Global and regional update - Middle East

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Foot-and-Mouth Disease
Global and regional update
Donald King
Vesicular Disease Reference Laboratory
[email protected]
FMD 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
FMD Reference Laboratory
2010-2014:
Changing patterns and threats
SAT 2 and O
North Africa
and West Eurasia
Multiple
East Asia
Asia 1
Detailed reports can be found at: www.wrlfmd.org
Recent submissions to WRLFMD
• Jan – Dec 2013: 401 samples
• 259 isolates
• Represent 5 FMDV serotypes:
O
A
Asia 1
SAT 1
SAT 2
• No virus isolated 32.4% of samples
• RT-PCR negative in 17.7% samples
• No serotype C since 2004
Field data from West Eurasia and North Africa
Sample submissions to WRL (last 10 years)
* Sequence
data only
*
Bulgaria
*
Samples sent to WRLFMD
(last shipment)
Bahrain
2013-14
Country
Year
2012
Yemen
2009
Somalia
2009
Lebanon
2009
Jordan
2006
2011
Recently circulating FMDV lineages
Viral lineage:
West EurAsia
(Middle East)
North Africa
✓
✓
✓
✓
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/ME-SA/PanAsia-2
A/ASIA/Iran-05
Asia-1
O/ME-SA/PanAsia-2
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
Sub-lineage nomenclature used to define
different viral genotypes
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
2014 2013 2012 2011
• ANT-10
Iran
Israel
Saudi Arabia
Turkey
UAE
Afghanistan
Pakistan
Libya
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
FAR-09
O/IRN/34/2009
O/IRN/64/2009
PanAsia-2
O/IRN/38/2009
O/IRN/35/2009
O/IRN/49/2009
O/IRN/65/2009
ME-SA
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
• FAR-09
Iran
Israel
PAT
Turkey
O/IRN/57/2009
O/IRN/87/2009
O/IRN/18/2010
O/PAK/16/2010
BAL-09
PUN-10
O/IRN/8/2005
O/IRN/88/2009
O/TUR/257/2008* (FMDI)
O/TUR/264/2009* (FMDI)
ANT-10
TER-08
SAN-09
PanAsia
Irn-2001
Ind-2001
Pak-98
O/IND/53/79 (AF292107)
O/IND/R2/75* (AF204276)
O1/Manisa/TUR/69 (AY593823)
SEA
EA-3
EA-2
EA-4
Epidemiology of FMDV in Bulgaria
(Burgas): 2011
© Daniel Dalet / d-maps.com
500 km
300 mi
• 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
Bulgaria
Kastamonu
Bursa
Gümüşhane
Eskişehir
Turkey
Antalya
Sivas
Ağrı
Iran
• Analysis included additional
sequences from Turkey and Israel
Complete FMDV sequences
recovered from Bulgaria
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
12LPN1
Closest
Turkish
virus
12LPN3
BUL/11/2011
BUL/30/2011
TCS tree showing linking samples
showing putative unsampled
intermediates (-O-)
Valdazo-Gonzalez et al., PLoS ONE (2012)
BUL/26/2011
BUL/20/2011
BUL/32/2011
Vaccine matching data (2013)
Serotype O (all O/ME-SA/PanAsia-2 lineages)
Matched
Vaccine strain
Not matched
Field isolate
O-3039
O/RUSSI
O-4625 O/Manisa A/2000 TAW/98
Iran 2012
Iran 2013
Pakistan 2012
Pakistan 2013
*
Palestinian AT 2013
UAE 2013
Turkey 2013
*
* Single values have yielded borderline matches
O/TUR
5/2009
A/ASIA/Iran-05
In the past 3 years: 8 sub-lineages:
2013 2012 2011
SIS-12
Pakistan and Iran
SIS-10
Iran, Iraq, Turkey and Russia
AFG-07
Afghanistan, Pakistan, Iran,
Turkey
HER-10
Afghanistan, Pakistan, Iran,
Kazakhstan, Kyrgyzstan
QAZ-11
Iran
FAR-11
Pakistan and Iran
ESF-10
Iran
BAR-08
Egypt and PAT
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
A/IRN/78/2009
A/AFG/6/2007
A/BAR/6/2008
A/AFG/10/2010
A/IRN/15/2012
A/IRN/9/2010
A/TUR/1/2008
A/IRN/1/2005 (EF208769)
A/TUR/33/2008
A/IRN/9/2011
Iran-99
Irn-96
Iran-87
SIS-10
Iran-05
ASIA
FAR-09
AFG-07
BAR-08
HER-10
SIS-12
ESF-10
ARD-07
EZM-07
QAZ-11
A/ASIA/Iran-05
• 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
Vaccine matching data (2013)
Serotype A (A/ASIA/Iran-05)
Matched
Vaccine strain
Not matched
A/IND A/Iran A22Irq A/TUR/
A/Eri98 17/82 2005 24/64 2006
Egypt 2013
BAR-08
Iran 2012
Iran 2013
SIS-10
Pakistan 2012
Pakistan 2012
Pakistan 2013
HER-10
SIS-12
FAR-11
Palestinian AT 2013 BAR-08
Turkey 2013
SIS-10
* Single values have yielded borderline matches
*
Asia 1
• 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 transboundary movements of O/PanAsia
and A/Iran-05
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
Sindh-08
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
Asia1/AFG/1/2001 (DQ121109)
Group I
Asia1/HKN/19/74
Asia1/Shamir/ISR/89
Asia1/IND/762/2003* (DQ101240)
Group III
Asia1/IND/14/95* (AF390678)
Asia1/IRN/10/2004 (DQ121119)
Group VIb
Asia1/YNBS/CHA/58 (AY390432)
Asia1/IND/63/72* (AY304994)
Asia1/IND/18/80 (DQ121116)
Group V
Asia1/PAK/1/54 (AY593795)
Changing global patterns:
SAT 2 in North Africa during 2012
• First FMD cases in Egypt due to
serotype SAT 2 since 1950
• Cases associated with high
mortality
100
Cameroon 2005
SAT2/LIB/40/2012
100
79
SAT2/LIB/41/2012
SAT2/LIB/39/2012
SAT2/SUD/1/2007 (GU566071)
SAT2/NIG/2/2007
97
93
SAT2/NIG/5/2008
SAT2/NIG/6/2008
89
SAT2/NIG/7/2008
SAT2/NIG/4/2008
100
SAT2/NIG/1/2008
98
SAT2/NIG/2/2008
SAT2/NIG/3/2008
• ~50% particularly in young animals
due to myocarditis
SAT2/NIG/8/2008
100
SAT2/LIB/1/2003
SAT2/LIB/7/2003
SAT2/NGR/15/2005
86
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)
• Sequence data supported at least
two introductions of SAT 2 FMDV
into Egypt
SAT2/ERI/1/98 (AY343933)
100
100
SAT2/ERI/4/98 (AY343934)
SAT2/EGY/9/2012
SAT2/EGY/11/2012
100
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
Within SAT 2 topotype VII
0.01
• 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 pools
Egypt- Recent FMD Outbreaks
Recent FMD outbreaks in Egypt have involved at least 3
serotypes and a number of different topotypes/lineages
1.
2.
3.
4.
5.
6.
7.
8.
O/ME-SA/Egy-72 (2006-2009)
O/ME-SA/PanAsia 2 (Egy-09) (2009 & 2011)
O/EA-3 (2012)
A/Africa/G-VII (Ken-05) (2006 & 2009)
A/Asia/Iran-05 (Bar-08) (2010-2011)
A/Africa/G-IV (ISM-12) (2012)
SAT2/VII/Alx-12 (2012)
SAT2/VII/Ghb-12 (2012)
Changing global patterns:
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)
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
O/UAE/4/2008
O/KUW/3/97 (DQ164904)
O/OMN/7/2001 (DQ164941)
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 20082009, Oman 2001, Bahrain 2001, Kuwait
1997).
Dr Ibrahim Eldaghayes
PanAsia
PanAsia-2
O1/Manisa/TUR/69 (AY593823)
SEA
K
c
a
b
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 tools
For 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
Available type-specific rRT-PCR tests
• O/ME-SA/PanAsia-2
• A/ASIA/Iran-05
• ASIA
For west Eurasian viruses
(Middle East)
• SAT 2 (topotype VII) – Ahmed et al., 2012
• O/ME-SA/Ind-2001 – Knowles et al., in prep
•
•
•
•
O
A
SAT1
SAT2
For East African viruses
For further information and protocols contact: WRLFMD
Simplified summary
Transboundary movement patterns of FMDV
O/ME-SA/PanAsia-2
A/ASIA/Iran-05
Asia-1
A/
SAT 2
AFRICA
?
O/ME-SA/Ind-2001
O/EA-3
• 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
Matched
Not matched
O/ME-SA/Ind-2001:
Vaccine strain
O/Manis
O/TUR
O-3039 O-4625
a
TAW/98 5/2009
Saudi Arabia 2013
Libya 2013
O/EA-3:
Egypt 2012
SAT2
SAT2
Eritrea ZIM/7/83
Egypt 2012
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