/2014 SRL 33/2014 SRL 34/2014 SRL 35/2014

BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BOVINE BUFFALO BUFFALO BUFFALO BUFFALO BOVINE BOVINE BOVINE

02-Mar-14 04-Apr-14 06-Apr-14 06-Apr-14 18-Jun-14 10-Jul-14 14-Jul-14 14-Jul-14 16-Jul-14 05-Aug-14 01-Sep-14 10-Sep-14 10-Sep-14 10-Sep-14 10-Sep-14 11-Sep-14 15-Sep-14 18-Sep-14

NEG NEG NEG NEG NEG NEG NEG NEG NEG O O O O O O NEG O O

POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS POS

FMDV GD FMDV GD FMDV GD FMDV GD FMDV GD FMDV GD FMDV GD FMDV GD FMDV GD O O O O O O FMDV GD O O

TOTAL:

18

Results

Abbreviations used in table: FMD(V) FMDV GD FMDV NGD VI/ELISA RT-PCR NVD NT

Foot-and-mouth disease (virus) Genome detected Genome not detected (samples submitted in Trizol, only rRTPCR carried out) FMDV serotype identified following virus isolation in cell culture and antigen ELISA Reverse transcription polymerase chain reaction on epithelial suspension for FMD (or SVD) viral genome No foot-and-mouth disease, swine vesicular disease or vesicular stomatitis virus detected Not tested

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

20

Table 3: Summary of samples collected and received to WRLFMD (October-December 2014) Virus isolation in cell culture/ELISA

o

Country

BAHRAIN EGYPT ETHIOPIA

HONG KONG SOUTH KOREA VIETNAM TOTAL

N of samples

3 28

16 2 10 32 91

FMD virus serotypes

NVD

O

A

C

SAT 1

SAT 2

SAT 3

Asia 1

3 9 -

2 -

-

-

2 -

-

-

15 16

1 12 25

13 15

-

-

2

-

-

-

-

-

-

RT-PCR for FMD (or SVD) virus (where appropriate) Positive

Negative

1 7 39

3 18 7 2 32 62

10 9 19

10 10

18 18

-

Sample results pending from previous report SRI LANKA TOTAL

18 18

8 8

-

-

Abbreviations used in table: VI / ELISA FMD SVD NVD NT RT-PCR

FMD (or SVD) virus serotype identified following virus isolation in cell culture and antigen detection ELISA foot-and-mouth disease swine vesicular disease no FMD, SVD or vesicular stomatitis virus detected not tested reverse transcription polymerase chain reaction for FMD (or SVD) viral genome

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

21

Table 4: Antigenic characterisation of FMD field isolates by matching with vaccine strains by 2dmVNT from October to December 2014 Vaccine Matching Studies for Serotype O FMDV by VNT

Sample Reference O/SRL/28/2014 O/SRL/30/2014 O/MAY/2/2014 O/MAY/3/2014

O 3039 M M M M

O BFS N N NT NT

O Manisa N N Borderline M

O TAW/98 M M Borderline M

O TUR/5/09 M Borderline N M

Vaccine Matching Studies for Serotype A FMDV by VNT

Sample Reference A/MAY/12/2013 A/MAY/20/2013 A/MAY/23/2013 A/CAR/4/2013 A/CAR/10/2013

A IRN/05 N N N N N

A22 IRQ M M M N N

A MAY/97 M M M NT NT

A TUR/06 M M N M M

Vaccine Matching Studies for Serotype SAT 2 FMDV by VNT

Sample Reference SAT 2/CAR/16/2013

SAT 2 ERI M

SAT 2 ZIM M

Abbreviations used in table:

M

Vaccine Match- r1 = > 0.3. Suggests that there is a close relationship between field isolate and vaccine strain. A potent vaccine containing the vaccine strain is likely to confer protection.

N

No Vaccine Match - r1 = < 0.3. Suggests that the field isolate is so different from the vaccine strain that the vaccine is unlikely to protect

Borderline

NT

Any r1 values between 0.28 to 0.32

Not tested against this vaccine

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

22

Annex 2 Recent FMD Publications (October-December 2014) cited by Web of Science (Pirbright Institute papers and authors are highlighted in BOLD) 1. Lefebvre, D.J., A.R. De Vleeschauwer, N. Goris, S. Van Borm, A. Chimirri, A.M. Monforte, B. Valdazo-Gonzalez, D.P. King, J. Neyts, and K. De Clercq, A thiazepino 4,5a benzimidazole derivative hampers the RNA replication of Eurasian serotypes of footand-mouth disease virus. Biochemical and biophysical research communications, 2014. 455(3-4): p. 378-81. 2. Reid, S.M., V. Mioulet, N.J. Knowles, N. Shirazi, G.J. Belsham, and D.P. King, Development of tailored real-time RT-PCR assays for the detection and differentiation of serotype O, A and Asia-1 foot-and-mouth disease virus lineages circulating in the Middle East. Journal of Virological Methods, 2014. 207: p. 146-153. 3. Fowler, V.L., B.M. Bankowski, B. Armson, A. Di Nardo, B. Valdazo-Gonzalez, S.M. Reid, P.V. Barnett, J. Wadsworth, N.P. Ferris, V. Mioulet, and D.P. King, Recovery of Viral RNA and Infectious Foot-and-Mouth Disease Virus from Positive Lateral-Flow Devices. Plos One, 2014. 9(10). 4. Bari, F.D., S. Parida, T. Tekleghiorghis, A. Dekker, A. Sangula, R. Reeve, D.T. Haydon, D.J. Paton, and M. Mahapatra, Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains. Vaccine, 2014. 32(44): p. 5794-5800. 5. Gonzales, J.L., M.A. Barrientos, L. Quiroga, D. Ardaya, O. Daza, C. Martinez, C. Orozco, J. Crowther, and D.J. Paton, Within herd transmission and evaluation of the performance of clinical and serological diagnosis of foot-and-mouth disease in partially immune cattle, herds. Vaccine, 2014. 32(47): p. 6193-6198. 6. Forrest, S., Z. Lear, M.R. Herod, M. Ryan, D.J. Rowlands, and N.J. Stonehouse, Inhibition of the foot-and-mouth disease virus subgenomic replicon by RNA aptamers. The Journal of general virology, 2014. 95(Pt 12): p. 2649-57. 7. Gao, Z.-L., J.-H. Zhou, J. Zhang, Y.-Z. Ding, and Y.-S. Liu, The silent point mutations at the cleavage site of 2A/2B have no effect on the self-cleavage activity of 2A of foot-and-mouth disease virus. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2014. 28: p. 101-6. 8. Delgado, A.H., B. Norby, H.M. Scott, W. Dean, W.A. McIntosh, and E. Bush, Distribution of cow-calf producers' beliefs about reporting cattle with clinical signs of foot-and-mouth disease to a veterinarian before or during a hypothetical outbreak. Preventive veterinary medicine, 2014. 117(3-4): p. 505-17. 9. Delgado, A.H., B. Norby, H.M. Scott, W. Dean, W.A. McIntosh, and E. Bush, Distribution of cow-calf producers' beliefs regarding gathering and holding their cattle and observing animal movement restrictions during an outbreak of foot-and-mouth disease. Preventive veterinary medicine, 2014. 117(3-4): p. 518-32. 10. East, I.J., S.E. Roche, R.M. Wicks, K. de Witte, and M.G. Garner, Options for managing animal welfare on intensive pig farms confined by movement restrictions during an outbreak of foot and mouth disease. Preventive veterinary medicine, 2014. 117(3-4): p. 533-41. 11. McReynolds, S.W., M.W. Sanderson, A. Reeves, and A.E. Hill, Modeling the impact of vaccination control strategies on a foot and mouth disease outbreak in the Central United States. Preventive veterinary medicine, 2014. 117(3-4): p. 487-504. 12. Su, C., X. Duan, R. Cao, J. Zheng, and P. Chen, Enhancement of mouse immune response by recombinant adenovirus co-expressing VP1-2A of foot-and-mouth disease virus and porcine IFN-alpha. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology, 2014. 30(11): p. 1129-32. 13. Bucafusco, D., S. Di Giacomo, J. Pega, M.S. Juncos, J.M. Schammas, M. Perez-Filgueira, and A.V. Capozzo, Influence of antibodies transferred by colostrum in the immune responses of calves to current foot-and-mouth disease vaccines. Vaccine, 2014. 32(48): p. 6576-82. 14. Richards, K.K., M.L. Hazelton, M.A. Stevenson, C.Y. Lockhart, J. Pinto, and L. Nguyen, Using exceedance probabilities to detect anomalies in routinely recorded animal health data, with particular reference to foot-and-mouth disease in Viet Nam. Spatial and spatio-temporal epidemiology, 2014. 11: p. 125-33. The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

23

15. Xin, A., M. Zhu, Q. Hu, H. Miao, Z. Peng, Y. He, L. Gao, and H. Li, Effect of amino acid mutation at position 127 in 3A of a rabbit-attenuated foot-and-mouth disease virus serotype Asia1 on viral replication and infection. Virologica Sinica, 2014. 29(5): p. 291-8. 16. Connolly, J., Dynamics of Change in the Aftermath of the 2001 UK Foot and Mouth Crisis: Were Lessons Learned? Journal of Contingencies and Crisis Management, 2014. 22(4): p. 209-222. 17. Ehizibolo, D.O., A.M. Perez, C. Carrillo, S. Pauszek, M. AlKhamis, I. Ajogi, J.U. Umoh, H.M. Kazeem, P.O. Ehizibolo, A. Fabian, M. Berninger, K. Moran, L.L. Rodriguez, and S.A. Metwally, Epidemiological Analysis, Serological Prevalence and Genotypic Analysis of Footand-Mouth Disease in Nigeria 2008-2009. Transboundary and Emerging Diseases, 2014. 61(6): p. 500-510. 18. Elhaig, M.M. and M.N. Elsheery, Molecular investigation of foot-and-mouth disease virus in domestic bovids from Gharbia, Egypt. Tropical Animal Health and Production, 2014. 46(8): p. 1455-1462. 19. Ferrari, G., L. Tasciotti, E. Khan, and A. Kiani, Foot-and-Mouth Disease and Its Effect on Milk Yield: An Economic Analysis on Livestock Holders in Pakistan. Transboundary and Emerging Diseases, 2014. 61(6): p. E52-E59. 20. Jamal, S.M., S.I. Shah, Q. Ali, A. Mehmood, M. Afzal, M. Afzal, and A. Dekker, Proper Quality Control of Formulated Foot-and-Mouth Disease Vaccines in Countries with Prophylactic Vaccination is Necessary. Transboundary and Emerging Diseases, 2014. 61(6): p. 483-489. 21. Lefebvre, D.J., A.R. De Vleeschauwer, N. Goris, D. Kollanur, A. Billiet, L. Murao, J. Neyts, and K. De Clercq, Proof of Concept for the Inhibition of Foot-and-Mouth Disease Virus Replication by the Anti-Viral Drug 2 '-C-Methylcytidine in Severe Combined Immunodeficient Mice. Transboundary and Emerging Diseases, 2014. 61(6): p. E89-E91. 22. Morgan, K.L., I.G. Handel, V.N. Tanya, S.M. Hamman, C. Nfon, I.E. Bergman, V. Malirat, K.J. Sorensen, and B.M.d.C. Bronsvoort, Accuracy of Herdsmen Reporting versus Serologic Testing for Estimating Foot-and-Mouth Disease Prevalence. Emerging Infectious Diseases, 2014. 20(12): p. 2048-2054. 23. Park, J.-H., K.-N. Lee, S.-M. Kim, H.-S. Lee, Y.-J. Ko, D.-S. Tark, Y.-K. Shin, M.-G. Seo, and B. Kim, Reemergence of Foot-and-Mouth Disease, South Korea, 2000-2011. Emerging Infectious Diseases, 2014. 20(12): p. 2158-2161. 24. Ringa, N. and C.T. Bauch, Impacts of constrained culling and vaccination on control of foot and mouth disease in near-endemic settings: A pair approximation model. Epidemics, 2014. 9: p. 18-30. 25. Singh, R., R. Deb, U. Singh, R. Alex, S. Kumar, S. Chakraborti, S. Sharma, G. Sengar, and R. Singh, Development of a tetra-primer ARMS PCR-based assay for detection of a novel singlenucleotide polymorphism in the 5' untranslated region of the bovine ITGB6 receptor gene associated with foot-and-mouth disease susceptibility in cattle. Archives of Virology, 2014. 159(12): p. 3385-3389. 26. Tekleghiorghis, T., R.J.M. Moormann, K. Weerdmeester, and A. Dekker, Serological Evidence Indicates that Foot-and-Mouth Disease Virus Serotype O, C and SAT1 are most Dominant in Eritrea. Transboundary and Emerging Diseases, 2014. 61(6): p. E83-E88. 27. Xiang, F. and P. Neal, Efficient MCMC for temporal epidemics via parameter reduction. Computational Statistics & Data Analysis, 2014. 80: p. 240-250. 28. Cao, Y., Adjuvants for foot-and-mouth disease virus vaccines: recent progress. Expert Review of Vaccines, 2014. 13(11): p. 1377-1385. 29. Diaz-San Segundo, F., C.C. Dias, M.P. Moraes, M. Weiss, E. Perez-Martin, A.M. Salazar, M.J. Grubman, and T. de los Santos, Poly ICLC increases the potency of a replicationdefective human adenovirus vectored foot-and-mouth disease vaccine. Virology, 2014. 468: p. 283-292. 30. Gullberg, M., C. Polacek, and G.J. Belsham, Sequence adaptations affecting cleavage of the VP1/2A junction by the 3C protease in foot-and-mouth disease virus-infected cells. Journal of General Virology, 2014. 95: p. 2402-2410. 31. Habiela, M., J. Seaga, E. Perez-Martin, R. Waters, M. Windsor, F.J. Salguero, J. Wood, B. Charleston, and N. Juleff, Laboratory animal models to study foot-and-mouth disease: a review with emphasis on natural and vaccine-induced immunity. Journal of General Virology, 2014. 95: p. 2329-2345.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

24

32. Huang, L., F. Zhang, Q. Tang, Y. Wei, H. Wu, L. Guo, Y. Fu, and C. Liu, A recombinant porcine circovirus type 2 expressing the VP1 epitope of the type O foot-and-mouth disease virus is infectious and induce both PCV2 and VP1 epitope antibodies. Applied Microbiology and Biotechnology, 2014. 98(22): p. 9339-9350. 33. Lin, Y.-L., C.-Y. Chang, C.-H. Pan, M.-C. Deng, H.-J. Tsai, and F. Lee, First Finding of Southeast Asia Topotype of Foot-and-Mouth Disease Virus in Kinmen, Taiwan, in the 2012 Outbreak. Journal of Veterinary Medical Science, 2014. 76(11): p. 1479-1485. 34. O'Donnell, V., J.M. Pacheco, M. Larocco, D.P. Gladue, S.J. Pauszek, G. Smoliga, P.W. Krug, B. Baxt, M.V. Borca, and L. Rodriguez, Virus-host interactions in persistently FMDV-infected cells derived from bovine pharynx. Virology, 2014. 468: p. 185-196. 35. Onozato, H., K. Fukai, R. Kitano, R. Yamazoe, K. Morioka, M. Yamada, S. Ohashi, K. Yoshida, and T. Kanno, Experimental infection of cattle and goats with a foot-and-mouth disease virus isolate from the 2010 epidemic in Japan. Archives of Virology, 2014. 159(11): p. 2901-2908. 36. Ruiz, V., A.C. Mignaqui, M.C. Nunez, E. Reytor, J.M. Escribano, and A. Wigdorovitz, Comparison of Strategies for the Production of FMDV Empty Capsids Using the Baculovirus Vector System. Molecular Biotechnology, 2014. 56(11): p. 963-970. 37. Sharma, G.K., S. Mahajan, R. Matura, S. Subramaniam, J.K. Mohapatra, and B. Pattnaik, Production and characterization of single-chain antibody (scFv) against 3ABC non-structural protein in Escherichia coli for sero-diagnosis of Foot and Mouth Disease virus. Biologicals, 2014. 42(6): p. 339-345. 38. Steinberger, J., I. Grishkovskaya, R. Cencic, L. Juliano, M.A. Juliano, and T. Skern, Foot-andmouth disease virus leader proteinase: Structural insights into the mechanism of intermolecular cleavage. Virology, 2014. 468: p. 397-408. 39. Velsko, S.P., J. Osburn, and J. Allen, Forensic interpretation of molecular variation on networks of disease transmission and genetic inheritance. Electrophoresis, 2014. 35(21-22): p. 3117-3124. 40. Zheng, W., X. Li, J. Wang, X. Li, H. Cao, Y. Wang, Q. Zeng, and S.J. Zheng, A critical role of interferon-induced protein IFP35 in the type I interferon response in cells induced by foot-andmouth disease virus (FMDV) protein 2C. Archives of Virology, 2014. 159(11): p. 2925-2935. 41. Moral-Lopez, P., E. Alvarez, N. Redondo, T. Skern, and L. Carrasco, L protease from foot and mouth disease virus confers eIF2-independent translation for mRNAs bearing picornavirus IRES. Febs Letters, 2014. 588(21): p. 4053-4059. 42. Fu, Y., Z. Lu, P. Li, Y. Cao, P. Sun, M. Tian, N. Wang, H. Bao, X. Bai, D. Li, Y. Chen, and Z. Liu, Development of a Blocking ELISA Based on a Monoclonal Antibody against a Predominant Epitope in Non-Structural Protein 3B2 of Foot-and-Mouth Disease Virus for Differentiating Infected from Vaccinated Animals. Plos One, 2014. 9(11). 43. Sucafusco, D., S. Di Giacomo, J. Pega, M.S. Juncos, J. Manuel Schammas, M. PerezFilgueira, and A. Victoria Capozzo, Influence of antibodies transferred by colostrum in the immune responses of calves to current foot-and-mouth disease vaccines. Vaccine, 2014. 32(48): p. 6576-6582. 44. Feng, Q., M.A. Langereis, and F.J.M. van Kuppeveld, Induction and suppression of innate antiviral responses by picornaviruses. Cytokine & Growth Factor Reviews, 2014. 25(5): p. 577-585. 45. Kritana, P., K. Taehyeung, K. Hyeontae, K.K. Youn, and S. Wongeun, Atmospheric pathway: A possibility of continuous outbreaks of foot-and-mouth disease in South Korea in 2010-2011. Computers and Electronics in Agriculture, 2014. 108: p. 95-104. 46. Ramirez-Carvajal, L., F.D.-S. Segundo, D. Hickman, C.R. Long, J. Zhu, L.L. Rodriguez, and T.d.l. Santos, Expression of Porcine Fusion Protein IRF7/3(5D) Efficiently Controls Foot-andMouth Disease Virus Replication. Journal of Virology, 2014. 88(19): p. 11140-11153. 47. Sharma, G.K., J.K. Mohapatra, S. Mahajan, R. Matura, S. Subramaniam, and B. Pattnaik, Comparative evaluation of non-structural protein-antibody detecting ELISAs for foot-andmouth disease sero-surveillance under intensive vaccination. Journal of Virological Methods, 2014. 207: p. 22-28. 48. Steinberger, J. and T. Skern, The leader proteinase of foot-and-mouth disease virus: structure-function relationships in a proteolytic virulence factor. Biological Chemistry, 2014. 395(10): p. 1179-1185.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

25

49. Xie, X., H. Wang, J. Zeng, C. Li, G. Zhou, D. Yang, and L. Yu, Foot-and-mouth disease virus low-fidelity polymerase mutants are attenuated. Archives of Virology, 2014. 159(10): p. 26412650. 50. Perez-Martin, E., F. Diaz-San Segundo, M. Weiss, D.F. Sturza, C.C. Dias, E. RamirezMedina, M.J. Grubman, and T. de los Santos, Type III Interferon Protects Swine Against Footand-Mouth Disease. Journal of Interferon and Cytokine Research, 2014. 34(10): p. 810-821. 51. Gonzalez-Magaldi, M., M.A. Martin-Acebes, L. Kremer, and F. Sobrino, Membrane Topology and Cellular Dynamics of Foot-and-Mouth Disease Virus 3A Protein. Plos One, 2014. 9(10). 52. Du, J., X. Guo, S. Gao, J. Luo, X. Gong, C. Hao, B. Yang, T. Lin, J. Shao, G. Cong, and H. Chang, Induction of protection against foot-and-mouth disease virus in cell culture and transgenic suckling mice by miRNA targeting integrin alpha v receptor. Journal of Biotechnology, 2014. 187: p. 154-161. 53. Ma, X., P. Li, X. Bai, P. Sun, H. Bao, Z. Lu, Y. Cao, D. Li, Y. Chen, Z. Qiao, and Z. Liu, Sequences outside that of residues 93-102 of 3A protein can contribute to the ability of footand-mouth disease virus (FMDV) to replicate in bovine-derived cells. Virus Research, 2014. 191: p. 161-171.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

26

Annex 3 RECOMMENDATIONS FROM WRLFMD® ON FMD VIRUS STRAINS TO BE INCLUDED IN FMDV ANTIGEN BANKS – December 2014 Note: Virus strains are NOT listed in order of importance

High Priority

Medium Priority

Low Priority

O Manisa O PanAsia-2 (or equivalent) O BFS or Campos A24 Cruzeiro Asia 1 Shamir A Iran-05 (or A TUR 06) A22 Iraq SAT 2 Saudi Arabia (or equivalent i.e. SAT 2 Eritrea) A Eritrea SAT 2 Zimbabwe SAT 1 South Africa A Malaysia 97 (or Thai equivalent such as A/NPT/TAI/86) A Argentina 2001 O Taiwan 97 (pig-adapted strain or Philippine equivalent) A Iran ‘96 A Iran ‘99 A Iran 87 or A Saudi Arabia 23/86 (or equivalent) A15 Bangkok related strain A87 Argentina related strain C Noville SAT 2 Kenya SAT 1 Kenya SAT 3 Zimbabwe

Note: new risk-based priorities for FMD-free countries are currently being discussed.

The content of this report is the property of WRLFMD®, The Pirbright Institute. Copies of all the individual reports cited herein can be obtained from The Pirbright Institute and prior to presentation, publication or any other public use of these data, please contact Dr Donald King, The Pirbright Institute, [email protected].

27