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Jemma Wadsworth1, Antonello Di Nardo1, Katarzyna Bachanek-Bankowska1,*, Souheyla Benfrid2, Sandra Blaise-Boisseau2,
Sabine Delannoy2, Andrew E Shaw1, Valerie Mioulet1, Aurore Romey2, Anthony Relmy2, Patrick Fach2, Labib Bakkali Kassimi2,
Donald P King1 & Nick J Knowles1
Jemma Wadsworth1, Antonello Di Nardo1, Katarzyna Bachanek-Bankowska1,*, Souheyla Benfrid2, Sandra Blaise-Boisseau2,
Sabine Delannoy2, Andrew E Shaw1, Valerie Mioulet1, Aurore Romey2, Anthony Relmy2, Patrick Fach2, Labib Bakkali Kassimi2,
Donald P King1 & Nick J Knowles1
COMPLETE GENOME ANALYSES OF FOOT-AND-MOUTH DISEASE VIRUSES BELONGING
TO SEROTYPES O, A AND SAT 2 IN EAST, WEST AND NORTH AFRICA
COMPLETE GENOME ANALYSES OF FOOT-AND-MOUTH DISEASE VIRUSES BELONGING
TO SEROTYPES O, A AND SAT 2 IN EAST, WEST AND NORTH AFRICA
29th October 2019
1 The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom. 2 Laboratoire de Santé Animale de Maisons-Alfort, UMR 1161 virologie, INRA, Ecole Nationale
Vétérinaire d’Alfort, ANSES, Université Paris-Est, 94700 Maisons-Alfort, France.* present affiliation: MSD Animal Health.
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FMD Virus PoolsFMD Virus Pools
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FMDV Historical Distribution in Pools 4 & 5FMDV Historical Distribution in Pools 4 & 5
1000 km
600 mi© Daniel Dalet / d-maps.com
ASIAIran-05ASIA
Iran-05
EURO-SAEURO-SA
G-IVG-IV
G-IG-I
G-VIG-VIG-VIIG-VII
G-VIIG-VII
ASIAIran-05ASIA
Iran-05
1000 km
600 mi© Daniel Dalet / d-maps.com
V & VIV & VI
IVIV
XIIIXIIIVIIVII
VVVV
VV19981998
1000 km
600 mi© Daniel Dalet / d-maps.com
2013-2015ME-SA
Ind-2001d
2013-2015ME-SA
Ind-2001d2011
ME-SAPanAsia-2
2011ME-SA
PanAsia-2
EA-3EA-3
EA-2EA-2
WAWA
EA-1, East Africa 1EA-2, East Africa 2EA-3, East Africa 3EA-4, East Africa 4ME-SA, Middle East-South AsiaWA, West Africa
In general, Pool 4 can be divided into two distinct areas, North (Sudan, Ethiopia, Eritrea) and South (Kenya, Uganda, Tanzania, Rwanda, Burundi, DR Congo).
Type OType O Type AType A Type SAT 2Type SAT 2
EA-1EA-1 2002Afr. buffalo
2002Afr. buffalo
VIIVII20002000VIIVII
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FMDV 2003-2019FMDV 2003-2019
1000 km
600 mi© Daniel Dalet / d-maps.com
20182018
EA-2EA-2
WAWA
2010201020072007
20182018
2012201220192019
20122012
2018201820182018
2018201820182018
20182018
20182018
EA-2, East Africa 2EA-3, East Africa 3EA-4, East Africa 4ME-SA, Middle East-South AsiaWA, West Africa
EA-3EA-3
1000 km
600 mi© Daniel Dalet / d-maps.com
G-IVG-IV
G-IG-I
G-VIG-VI
G-VIIG-VII
G-VIIG-VII
2006-2009G-VII
2012-2018G-IV
2006-2009G-VII
2012-2018G-IV
20162016
2004-062004-06
20052005
2009-162009-162000-162000-16
2017201720172017
1000 km1000 km
600 mi600 mi© Daniel Dalet / d-maps.com© Daniel Dalet / d-maps.com
IV
2014-18
2007-172016
2007-142005-15
20052014 2014
2009
2012-1820032012
2018
VII 2015
1000 km
600 mi© Daniel Dalet / d-maps.com
IVIV
2014-182014-18
2007-172007-1720162016
2007-142007-142005-152005-15
2005200520142014 20142014
20092009
2012-182012-182003201220032012
20182018
VIIVII 20152015
Type OType O Type AType A Type SAT 2Type SAT 2
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Serotype Topotype Lineage VP1* Complete genomes*
O EA-3 - ~500† 56 (49 new)A AFRICA G-IV ~160 35 (27 new)
SAT 2 VII various ~190 36 (29 new)Total(s) ~850 127 (105 new)
Nucleotide SequencesNucleotide Sequences
* Including published sequences and sequences from ANSES
VP1: Sanger sequencing (ABI)CG: Next Generation Sequencing (Illumina MiSeq)
Country Year(s) O A SAT 2Algeria 2018 4Burkina Faso 2018 3Cameroon 2000-2013 5 2Côte d'Ivoire 2018 3Egypt 2012-2017 4 3 7Eritrea 1997-2006 2 1Ethiopia 2013-2019 5 2 3Gambia 2018 1Guinea 2018 3Israel 2017 1Libya 2003-2012 2Mali 2004 1Mauritania 2014-2018 1 1Morocco 2019 4Niger 2005 1Nigeria 1982-2016 4 6 5Oman 2015 1Palestine 2017 1Sierra Leone 2018 1Senegal 2009-2018 1 1South Sudan 2017 1Sudan 1977-2017 10 7 5Togo 2005 1Tunisia 2019 2Totals 49 27 29
New genome sequences
† see poster EPI 2 (Session 2) - Souheyla Benfrid et al.: Molecular epidemiology of foot-and-mouth disease virus O/EA-3: a recent transboundary emergence in North Africa (2017-2019).
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Other related presentations at this meetingOther related presentations at this meeting
Poster EPI 10 (Session 5) – Hussaini Ularamu et al.: Recent incursion of foot-and-mouth disease (FMD) serotype O East Africa topotype 3 (O/EA-3) in North Central Nigeria.
Poster EPI 19 (Session 7) – Mohamed Soltan et al.: Genetic characterization of foot-and-mouth disease virus (FMD) serotypes in Egypt (2016-2017) and identification of a new lineage of serotype O topotype EA-3.
Poster EPI 20 (Session 7) – Mohamed Soltan et al.: Emergence of foot-and-mouth disease virus, Lib-2 lineage of topotype VII, serotype SAT2 in Egypt 2018.
Poster EPI 21 (Session 7) – David Lefebvre et al.: Continued circulation of foot-and-mouth disease virus in Nigeria.
Poster EPI 24 (Session 7) – David Ehizibolo et al.: Reemergence of the novel topotype of foot-and-mouth disease virus serotype SAT 1 in Nigeria and Cameroon.
www.pirbright.ac.uk / www.anses.fr0.05
P3-coding regionP3-coding region
0.5
P1-coding regionP1-coding region
0.05
P2-coding regionP2-coding region
0.5
L-co
ding
regi
onL-
codi
ng re
gion Maximum Likelihood trees
(substitution model=GTR+G+I)167 genome sequences
Maximum Likelihood trees(substitution model=GTR+G+I)167 genome sequences
A/AFRICA/G-IV 32A/AFRICA/G-VI 4A/AFRICA/G-VII 1O/EA-3 56O/EA-4 9O/WA 4SAT1/V 1SAT1/VI 2SAT1/VII 3SAT1/IX 1SAT1/X 9SAT1/XI 1SAT2/V 4SAT2/VII 12SAT2/VII/Alx-12 11SAT2/VII/Ghb-12 5SAT2/VII/Lib-03 1SAT2/VII/Lib-12 8SAT2/XIII 3Total 167
OASAT 1SAT 2
OASAT 1SAT 2
OASAT 1SAT 2
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O/CIV/8/99 O/NIG/1/2016
O/NIG/1/2014WA
O/ETH/21/2013 O/ETH/22/2013 O/ETH/2/2006 MH053313
O/ETH/3/2004 MH053311 O/ETH/1/2007 MH053314
O/ISR/1/2017 O/PAT/2/2017 O/ETH/3/2017
O/SUD/2/2017 O/SSD/6/2017
O/EGY/14/2015 O/ETH/19/2018
O/EGY/10/2014 O/EGY/18/2014 O/NIG/10/2016
O/BKF/1/2018 O/BKF/9/2018 O/BKF/4/2018 O/SEL/13/2018 O/ALG/1/2018
O/SEN/1/2018 O/GAM/1/2018 O/GHA/Asu/10/2018 LC456871 O/GHA/Asu/9/2018 LC456870 O/GHA/Asu/11/2018 LC456872 O/GHA/Asu/12/2018 LC456873
EA-3
10099
100100
100
99
99
100
100
87
100
87
95
99
100
92
98
99
0.020
FMDV O & A P1FMDV O & A P1
West Africa& the Magreb
The Magreb(Northwest Africa)
Plus:Cote d’IvoireGuineaMauritaniaMoroccoTunisia(ANSES)
A/NIG/5/15 MG725875 A/NIG/6/15 MG725876
A/NIG/1/15 MG725873 A/ALG/1/2017 MG913340
A/NIG/2/2011 A/CAR/4/2013 A/CAR/10/2013 A/NIG/3/15 MG725874
A/NIG/1/13 MG725872 A/NIG/3/2013 A/NIG/7/2013 A/NIG/6/2013 A/NIG/8/2013
A/MAI/4/2004 A/CAR/12/2000
A/TOG/9/2005 A/CAR/60/2012
A/NIG/3/2009 A/CAR/36/2005
A/ERI/3/97 A/SUD/3/77 A/EGY/3/2016 A/ETH/19/2015 CJK
A/EGY/2/2018 A/SUD/12/2013 CJK A/SUD/13/2013
A/ETH/40/2018 A/SUD/1/2013
A/EGY/30/2012 A/SUD/1/2011
A/ERI/5/2006 A/SUD/3/2006
G-IV
G-I A/UGA/42/2019
99100
100
10099
99
99
87100
100
76
100
99
100
77
73
100
100100
100
100
84
100
86
100
0.020
West Africa &the Magreb
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FMDV SAT 2 P1FMDV SAT 2 P1XIII SAT2/ETH/24/2010
SAT2/MFNP-4/UGA/2002 FJ461346
SAT2/EGY/20/2014
SAT2/EGY/24/2014 KY825720
SAT2/EGY/5/2015
Alx-12
SAT2/EGY/9/2012 JX014255
SAT2/PAT/1/2012 JX014256
SAT2/EGY/3/2012 KC440884
Ghb-12
SAT2/NIG/3/2012
SAT2/GHA/Tul/2/2018 LC456874
SAT2/GHA/Tul/5/2018 LC456875
SAT2/CAR/16/2013
SAT2/EGY/31/2018
SAT2/EGY/34/2018
Lib-12
100
100
100
100
100
77
70
89
100
100
0.020
West Africa
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Breakpoints
Recombination rate
5’ UTR5’ UTR L VP4 VP2 VP3 VP1 2A 2B 2C 3A 3B 3C 3’ 3’ 3D
Recombination analysesRecombination analyses
Based on 127 genome sequences of:O/EA-3A/AFRICA/G-IVSAT2/VII
genome-wide map of site-by site variations in recombination ratesρ=0.13 [0.11 – 0.16] rho is the average recombination rate [confidence intervals] per siteρ/θ= 2.26 this is the ratio of recombination rate/mutation rate per site
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5’ UTR5’ UTR L VP4 VP2 VP3 VP1 2A 2B 2C 3A 3B 3C 3’ 3’ 3D
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• Intertypic recombination appears to be common. Intratypicrecombination was not tested but it would be assumed to be at least as common.
• The three main (northern) East African lineages of O and A appear to have spread independently into Egypt and West Africa (and from there into the Magreb). The directional spread of SAT 2 is less clear since the earliest reports are in Eritrea (1998) and Cameroon (2000).
• Changes in trade (and politics – ‘the Arab Spring’ – 2010 on) may have led to the increased spread of disease.
• New roads crossing the Sahara desert may have increased movements of animals and their products.
• This and other studies have shown that FMD Pool 4 (East Africa) viruses can be subdivided into two sub-pools, North and South.
ConclusionsConclusions
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• What role does recombination play in the epidemiology, evolution and pathogenicity of FMDV?
• What will happen to the FMDV lineages that were previously present in West Africa?• Disappear• Co-exist• Re-emerge in subsequent years
• Are FMDV Pools 4 (northern part) and 5 merging into a single pool?
QuestionsQuestions
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AcknowledgementsAcknowledgementsWest AfricaDr Habibata Ouermi & Dr Joseph
Savadogo (Burkina Faso)Dr Ndamkou Ndamkou Christian & Dr
Mark Bronsvoort (Cameroon)Dr M’Bétiégué Coulibaly (Côte d'Ivoire)Dr Momar Talla Seck (Gambia/Senegal)Dr Mamadou Lamarana Souare
(Guinea)Dr Mohamed Yahya Bah (Mauritania)Dr Hussaini Ularamu (Nigeria)Dr Tesfai Tseggai (Sierra Leone)
East AfricaDr Daniel Gizaw & Dr Yeneneh Tesfaye
Alemu (Ethiopia)Dr Abraham Sangula (South Sudan)Dr Yazeed A. Raouf (Sudan)
Middle EastDr Boris Gelman (Israel/Palestine)
North AfricaDr Hafsa Madani & Dr Hadj Amar (Algeria)Dr Mohamed Attia & Dr Iman Farag (Egypt)Dr Ibrahim Mohamed Eldaghayes & Dr
Milad A Farhat (Libya)Dr El Abrak Abderrahman (Morocco)Dr Malek Zrelli (Tunisia)
Dr Emiliana Brocchi (IZSLER, Italy)
Work at Pirbright was funded by Defra UK (SE2943 & SE2944) & EuFMD
Work at ANSES was funded by EuFMD & Boehringer Ingelheim
We would like to thank the following people (and their teams) for kindly providing the samples used in this study: