molecular epidemiology of foot-and-mouth disease virus in tanzania - usda kasanga.gfra... ·...
TRANSCRIPT
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