Molecular Epidemiology of Foot-and-Mouth Disease Virus in Tanzania

Christopher Kasanga1, Raphael Sallu2, Chanasa Mpelumbe-Ngeleja2, Jemma Wadsworth3, Nigel Ferris3,

Geoff Hutchings3, Sarah Cleaveland4, Tiziana Lembo4,

Philemon Wambura1, Mmeta Yongolo2, Nick Knowles3, Donald King3 and Mark Rweyemamu1

1Sokoine University of Agriculture, Morogoro, Tanzania2Central Veterinary Laboratory, Tanzania

3Institute for Animal Health, Pirbright, United Kingdom4University of Glasgow, United Kingdom

GFRA Scientific Workshop, Hazyview, RSA: 17th April 2012

FMD in TanzaniaFMD in TanzaniaFMD in TanzaniaFMD in TanzaniaFMD in TanzaniaFMD in TanzaniaFMD in TanzaniaFMD in Tanzania

• Foot-and-mouth disease (FMD) is endemic in Tanzania

• First FMD outbreak reports ~ 1954

• Animal affected: Cattle, Pigs, small ruminants, wild animals

• Outbreaks occur in different geographic regions

• Factors associated with outbreaks are not clearly known

FMD virus (FMDV) FMD virus (FMDV) FMD virus (FMDV) FMD virus (FMDV) FMD virus (FMDV) FMD virus (FMDV) FMD virus (FMDV) FMD virus (FMDV)

• Aphthovirus of the family picornaviridae

• Non-enveloped, icosahedral virus, 26 nm in diameter

• +ve sense ss RNA virus

• Seven serotypes exist: A, O, C, Asia 1 and SAT1-3)

• Displays high genetic and antigenic variation

FMDV genome orientationFMDV genome orientationFMDV genome orientationFMDV genome orientationFMDV genome orientationFMDV genome orientationFMDV genome orientationFMDV genome orientation

L 2A 3CPrimary cleavages

Poly(C)

L1A 1B 1C 1D

2A 2B 2C 3A 3B 3C 3D

Secondary cleavages 1B/RNA? 3C 3C 3C 3C 3C 3C

Kilobases

0 1 2 3 4 5 6 7 8

Protease

Carboxy-terminal

self-cleaving

ProteaseCapsid NTP binding* Polymerase

Genome-linked

(VPg)

* putative functions

Membrane-binding

VP4 VP2 VP3 VP1VPG

5’UTR

AAA (n)

3’UTR

variable VP1 region

sequences used for isolate characterisation

Samples and analysisSamples and analysisSamples and analysisSamples and analysisSamples and analysisSamples and analysisSamples and analysisSamples and analysis

• 231 samples (epithelial tissues, probang samples, and whole blood) were submitted to the WRLFMD from 1967 to 2009 for analysis

• Lab analysis for FMDV was conducted by VI, CF, Antigen ELISA, RT-PCR and sequencing of the VP1 gene

• Phylogenies of VP1 sequences were determined by neighbor-joining method

Detection rate of FMDV Detection rate of FMDV Detection rate of FMDV Detection rate of FMDV Detection rate of FMDV Detection rate of FMDV Detection rate of FMDV Detection rate of FMDV

• Detection rate varied with time and geographic location• Are the correct samples being collected? • Preservation of the samples?

Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes Detection frequency of FMDV serotypes

27

1549

13

Geographic distribution of serotypes Geographic distribution of serotypes Geographic distribution of serotypes Geographic distribution of serotypes Geographic distribution of serotypes Geographic distribution of serotypes Geographic distribution of serotypes Geographic distribution of serotypes

Map of Map of Map of Map of AfricaAfricaAfricaAfrica

Map of TanzaniaMap of TanzaniaMap of TanzaniaMap of Tanzania

Veterinary Investigation Centre

Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““AAAA””””Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““AAAA””””

Coloured blue: Tanzania strains, which belong to the Africa GColoured blue: Tanzania strains, which belong to the Africa GColoured blue: Tanzania strains, which belong to the Africa GColoured blue: Tanzania strains, which belong to the Africa G----IIII

A/TAN/4/2009A/TAN/39/2009

A/TAN/11/2009A/TAN/47/2009A/TAN/40/2009A/TAN/42/2009

A/KEN/8/2008A/TAN/9/2009

A/TAN/11/2008A/TAN/12/2008

A/BUN/4/90A/MAL/5/81

A/UGA/1/2002A/ZAM/90

A/TAN/4/80A/TAN/2/68 (T626/68)

A/TAN/3/68 (T809/67)A/KEN/42/66 (K18/66)

A/SOM/1/78

G-I

A/EGY/1/72 (EF208756)A21/Lumbwa/KEN/64 (AY593761) G-II

A/SUD/3/77 (GU566064)A/UGA/13/66 G-III-IV

G-VA/GHA/16/73

G-VIA/NGR/2/73

AFRICA

A5/Allier/FRA/60 (AY593780)A12/UK/119/32 (M10975)

A24/Cruzeiro/BRA/55 (AY593768)A/Alem/ARG/81 (AJ306219)

A11/GER/29 (AGB)(EU553852)

EURO-SA

A23/Kitale/KEN/64 (AY593766)A15/Bangkok/TAI/60 (AY593755)

A/IRN/1/96 (EF208771)A/TAI/7/2003A/TAI/2/97 (EF208778)A/TAI/118/87* (EF208777)

A/IRN/2/87 (EF208770)A22/IRQ/64 (AY593763)

A/IRN/22/99 (EF208772)A/AFG/6/2007A/BAR/6/2008

A/TUR/1/2008A/IRN/1/2005 (EF208769)

A/TUR/33/2008

ASIA

100

95

100

100

94

100

99

78

95

92

100

100

98

100

87

97

79

95

93

0.02

Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““OOOO””””Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““OOOO””””

Coloured red: Tanzania strains, which belong to the EAColoured red: Tanzania strains, which belong to the EAColoured red: Tanzania strains, which belong to the EAColoured red: Tanzania strains, which belong to the EA----2 topotype2 topotype2 topotype2 topotype

O/MAL/1/98 (DQ165074)O/TAN/9/98

O/TAN/1/2004O/TAN/16/2008

O/TAN/2/2004O/TAN/12/2004

O/KEN/5/2002 (DQ165073)O/UGA/3/2002 (DQ165077)

O/TAN/29/2009O/TAN/5/2009O/TAN/44/2009

O/TAN/1/85O/TAN/14/2004O/TAN/17/2004

EA-2

O/ETH/58/2005 (FJ798141)O/UGA/17/98 (HM211075)

EA-4

O/ETH/3/2004 (FJ798109)O/ETH/1/2007 (FJ798137)

O/ETH/2/2006 (FJ798127)O/SUD/2/86 (DQ165075)

EA-3

O/CIV/8/99 (AJ303485)O/GHA/5/93 (AJ303488)

WA

O/K40/84*O/UGA/5/96 (AJ296327)

O/KEN/64/2009O/K83/79* (AJ303511)

EA-1

O/MYA/7/98 (DQ164925)O/TAI/189/87* (TRRL)

O/CAM/3/98 (AJ294910)

SEA

O/IND/R2/75* (AF204276)O1/Manisa/TUR/69 (AY593823)O/PAK/16/2003 (DQ165068)

O/IND/53/79 (AF292107)O/IRN/8/2005

O/UKG/35/2001 (AJ539141)O/IRN/61/2001 (DQ164896)

O/BHU/3/2009O/UAE/4/2008

O/KUW/3/97 (DQ164904)O/OMN/7/2001 (DQ164941)

ME-SA

O/PHI/7/96 (AJ294926)O/Yunlin/TAW/97 (AF308157)

O/HKN/6/83 (AJ294919)O/HKN/21/70 (AJ294911)

CATHAY

O/ISA/9/74 (AJ303502)O/ISA/8/83 (AJ303503)

O/ISA/1/62 (AJ303500)

ISA-1

O/ISA/1/74 (AJ303501)O/JAV/5/72 (AJ303509)

ISA-2

O/Corrientes/ARG/06 (DQ834727)O2/Brescia/ITL/47 (M55287)O1/BFS 1860/UK/67 (AY593815)

O3/VEN/51 (AJ004645)

EURO-SA

100

100

96

100

96

100

100

76

100

100

100

100

99

100

100

99

84

89

84

99

100

94

84

96

92

98

97

90

73

77

78

87

96

0.02

Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““SAT1SAT1SAT1SAT1””””Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““SAT1SAT1SAT1SAT1””””

Coloured red: Tanzania strains, which belong to the NWZ and otheColoured red: Tanzania strains, which belong to the NWZ and otheColoured red: Tanzania strains, which belong to the NWZ and otheColoured red: Tanzania strains, which belong to the NWZ and other topotyper topotyper topotyper topotype

SAT1/TAN/19/99

SAT1/TAN/25/99

SAT1/TAN/26/99

SAT1/TAN/60/99

SAT1/TAN/21/99

SAT1/TAN/51/99

SAT1/KEN/11/2005

SAT1/KEN/9/2009

SAT1/KEN/8/2009

SAT1/KEN/103/2010

SAT1/KEN/18/2005

SAT1/KEN/10/2006

SAT1/TAN/15/2008

SAT1/ZAM/1/2009

SAT1/TAN/1/96

SAT1/TAN/2/71

SAT1/T155/71

SAT1/TAN/5/96

SAT1/KEN/123/2009

SAT1/MAL/1/2001

SAT1/MAL/2/2000

SAT1/ZAM/3/2000

SAT1/TAN/3/80

SAT1/TAN/2/77

SAT1/TAN/18/99

SAT1/TAN/43/99

SAT1/TAN/6/99

SAT1/TAN/37/99

SAT1/ZAM/1/2004

NWZ

SAT1/ZIM/23/2003

SAT1/RV/11/37 (AY593839)

SAT1/RHO/5/66 (AY593846)SEZ

SAT1/BEC/1/48 (AY593838)

SAT1/BOT/1/68 (AY593845)

SAT1/UGA BUFF/21/70 buffalo

SAT1/UGA/1/97 (AY442012)

WZ

SAT1/SUD/3/76 (AY441996)

SAT1/ISR/4/62 (AY593844)

SAT1/UGA/13/74 (AY442010)

SAT1/TAN/3/72

SAT1/ETH/3/2007 (FJ798154)

SAT1/NIG/11/75 (AF431711)

100

81

100

93

100

71

100

100

100

99

100

96

90

73

76

100

0.05

RecommendationsRecommendationsRecommendationsRecommendationsRecommendationsRecommendationsRecommendationsRecommendations

• FMD outbreak investigation:– More sample collection and appropriate diagnosis is needed

• Research to describe the complex epidemiology and endemicity of FMD in Tanzania and other parts of Africa is needed

• Molecular characterisation and analysis of many FMD samples is needed to elucidate the phylodynamics and evolutionary nature of FMDV

• Cross-protection and vaccine-matching of the field isolates to available vaccines is required

Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““SAT2SAT2SAT2SAT2”””” (i)(i)(i)(i)Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““SAT2SAT2SAT2SAT2”””” (i)(i)(i)(i)

Coloured blue: Tanzania strains, which belong to the IV topotypeColoured blue: Tanzania strains, which belong to the IV topotypeColoured blue: Tanzania strains, which belong to the IV topotypeColoured blue: Tanzania strains, which belong to the IV topotype

SAT2/TAN/4/2004

SAT2/TAN/9/2004

SAT2/TAN/6/2004

SAT2/TAN/21/2004

SAT2/KEN/22/2004

SAT2/KEN/8/2005

SAT2/KEN/7/2007

SAT2/KEN/22/2007

SAT2/TAN/43/2009

SAT2/TAN/1/2010

SAT2/ETH/1/90 (1989)(AY343935)

SAT2/TAN/1/75 (AY343970)

SAT2/K65/82 (Kenya)

SAT2/KEN/1/84 (K7/84) (AY344505)

IV

SAT2/BOT/P3/98 (buffalo 29) (AF367124)

SAT2/RHO/1/48 (AY593847)I

SAT2/MAL/1/2003

SAT2/SA/106/59 (AY593848)

SAT2/ZIM/14/2002

III

SAT2/ZIM/5/81 (EF134951)

SAT2/ZIM/7/83 (AF136607)II

SAT2/GHA/2/90 (AF479415)

SAT2/NIG/2/75 (AF367139)XI

VISAT2/ANG/4/74 (AF479417)

VSAT2/GAM/8/79 (AF479410)

SAT2/ETH/2/2007 (FJ798161)

SAT2/SUD/6/77 (AY343939)

SAT2/ETH/2/91 (AY343938)

XIII

SAT2/CAR/8/2005

SAT2/SAU/6/2000 (AF367135)XIV

SAT2/RWA/1/2000* (AF367134)

SAT2/ZAI/1/74 (DQ009737)XII

SAT2/KEN/3/57 (AJ251473)

SAT2/KEN/2/84 (AY343941)IX

VIIISAT2/UGA/51/75 (AY343963)

SAT2/UGA/19/98 (AY343969)

SAT2/ZAI/1/82 (AF367100)VII

100

100

100

100

99

99

100

96

84

99

99

100

88

100

97

91

70

99

81

0.05

Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““SAT2SAT2SAT2SAT2”””” (ii)(ii)(ii)(ii)Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype Phylogenetic tree: serotype ““““SAT2SAT2SAT2SAT2”””” (ii)(ii)(ii)(ii)

Coloured blue: Tanzania strains, which belong to the IV topotypeColoured blue: Tanzania strains, which belong to the IV topotypeColoured blue: Tanzania strains, which belong to the IV topotypeColoured blue: Tanzania strains, which belong to the IV topotype0.05

Note: Note: Note: Note: The tree include virusesisolated in 2010-2011

Discussion and conclusionDiscussion and conclusionDiscussion and conclusionDiscussion and conclusionDiscussion and conclusionDiscussion and conclusionDiscussion and conclusionDiscussion and conclusion

• Serotypes A, O, SAT1 and SAT2 are the main cause of FMD outbreaks in Tanzania

• FMDV isolates so far detected in Tanzania are genetically related to lineages and topotypes from West and East Africa

• Presence of multiple serotypes and topotypes complicates FMD control in the region

• Understanding the spatio-temporal distribution, epidemiology, genetic and antigenic characteristics of circulating FMDV is a pre-requisite for control of FMD in Tanzania and other parts of Africa

AcknowledgementAcknowledgementAcknowledgementAcknowledgementAcknowledgementAcknowledgementAcknowledgementAcknowledgement

Directors: Directors: Directors: Directors: CVL and DVS in Tanzania