FMD Reference Laboratory

Foot-and-Mouth Disease Global and regional update

Donald KingVesicular Disease Reference Laboratory

donald.king@pirbright.ac.ukFMD Ref Lab Team: Valerie Mioulet, Nick Knowles, Anna Ludi, Ginette Wilsden,

Bryony Armson, Pip Hamblin, Kasia Bachanek-Bankowska, Kelly Adams, Jemma Wadsworth, Begoña Valdazo-González, Britta Wood, Barsha Thapa,

Bob Statham, Ashley Gray, Trish Ryder, Sarah Belgrave, David Paton

2010-2014: Changing patterns and threats

SAT 2 and O North Africaand West Eurasia

Asia 1

MultipleEast Asia

Detailed reports can be found at: www.wrlfmd.org

• Jan – Dec 2013: 401 samples• 259 isolates• Represent 5 FMDV serotypes:

• No virus isolated 32.4% of samples• RT-PCR negative in 17.7% samples• No serotype C since 2004

Recent submissions to WRLFMD

Field data from West Eurasia and North AfricaSample submissions to WRL (last 10 years)

Bulgaria

2013-14

2012

2011

Bahrain

*

*

* Sequence data only

Country YearYemen 2009

Somalia 2009

Lebanon 2009

Jordan 2006

Samples sent to WRLFMD (last shipment)

Recently circulating FMDV lineages

Viral lineage: West EurAsia(Middle East)

North Africa

O/ME-SA/PanAsia-2 ✓ ✓A/ASIA/Iran-05 ✓ ✓Asia-1 ✓ ✗O/ME-SA/Ind-2001 ✓ ✓SAT 2 topotype VII ✓ ✓SAT 2 topotype IV ✓ ✗A/AFRICA/G-IV ✗ ✓A/AFRICA/G-VII ✗ ✓O/ME-SA/Sharqia-72 ✗ ✓O/EA-3 ✓ ✓

O/TUR/31/2013 O/TUR/33/2013 O/TUR/38/2013 O/TUR/27/2013

O/TUR/26/2013 O/TUR/12/2013 O/TUR/25/2013 O/TUR/24/2013 O/TUR/29/2013

O/TUR/36/2013 O/TUR/37/2013

O/ISR/1/2013 O/ISR/2/2013 O/ISR/3/2013

O/ISR/3/2014 O/ISR/4/2014 O/ISR/2/2014 O/ISR/1/2014

O/PAT/13/2013 O/PAT/14/2013

O/ISR/5/2014 O/ISR/6/2014

O/SAU/1/2009 O/SAU/2/2009 O/IRN/41/2009 O/IRN/52/2009 O/IRN/79/2009

O/IRN/42/2009 O/IRN/76/2009 O/IRN/34/2009

O/IRN/64/2009 O/IRN/38/2009 O/IRN/35/2009

O/IRN/49/2009 O/IRN/65/2009 O/IRN/68/2009 O/IRN/83/2009

O/IRN/89/2009 O/IRN/31/2009 O/IRN/51/2009

O/IRN/60/2009 O/IRN/81/2009

O/IRN/61/2009 O/IRN/80/2009 O/IRN/43/2009 O/IRN/66/2009 O/IRN/75/2009 O/IRN/84/2009 O/IRN/56/2009 O/IRN/21/2012

O/IRN/2/2013 O/IRN/62/2011 O/IRN/71/2011 O/IRN/77/2011 O/IRN/57/2009

O/IRN/87/2009

FAR-09

BAL-09 O/IRN/18/2010PUN-10 O/PAK/16/2010

O/IRN/8/2005ANT-10 O/IRN/88/2009TER-08 O/TUR/257/2008* (FMDI)SAN-09 O/TUR/264/2009* (FMDI)

PanAsia-2

PanAsia Irn-2001 Ind-2001

Pak-98 O/IND/53/79 (AF292107)

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

ME-SA

SEA EA-3

EA-2 EA-4

WA EA-1

CATHAY ISA-1 ISA-2 EURO-SA

100

100

99

100

99

100

99

88

8677

8572

99

98

89

99

99

86

87

99

88

89

99

0.02

O/ME-SA/PanAsia-2

2014 2013 2012 2011• ANT-10Iran        Israel        Saudi Arabia        Turkey        UAE        Afghanistan        Pakistan        Libya        

• FAR-09Iran        Israel        PAT        Turkey        

Sub-lineage nomenclature used to define different viral genotypes

Epidemiology of FMDV in Bulgaria (Burgas): 2011

500 km

300 mi

© Daniel Dalet / d-maps.com

Bulgaria

Turkey IranAntalya

BursaSivas AğrıEskişehir

Gümüşhane

Kastamonu

• Incursion of FMD into a FMD-free (without vaccination) country in Europe

• O/ME-SA/PanAsia-2ANT10

• Use of full genome sequence data generated in real-time to show how sequences are related

• Analysis included additional sequences from Turkey and Israel

Complete FMDV sequences recovered from Bulgaria

Valdazo-Gonzalez et al., PLoS ONE (2012)

Full genome sequence data:•provides evidence for single introduction into Bulgaria from Turkey•long branches indicative of unsampled infection

• either in 4 villages with seropositive domesticated animals• or wildlife (wild boar)

BUL/1/2010

12LPN3

12LPN1

BUL/11/2011

BUL/26/2011BUL/30/2011

BUL/32/2011

BUL/20/2011

Closest Turkish

virus

TCS tree showing linking samples showing putative unsampled intermediates (-O-)

Vaccine matching data (2013)Serotype O (all O/ME-SA/PanAsia-2 lineages)

Field isolate O-3039 O-4625 O/Manisa

O/RUSSIA/

2000 TAW/98O/TUR 5/2009

       

Iran 2012     

Iran 2013     

       

Pakistan 2012  

Pakistan 2013 *    

       

Palestinian AT 2013       

UAE 2013         

Turkey 2013 * 

* Single values have yielded borderline matches

Vaccine strainMatched

Not matched

A/AFG/140/2010 A/AFG/163/2010 A/AFG/128/2010 A/AFG/125/2010 A/IRN/125/2010 A/IRN/151/2010

A/PAK/37/2010 A/IRQ/5/2010

A/IRN/24/2011 A/TUR/26/2011

A/TUR/40/2010 A/TUR/1538/2010* (FMDI)

A/IRN/4/2011 A/IRN/5/2011 A/IRN/18/2011 A/IRN/30/2011 A/IRN/20/2011 A/IRN/52/2011 A/TUR/14/2011 A/TUR/3/2011 A/TUR/37/2011

A/TUR/63/2011 A/TUR/60/2011

A/TUR/9/2011* (FMDI) A/TUR/6/2011 A/TUR/13/2011 A/TUR/21/2011 A/TUR/24/2011 A/TUR/10/2011 A/TUR/43/2011

A/TUR/5/2011 A/TUR/23/2011

A/TUR/30/2011 A/TUR/35/2011 A/TUR/11/2011

A/TUR/18/2011 A/TUR/47/2011

A/TUR/29/2011 A/TUR/64/2011

A/TUR/16/2011 A/TUR/22/2011

A/TUR/41/2011 A/TUR/7/2011 A/TUR/3/2012

A/TUR/36/2011 A/TUR/5/2012

A/TUR/1/2013 A/TUR/10/2013 A/TUR/7/2013

A/TUR/11/2013 A/IRQ/A218/2012* (FMDI)

A/IRQ/A233/2012* (FMDI) A/IRQ/A223/2012* (FMDI)

A/IRQ/A222/2012* (FMDI) A/IRN/31/2012

A/IRQ/2012* (JUST) A/TUR/6/2012

A/TUR/4/2013 A/TUR/9/2013 A/TUR/14/2013

A/TUR/30/2013 A/TUR/1233/2012* (FMDI)

A/TUR/1204/2012* (FMDI) A/TUR/6/2013

A/TUR/16/2013 A/TUR/18/2013 A/TUR/19/2013 A/TUR/21/2013 A/TUR/35/2013

A/TUR/22/2013 A/TUR/23/2013

SIS-10

FAR-09 A/IRN/78/2009AFG-07 A/AFG/6/2007BAR-08 A/BAR/6/2008HER-10 A/AFG/10/2010SIS-12 A/IRN/15/2012ESF-10 A/IRN/9/2010ARD-07 A/TUR/1/2008

A/IRN/1/2005 (EF208769)EZM-07 A/TUR/33/2008QAZ-11 A/IRN/9/2011

Iran-05

Iran-99 Irn-96

Iran-87 A22

Thai-87 Sea-97

A15

ASIA

EURO-SA AFRICA

98

98

96

99

90

72

9271

99

99

99

87

93

82

97

91

99

97

80

72

74

0.02

A/ASIA/Iran-052013 2012 2011

SIS-12Pakistan and Iran

     

SIS-10Iran, Iraq, Turkey and Russia

     

AFG-07Afghanistan, Pakistan, Iran, Turkey      

HER-10Afghanistan, Pakistan, Iran, Kazakhstan, Kyrgyzstan      

QAZ-11Iran

     

FAR-11Pakistan and Iran

     

ESF-10Iran

     

BAR-08Egypt and PAT

     

In the past 3 years: 8 sub-lineages:

• Replaced the A-Iran-96 and A-Iran-99 strains that were previously circulating in the west Eurasian region

• Initially A22/Iraq vaccine provided protection

• After 2006, a new vaccines were required (A/Iran2005 and A/TUR/2006)

• Evidence that these vaccines are now no longer fully matched using in-vitro tests

• Full capsid sequences reveal amino acid changes in antigenic sites that may underpin these antigenic changes

Upadhyaya et al., (2013) Vaccine

A/ASIA/Iran-05

Vaccine matching data (2013)Serotype A (A/ASIA/Iran-05)

A/Eri98A/IND 17/82

A/Iran 2005 A22Irq

24/64

A/TUR/2006

Egypt 2013 BAR-08 

Iran 2012  Iran 2013 SIS-10  

 

Pakistan 2012 HER-10Pakistan 2012 SIS-12 *Pakistan 2013 FAR-11

 

Palestinian AT 2013 BAR-08   

Turkey 2013 SIS-10

Vaccine strainMatched

Not matched

* Single values have yielded borderline matches

Asia1/AFG/51/2011 Asia1/AFG/55/2011 Asia1/AFG/48/2011

Asia1/PAK/81/2011 Asia1/PAK/67/2011 Asia1/PAK/60/2011 Asia1/PAK/56/2011 Asia1/PAK/53/2011 Asia1/PAK/50/2011 Asia1/PAK/37/2011 Asia1/PAK/33/2011 Asia1/PAK/14/2011 Asia1/PAK/11/2011 Asia1/PAK/111/2010 Asia1/PAK/106/2010 Asia1/PAK/108/2010 Asia1/PAK/7/2011 Asia1/PAK/12/2011 Asia1/PAK/15/2011 Asia1/PAK/35/2011 Asia1/PAK/39/2011 Asia1/PAK/51/2011 Asia1/PAK/54/2011 Asia1/PAK/57/2011 Asia1/PAK/61/2011 Asia1/PAK/68/2011 Asia1/PAK/17/2011

Asia1/PAK/83/2011 Asia1/IRN/49/2011 Asia1/PAK/110/2010 Asia1/PAK/8/2011 Asia1/PAK/13/2011 Asia1/PAK/16/2011 Asia1/PAK/36/2011 Asia1/PAK/49/2011 Asia1/PAK/52/2011 Asia1/PAK/55/2011 Asia1/PAK/58/2011 Asia1/PAK/64/2011 Asia1/PAK/69/2011 Asia1/PAK/89/2011 Asia1/PAK/90/2011 Asia1/AFG/66/2011 Asia1/AFG/68/2011 Asia1/AFG/73/2011 Asia1/AFG/78/2011 Asia1/IRN/33/2011 Asia1/IRN/38/2011 Asia1/AFG/40/2011

Asia1/PAK/2/2012 Asia1/PAK/3/2012 Asia1/PAK/1/2012

Asia1/PAK/11/2012 Asia1/PAK/36/2012

Asia1/PAK/37/2012 Asia1/IRN/47/2011

Asia1/PAK/10/2013 Asia1/PAK/45/2012 Asia1/PAK/46/2012

Asia1/PAK/18/2012 Asia1/PAK/19/2012

Asia1/PAK/29/2012 Asia1/PAK/9/2013 Asia1/PAK/14/2013 Asia1/PAK/8/2013 Asia1/PAK/7/2013

Asia1/PAK/21/2012 Asia1/PAK/24/2012 Asia1/PAK/25/2012 Asia1/PAK/26/2012 Asia1/PAK/30/2012

Asia1/PAK/10/2012 Asia1/PAK/22/2012 Asia1/PAK/27/2012 Asia1/PAK/35/2012

Asia1/PAK/4/2012 Asia1/PAK/5/2012 Asia1/PAK/42/2012 Asia1/PAK/23/2013

Asia1/PAK/8/2008

Sindh-08

Group I Asia1/AFG/1/2001 (DQ121109) Asia1/HKN/19/74

Asia1/Shamir/ISR/89Group III Asia1/IND/762/2003* (DQ101240)

Asia1/IND/14/95* (AF390678)Group VIb Asia1/IRN/10/2004 (DQ121119)

Asia1/YNBS/CHA/58 (AY390432) Asia1/IND/63/72* (AY304994)

Group V Asia1/IND/18/80 (DQ121116) Asia1/PAK/1/54 (AY593795)

9978

99

99

99

98

99

98

99

99

96

99

86

90

97

94

85

76

71

79

0.02

• Emergence of a Asia 1 lineage (Sindh-08) with poor match Asia 1 Shamir (ISR/3/89)• First recognised in Pakistan (2008)

• However in-vivo potency test using >6PD50 Shamir vaccine does protect

• Lineage has now spread westward into Afghanistan, Iran, Turkey and Bahrain

• Spread mirrors recent trans-boundary movements of O/PanAsia and A/Iran-05

Asia 1

Changing global patterns: SAT 2 in North Africa during 2012

Cameroon 2005

SAT2/LIB/40/2012 SAT2/LIB/41/2012 SAT2/LIB/39/2012

SAT2/SUD/1/2007 (GU566071) SAT2/NIG/2/2007 SAT2/NIG/5/2008

SAT2/NIG/6/2008 SAT2/NIG/7/2008

SAT2/NIG/4/2008 SAT2/NIG/1/2008 SAT2/NIG/2/2008 SAT2/NIG/3/2008 SAT2/NIG/8/2008

SAT2/LIB/1/2003 SAT2/LIB/7/2003

SAT2/NGR/15/2005 SAT2/SEN/27/2009

SAT2/EGY/2/2012 SAT2/SAU/6/2000 (AF367135)

SAT2/CAR/P12/2000 (VDI 44/1)(HM211082) SAT2/ERI/12/98 (AF367126)

SAT2/ERI/1/98 (AY343933) SAT2/ERI/4/98 (AY343934)

SAT2/EGY/9/2012 SAT2/EGY/11/2012

SAT2/EGY/13/2012 SAT2/EGY/6/2012 SAT2/EGY/10/2012 SAT2/EGY/14/2012 SAT2/EGY/15/2012

SAT2/EGY/3/2012 SAT2/EGY/4/2012 SAT2/EGY/5/2012

100

100

79

89

97

98

100

93

100

86

100

100

100

0.01

• First FMD cases in Egypt due to serotype SAT 2 since 1950

• Cases associated with high mortality • ~50% particularly in young animals

due to myocarditis

• Sequence data supported at least two introductions of SAT 2 FMDV into EgyptWithin SAT 2 topotype VII

• Distinct from other contemporary SAT 2 lineages in the Middle East and North Africa • topotype VII from Libya • topotype IV from Bahrain

In partnership with the Animal Health Research Institute, Egypt

North Africa: cross-roads between poolsEgypt- Recent FMD Outbreaks

Recent FMD outbreaks in Egypt have involved at least 3 serotypes and a number of different topotypes/lineages

1.O/ME-SA/Egy-72 (2006-2009)2.O/ME-SA/PanAsia 2 (Egy-09) (2009 & 2011)3.O/EA-3 (2012)4.A/Africa/G-VII (Ken-05) (2006 & 2009)5.A/Asia/Iran-05 (Bar-08) (2010-2011) 6.A/Africa/G-IV (ISM-12) (2012)7.SAT2/VII/Alx-12 (2012)8.SAT2/VII/Ghb-12 (2012)

Changing global patterns: Serotype O from Indian sub-continent in Libya and Saudi Arabia

• Recent report (Nov. 2013)• Samples collected in Libya in Sept/Oct

2013 - submitted via IZSLER (Brescia)• Samples collected in Saudi Arabia in

Aug/Nov 2013• O/ME-SA/Ind-2001 lineage most

closely related to viruses from Bhutan and India• O/ME-SA/PanAsia-2 and O/EA3

previously reported in the country• O/ME-SA/Ind-2001 lineage normally

restricted to the Indian sub-continent • only previously caused FMD outbreaks in

the Middle East (Iran 2009, UAE 2008-2009, Oman 2001, Bahrain 2001, Kuwait 1997).

O/BAN/23/2009 (HQ630684) O/IND/182/2010* (KC506478) O/IND/132/2010* (KC506472) O/IND/27/2012* (KC506510) O/IND/29/2010* (KC506455) O/BAN/26/2009 (HQ630687) O/BAN/25/2009 (HQ630686)

O/BAN/27/2009 (HQ630688) O/BAN/11/2009 (HQ630682)

O/IND/148/2010* (KC506474) O/IND/102/2010* (KC506466) O/IND/30/2010* (KC506456) O/BAN/2/2009 (HQ630677)

O/IND/181/2010* (KC506477) O/BAN/28/2009 (HQ630689) O/BAN/29/2009 (HQ630690) O/BAN/30/2009 (HQ630691) O/BAN/31/2009 (HQ630692) O/IND/104/2010* (KC506467) O/BAN/9/2009 (HQ630681)

O/IND/32/2012* (KC506511) O/IND/4/2011* (KC506485)

O/IND/5/2011* (KC506486) O/IND/6/2011* (KC506487)

O/IND/2/2011* (KC506484) O/IND/38/2011* (KC506492)

d

O/BHU/1/2013 O/SAU/1/2013

O/SAU/4/2013 O/SAU/3/2013 O/SAU/6/2013 O/SAU/7/2013 O/SAU/8/2013

O/LIB/16/2013 O/LIB/1/2013 O/LIB/4/2013 O/LIB/5/2013 O/LIB/7/2013 O/LIB/11/2013 O/LIB/12/2013 O/LIB/22/2013 O/LIB/13/2013 O/LIB/17/2013 O/LIB/2/2013 O/LIB/3/2013 O/LIB/6/2013

KAR-13

c O/UAE/4/2008a O/KUW/3/97 (DQ164904)b O/OMN/7/2001 (DQ164941)

Ind-2001

PanAsia PanAsia-2

O1/Manisa/TUR/69 (AY593823)

ME-SA

SEA EA-2

EA-3 EA-4

WA EA-1

CATHAY ISA-1

ISA-2 EURO-SA

100

100

99

100

99

100

76

98

78

97

8684

96

71

91

8878

92

96

85

95

94

98

95

100 87

87

99

0.02

Dr Ibrahim Eldaghayes

OIE/FAO FMD Lab Network in action: Sharing samples and sequence data - O/ME-SA/Ind-2001

• Involved PD-FMD, IZSLER and Pirbright

• Molecular phylogenies of FMD viruses from SAU and LIB

• Indicates multiple independent introductions of this lineage from the Indian sub-continent

• KAR-13 sub-lineage that is widespread in the region

• Reports provided to OIE, FAO and local authorities (can be found at: www.wrlfmd.org)

New tailored diagnostic toolsFor endemic countries where multiple lineages are circulating

• Specific real-time RT-PCR assays• For detection and differentiation of different FMDV

lineages • Assays evaluated against circulating strains

• O/ME-SA/PanAsia-2• A/ASIA/Iran-05• ASIA

• SAT 2 (topotype VII) – Ahmed et al., 2012• O/ME-SA/Ind-2001 – Knowles et al., in prep

• O• A• SAT1• SAT2

Available type-specific rRT-PCR tests

For further information and protocols contact: WRLFMD

For East African viruses

For west Eurasian viruses (Middle East)

Simplified summaryTransboundary movement patterns of FMDV

?O/ME-SA/Ind-2001

O/ME-SA/PanAsia-2A/ASIA/Iran-05Asia-1

O/EA-3

SAT 2 A/AFRICA

• Are these patterns predictable?• Understanding epidemiology of FMD provides a basis

to estimate threats of new virus incursions• Phylogeography analysis is underway

Acknowledgements

• Support for the WRLFMD and research projects

• Collaborating FMD Reference Laboratories and field teams

• Partners within the OIE/FAO FMD Network

FMD Reference Laboratory

Supplementary in-vitro vaccine matching data

O-3039 O-4625O/

Manisa TAW/98O/TUR 5/2009

Saudi Arabia 2013   

Libya 2013   

Egypt 2012

SAT2Eritrea

SAT2ZIM/7/83

Egypt 2012

Vaccine strain

O/ME-SA/Ind-2001:

O/EA-3:

Matched

Not matched