COMPLETE GENOME ANALYSES OF FOOT- AND -MOUTH … · / Jemma Wadsworth 1, Antonello Di Nardo 1,...

www.pirbright.ac.uk / www.anses.fr

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.


FMD Virus PoolsFMD Virus Pools


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


V & VIV & VI

IVIV

XIIIXIIIVIIVII

VVVV

VV19981998

1000 km


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


FMDV 2003-2019FMDV 2003-2019

1000 km


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


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


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


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).


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


0.05


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


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


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


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


5’ UTR5’ UTR L VP4 VP2 VP3 VP1 2A 2B 2C 3A 3B 3C 3’ 3’ 3D


• 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


• 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


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:

COMPLETE GENOME ANALYSES OF FOOT- AND -MOUTH … · / Jemma Wadsworth 1, Antonello Di Nardo 1,...

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