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Appendix 43
“New tools and challenges for progressive control”Open Session of the EuFMD Research Group, Vienna (Austria) 29 September ‐ 1 October 2010
Foot-and-Mouth Disease Virus Genotype Definitions and NomenclatureNick J. Knowles, Jemma Wadsworth, Jef M. Hammond and Donald P. King
Institute for Animal Health, Pirbright Laboratory,Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK.
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Introduction• Foot-and-mouth disease viruses (FMDV) belonging to each of the
serotypes have been classified into a number of topotypes (VP1 genotypes which occupy distinct geographical niches).
• Currently, these number 11 for type O, 3 for type A, 3 for type C, 1 for type Asia 1, 9 for type SAT 1, 14 for type SAT 2 and 5 for type SAT 3.
• There are also a number of older viruses which are distinct or difficult to place within this framework.
• Within topotypes viruses are sometimes placed in named clusters, called genotypes, lineages or strains, which do not necessarily have consistent defining criteria.
2
Material & Methods• Phylogenetic trees were generated using the Neighbor-
joining (N-J) method with bootstrap re-sampling (MEGA 4.0).
• Bayesian evolutionary analysis was performed using the BEAST software package. The Bayesian Markov Chain Monte Carlo (MCMC) method, using virus isolation times, was used to generate dated trees.
• VP1 sequences of the prototype viruses were used in the construction of both trees.
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Results• In general the tree topology was similar using the two
methodologies, however, the Bayesian trees were more informative concerning the evolution and dating of the viruses.
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FMDV O•EURO-SA (Europe-South America)•ISA-1 (Indonesia 1)•ISA-2 (Indonesia 2)
•ME-SA (Middle East-South Asia)•SEA (Southeast Asia)•EA-1 (East Africa 1)•EA-2 (East Africa 2)•EA-3 (East Africa 3)•EA-4 (East Africa 4)•WA (West Africa)
•CATHAY (Far East)
•AFRICA?
•AFRICA•G-I•G-II•G-III•G-IV•G-V•G-VI•G-VII
•ASIA•EURO-SA
•AFRICA•ASIA•EURO-SA
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FMDV A FMDV C
FMDV Asia 1•ASIA
O/CAM/3/98
A24/Cruzeiro/BRA/55
O/SUD/2/86
A/TAI/118/87
Asia1/IND/63/72
O1/Manisa/TUR/69
As1/IND/14/95
O/ETH/3/2004
O/IND/53/79
A/NGR/2/73
O/CIV/8/99
A/SUD/3/77
A/EGY/1/72
A15/Bangkok/TAI/60
O/Corrientes/ARG/06
C/GER/c26
A/IRN/1/96
O2/Brescia/ITL/47
C1/Santa_Pau/SPA/70
O/ETH/58/2005
O/UGA/3/2002
O/ISA/9/74
C/N65/Tadjikistan/USSR/67
O/Yunlin/TAW/97
As1/IRN/10/2004
O/HKN/6/83
O/ETH/2/2006
O/UKG/35/2001
O/SUD/62/63
As1/IND/762/2003
O/K83/79
A/IRN/1/2005
O/ISA/1/74O/JAV/5/72
C/PHI/7/84
As1/PAK/1/54
C3/Resende/BRA/55
As1/HKN/19/74
O3/VEN/51
A23/Kitale/KEN/64
O/K40/84
O/TAN/2/2004
C/UKG/149/34
C3/Indaial/BRA/71(78)
O1/BFS_1860/UK/67
O/ETH/1/2007
O/IRN/8/2005
A/IRN/2/87
C/IND/51/79
A/GHA/16/73
O/MYA/7/98
A/UGA/13/66
O/PHI/7/96
O/HKN/21/70
O/IND/R2/75
A11/GER/29
O/ISA/8/83
O/KEN/5/2002
A21/Lumbwa/KEN/64
O/UGA/17/98
As1/YNBS/CHA/58
A/KEN/42/66
A/IRN/22/99
As1/AFG/1/2001
C/KEN/32/70
As1/Shamir/ISR/89
O/GHA/5/93
O/ISA/1/62
A/Alem/ARG/81A12/UK/119/32
O/MAL/1/98
C/ETH/1/71
As1/IND/18/80
O/TAI/189/87
O/UGA/5/96
A22/IRQ/64
74.9669
56.1172
75.1104
38.5151
45.8859
90.3356
43.1733
75.7157
79.31
118.6734
54.9277
90.2554114.5486
136.4071
51.2784
66.9976
70.8175
79.5978
66.1745
87.9046
100.1505
35.9039
47.1699
37.1958
359.0329
26.7117
28.8446
71.1323
67.601
106.3017
30.4719
62.6362
105.9441
56.2367
98.4513
26.3657
89.2675
76.5078
36.5147
128.2172
55.3432
107.4232
257.7132
95.1057
70.1486
51.3784
31.3679
78.3674
89.3394
70.8911
127.4734
85.5037
100.2248
24.9942
79.0683
42.3732
79.9635
73.5995
306.9279
76.3459
48.9
106.4941
135.6281
60.8478
105.0769
85.8809
114.9956
91.7334
119.1207
123.4639
414.2077
146.3516
61.7553
78.5225
116.8245
120 years ago
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Asia 1
O
A
C
ASIA
EURO-SA
EA-1
EA-2
AFRICA
ASIAEURO-SA
AFRICA
EA-3EA-4
ME-SA
SEA
CATHAY
ISA-1ISA-2
EURO-SA
WA
ASIA
Model: GTR+I+γConstant populationChain: 20,000,000Burn-in: 10%
Maximum cladecredibility tree
Appendix 43
“New tools and challenges for progressive control”Open Session of the EuFMD Research Group, Vienna (Austria) 29 September ‐ 1 October 2010
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FMDV C Topotypes1926-2004
EURO-SA
AFRICA
ASIA
C1/Cadelbosco di Sopra/89C1/Villa Sesso/89
C1/S.Palo dEute/89C1/Villa Colli/89
C1/Brescia/64C1/Brescia/ITL/64
C1/Modena/89C1/Poutecchio Bibhieur/Italy/89
C1/Oberbayern/FRG/60 (X00130)C1/Perugia/ITL/63
C1/Santa Pau/SPA/70 (AJ133357)C1/Santa Pau/70
C/HUN/1/72C/USSR/2/90
C1/Noville/SWI/65C1/Noville/SWI/65 (AY593804)
C1/Detmold/FRG/60C/Cotes du Nord/FRA/74C1/Oberbayern/FRG/60 (AY593805)C/POR/2/80
C/Pyrenees Atlantiques/FRA/80C1/Serra de Daro/SPA/81 (C-S15)
C1/Barcelona/SPA/82 (C-S30)C/BEL/1/72
C/AUR/4/73C1/Vosges/FRA/60 (EVD)C1/Turup/DEN/61C1/Vosges/FRA/60
C1/Bombay/IND/64 (IVRI)C1/Loupoigne/BEL/53 (1)C1/Loupoigne/BEL/53C/CZE/3/89C1/Loupoigne/BEL/53 (2)C/FRA/2/66
C1/Haute Loire/FRA/69C2/Pando/URU/44
C2/Pando/URU/44 (EVD)C4/TDF/ARG/66 (AY593808)
C4/TDF/ARG/66C2/997/UK/53C2/997/UK/53 (EVD)
C/Leticia/COL/67C/Leticia/COL/70
C/General Roca/Cordoba/ARG/02/93 (AJ3062C/General Villegas/BA/ARG/93 (AJ306217)
C3/Sao Jose dos Campos/BRA/72C3/Goias/88
C3/Chaco/PAR/74C3/Cordoba/ARG/85 (L29062)C3/ARG/85 (AJ007347)
C/General Lamadrid/ARG/93 (AJ306213)C3/ARG/85 (M19762)
C/Salto/BA/ARG/91 (AJ308703)C3/San Antonio de Giles/ARG/92 (AJ308704
C/ANG/3/73C3/Indaial/BRA/71(78) (M90376)
C3/Indaial/BRA/71 (J02184)C3/Alegrete/BRA/82
C3/Santa Fe/ARG/75C3/Indaial/BRA/71 (K01202)
C3/Indaial/BRA/71 (AY593806)C/PHI/7/84 VS
C/PHI/6/89C/PHI/3/88
C/PHI/11/89C/PHI/3/94
C/PHI/4/94C3/PAR/69
C5/ARG/69 (AY593809)C5/BEL/1/69
C5/ARG/69C3/ARG/84 (M19761)
C/PHI/7/76C/PHI/1/79
C/ISR/4/70C/LEB/3/69C3/Resende/BRA/55 (AY593807)C3/ARG/83 (EVD)
C3/ARG/83C3/Resende/BRA/55 (M19760)C3/Resende/55
CGC WRLC1/GER/c.26 (CGC) (Madrid)
C/UKG/149/34 (AY593810)
EURO-SA
C/KEN/1/2004 (K6/04)C/KEN/32/70 (K267/67)C/KEN/5/96 (K14/96)C/K221/83 (Kenya)
C/ETH/1/71C/ETH/6/2005
C/ETH/7/2005
AFRICAC/CEY/4/71
C/SRL/4/78C/SRL/1/84
C/IND/3/83C/KUW/2/82
C/IND/9/82C/IND/7/76
C/IND/14/80C/IND/12/82C/IND/51/79 (IND/42/77*)C/IND/1/82
C/SAU/1/84C/SAU/12/84
C/NEP/35/96C/IND/63/96* (1991 IVRI)C/IND/147/93* (IVRI)
C/IND/26/93* (IVRI)C/IND/146/93* (IVRI)
C/NEP/1/94C/NEP/10/93
C/IND/66/96* (1991 IVRI)C/NEP/124/90
C/IND/67/96* (1991 IVRI)C/IND/64/96* (1991 IVRI)
C/IND/65/96* (1991 IVRI)C/IND/8/93* (1992 IVRI)
C/BAN/1/92C/BAN/2/92
C/BHU/10/91C/IND/89/92* (1991 IVRI)
C/BHU/7/91C/IND/9/93* (1992 IVRI)
C/IND/7/92* (1991 IVRI)C/IND/136/92* (IVRI)
ASIA0.02
Topotype not known
NJ tree
0.0100.0200.0300.0400.0500.0
A24/Cruzeiro/BRA/55
SAT3/BEC/20/61
SAT2/KEN/3/57
SAT3/BEC/1/65
SAT3/SA/57/59
SAT2/RHO/1/48
SAT2/ETH/2/91
SAT2/ZAI/1/82
SAT1/T155/71
SAT1/UGA/1/97
SAT1/BEC/1/48
SAT2/NIG/2/75
SAT3/KNP/10/90
SAT2/GAM/8/79
SAT1/BOT/1/68
SAT3/ZIM/P25/91_(UR-7)
SAT1/UGA/13/74
SAT2/ZAI/1/74
SAT2/ZIM/14/2002
SAT1/UGA_BUFF/21/70
SAT2/BOT/P3/98_(B29)
SAT1/RHO/5/66
SAT3/ZAM/P2/96_(MUL-4)
SAT2/RWA/1/2000
SAT2/ETH/1/90
SAT3/UGA/2/97
SAT2/KEN/1/84
SAT2/SAU/6/2000
SAT1/NIG/11/75
SAT1/ETH/3/2007
SAT1/ISR/4/62
SAT2/KEN/2/84
SAT2/SA/106/59
SAT2/GHA/2/90
SAT2/UGA/19/98
SAT2/ZIM/7/83
SAT2/UGA/51/75
SAT3/UGA_BUFF/27/70
SAT2/CAR/8/2005
SAT2/ETH/2/2007
SAT1/ZIM/23/2003
SAT2/SUD/6/77
SAT2/ZIM/5/81
SAT1/SUD/3/76
SAT1/RV/11/37
SAT2/ANG/4/74
137.6382
167.8403
210.5827
97.3099
92.4326
455.4043
87.1995
155.4316201.9919
141.6076
101.3106
260.7143
111.3776
79.9792
359.9438
189.4959
199.7192
101.4153
109.5911
88.4598
229.1244
96.0793
86.594
96.9347
179.8027
240.2197
212.559
173.5708
112.3445
176.1991
143.9747
90.5951
140.8263
76.8002
173.2776554.8243
146.1399
35.5257
143.8035
145.8174
62.7246
184.3056
115.6589
123.2546
120 years ago
SAT 3
SAT 2
SAT 1
8
Model: GTR+I+γConstant populationChain: 20,000,000Burn-in: 10%
Maximum cladecredibility tree
SAT 1 topotypes
I
II
III
IV
V
VI
VII
VIII
IX
NSA-1 (North Southern Africa 1)
ESA-1(East Southern Africa 1)
WSA-1(West Southern Africa 1)
EA-1(East Africa 1)
EA-2(East Africa 2)
EA3(East Africa 3)
EA-4(East Africa 4)
WA-1(West Africa 1)
NCA-1(North Central Africa 1)
9
SAT 2 topotypes
WA-2(West Africa 2)
NCA-1(North Central Africa 1)
CA-1(Central Africa 1)
EA-2(East Africa 2)
EA-3(East Africa 3)
EA4(East Africa 4)
EA-5(East Africa 5)
CA-2(Central Africa 2)
ESA-1(East Southern Africa 1)
WSA-1(West Southern Africa 1)
WSA-2(West Southern Africa 2)
EA-1(East Africa 1)
WA-1(West Africa 1)
WSA-3(West Southern Africa 3)
GUINEA
IIIIIIIVVVIVIIVIIIIXXXIXIIXIIIXIV
10
SAT 3 topotypesESA-1
(East Southern Africa 1)NSA-1
(North Southern Africa 1)
NSA-2(North Southern Africa 2)
EA-1 East Africa 1)
WSA-1 (West Southern Africa 1)
I
II
III
IV
V
11
Bayesian analyses• Within-topotype diversity only dates back less than 120 years
• This suggests that almost all type O, A and C viruses were introduced into Africa following the African Rinderpest Pandemic of the 1890’s.
▫ Type O: two introductions, probably from Asia, i) the ancestor of EA-1/EA-3/EA-4/WA and ii) the ancestor of EA-2.
▫ Type A: one introduction from Europe or Asia.
▫ Type C: one introduction from Europe or Asia (possibly in the 1940’s) and one from South America circa 1973.
12
Appendix 43
“New tools and challenges for progressive control”Open Session of the EuFMD Research Group, Vienna (Austria) 29 September ‐ 1 October 2010
Summary• The topotypes of FMDV O, A and C have been assigned
geographically-based names (e.g. O WEST AFRICA), while those belonging to the SAT types have been given arbitrary numbers (in Roman numeral format).
• We suggest that the former system is more informative and should be adopted for the SAT topotypes.
• Using both Bayesian and distance methods to construct trees provides a better basis for the definition of genetic groupings below the level of serotype.
13
Questions
• How should we define FMDV topotypes?
• How should we define FMDV strains or named lineages?
14
Acknowledgements
• Funding from Defra, UK
15