Open Session of the EuFMD: 2012, Jerez de la Frontera, Spain
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1 Appendix 35 Virus Pools Pool 3, Pool 5 Local Differences in Circulation: What Have We Learnt from Patterns of FMD Persistence and Spread?, SAT 1, Pool 1, Pool 7, Nick J. Knowles Endemic Pool 4 ntermediate, sporadic Molecular Characterisation & Diagnostics Group A,, SAT 1,, 3 Free with vaccination SAT 1,, 3 Countries with multiple zones: FMD-free, free with vaccination or not free Free. Virus present in game parks Pool positions are approximate and colours indicate that there are three principal pools, two of which can be subdivided into overlapping areas Free East Asia Pool 1 Pool 1 FMDV type A, sia km 300 mi ASA / Sea-, /CATHAY //PanAsia // /SEA/Mya- 17 /CATHAY sia 1,, 7 /CATHAY A/ASA/Sea- Asia1/ASA/nd- Asia1/ASA/Sea, 0 km A/VT//009 (HQ116378) A/VT/8/009 (HQ116384) A/HuBWH/CHA/009 (JF7355) A/VT/4/008 (HQ1163) A/VT/5/008 (HQ1163) A/TA/18/008 (HQ116346) A/TA/5/009 (HQ116348) A/TA/17/008 (HQ116345) A/TA/10/009 (HQ116353) A/VT/8/008 (HQ1163) A/VT/6/008 (HQ116374) A/VT/3/009 (HQ116379) A/MAY/9/009 (HQ116306) A/VT/1/009 (HQ116377) A/VT//008 (HQ1163) A/MAY//009 (HQ116305) A/LA/4/008 (HQ11695) A/TA/16/008 (HQ116344) A/TA/19/008 (HQ116347) A/TA/15/008 (HQ116343) A/TA/6/009 (HQ116349) A/SKR//010 (JQ0331) A/Pochun/KR/010* (GU4415) A/VT/3/008 (HQ1163) A/VT/5/009 (HQ116381) A/VT/6/009 (HQ1163) A/VT/7/008 (HQ116375) A/TA/13/008 (HQ116341) A/TA/14/009 (HQ116354) A/TA/4/008 (HQ116336) A/TA/8/009 (HQ116351) A/TA/7/009 (HQ116350) A/VT/1/010 (JQ033) A/TA/8/008 (HQ116337) A/TA//006 (HQ11635) A/MAY/1/008 (HQ116303) A/MAY/3/007 (HQ11630) A/TA/11/007 (HQ116335) A/CAM/1/006 (HQ116) A/CAM//008 (HQ116) A/LA/7/006 (EU667458) A/LA/1/006 (003)(EU667456) A/TA/1/006 (HQ11634) A/MAY/1/007 (HQ116301) A/TA/3/007 (HQ116334) A/TA/118/* (EF077) A/TA// (EF078) 0.01 /MG/3/010 (JQ0310) /MG/4/010 (JQ0311) /MG/56/010* (JQ036) /MG/1/010 (JQ0308) /MG//010 (JQ0309) /RUS/Aug 010 (JQ0330) /MG/C3/010* (JQ035) /MG/5/010 (JQ031) /MG/7/010 (JQ0314) /MG/77/010* (JQ038) /MG/6/010 (JQ0313) /MG/9/010 (JQ0315) /MG/66/010* (JQ037) /TA/1/009 (HQ11660) /TA/13/009 (HQ11661) /MAY/0/009 (HQ11618) /TA/19/009 (HQ11666) /TA/3/009 (HQ116) /VT//010 (JQ03) /LA/1/009 (HQ1161) /TA/3/009 (HQ11658) /MAY/8/009 (HQ11616) /TA/18/009 (HQ11665) /MYA//008 (HQ1166) /TA/4/009 (HQ11659) /TA/5/008 (HQ1165) /TA//008 (HQ11650) /TA/6/008 (HQ11653) /TA//009 (HQ11657) /LA//008 (HQ1161) /MAY/5/009 (HQ11613) /LA/1/007 (HQ116175) /MYA/3/008 (HQ1167) /MYA/1/009 (JQ0318) /TA/0/009 (HQ11667) /VT/5/010 (JQ033) /MYA//006 (HQ1165) /MYA/3/009 (JQ0317) /MYA/1/006 (JQ0316) /HLJC1/03 (China) (DQ1143) /MG/004 (JQ034) /MYA/3/010 (JQ0319) /MYA/11/009 (HQ1163) /MYA/5/009 (HQ1168) /TA//009 (HQ11669) /HKN/1/010 (JQ0301) /HKN/6/010 (JQ030) /HKN/19/010 (JQ0305) /NC/CHA/010 (HQ650) /MY/CHA/010 (HQ65079) /GZ/CHA/010 (JN) /SKR/4/010 (JQ030) /VN/YB08/010 (HQ608) /HKN/7/010 (JQ0303) /HKN/9/010 (JQ0304) /HKN/1/011 (JQ0306) /HKN//011 (JQ0307) /DY/CHA/010 (HQ65078) /CHA/31/010* (JF7356) /BY/CHA/010 (JN) /TZ/CHA/010 (HQ65081) /JPN/MZ1/010 (AB6103) /RUS/Jul 010 (JQ039) /SKR/5/010 (JQ031) /TA/1/* Pool 1 FMDV type SEA / Mya Southern Asia 0 km (/PanAsia) (/) (/nd-001d) A (ASA/unnamed) (ASA/unnamed), 0.01 pen Session of the EuFMD: 01, Jerez de la Frontera, Spain 1
2 PanAsia nd-001d /BAN/5/009 (HQ6306) /BAN/7/009 (HQ630688) /BAN/6/009 (HQ6306) /BHU//009 /NEP/5/010 /BHU/3/009 /BHU/16/009 /NEP/3/010 /BHU/19/009 /NEP/1/010 /BHU/8/009 /BHU/9/009 /BHU/10/009 /BAN/11/009 (HQ6306) /BHU/6/009 /BHU/18/009 /NEP/17/010 /BAN/3/009 (HQ630684) /APR11/ND/009 (JX0611) /APR1/ND/009 (JX061) /BHU/5/009 /NEP/15/010 /NEP/16/010 /BHU/4/009 /NEP/6/010 /BHU/7/009 /KAM0110/ND/010 (JX0616) /KAM010/ND/010 (JX0617) /RN//009 /BAN//009 (HQ630677) /BAN/9/009 (HQ630681) /BHU/41/009 /BHU/37/009 /BHU/40/009 /NEP/11/010 /BHU/5/009 /BHU/6/009 /BHU/0/009 /BHU/3/009 /RKo0810/ND/010 (JX061) /NEP/9/010 /UPMe9/ND/009 (JX0610) /KEKm9/ND/009 (JX0614) /KAM0410/ND/010 (JX0618) /KEKm0610/ND/010 (JX0619) /NEP/1/010 /BAN/8/009 (HQ6306) /BAN/9/009 (HQ6306) /BAN/30/009 (HQ630691) /BAN/31/009 (HQ6306) /NEP/7/010 /BAN/1/009 (HQ6306) /KEPt00/ND/010 (JX060) /CHRn0509/ND/009 (JX0609) /PUJ011/ND/01 (JX064) /NEP/5/008 (HQ630693) /NEP/7/008 /NEP//009 (HQ6306) /NEP/3/009 /TNNa111/ND/011 (JX063) /GUK609/ND/009 (JX0613) /GUK9/ND/009 (JX0615) /UAE/4/008 /KUW/3/ (DQ1644) /MN/7/001 (DQ1641) /RN/61/001 (DQ1648) /ND/77/00* (PD-FMD) /APMb05/ND/005 (JX0604) /APG1005/ND/005 (JX0606) /MAP01/ND/011 (JX06) /PP1440/ND/00 (JX05) /RAB0503/ND/003 (JX0595) /WBN1310/ND/00 (JX0591) /RC103/ND/003 (JX05) /TUR//001 (DQ1645) /TUR/5/06/01* (DQ517) /RN/67/001 (DQ1648) /Tibet/CHA// /UKG/35/001 (AJ539141) /YEM/6/ /SAU/36/ /SAU/38/ (AJ31) /PAK/16/003 (DQ165068) /ND/53/79 (AF107) /ND/R/75* (AF04) 1/Manisa/TUR/69 (AY5933) EA-1 EA- SEA EA-4 Asia1/ND/3/01* (PD-FMD) Asia1/ND/3/01* (PD-FMD) Asia1/ND/3/01* (PD-FMD) CATHAY SA-1 SA- EUR-SA Asia1/ND/438/01* (PD-FMD) Asia1/ND/388/01* (PD-FMD) Asia1/ND/43/01* (PD-FMD) Asia1/ND/3/01* (PD-FMD) Asia1/ND/139/0* (DQ1014) Asia1/ND/34/01* (PD-FMD) Asia1/ND/335/01* (PD-FMD) Asia1/ND/175/004* (DQ10137) Asia1/ND/354/01* (PD-FMD) Asia1/ND/3/01* (PD-FMD) Asia1/ND/60/0* (DQ10143) Asia1/ND/61/0* (PD-FMD) Asia1/ND/1/0* (001) (PD-FMD) Asia1/ND/141/0* (PD-FMD) Asia1/ND/1/0* (DQ10144) Asia1/ND/38/004* (PD-FMD) Asia1/ND/388/004* (DQ10135) Asia1/ND/140/01* (PD-FMD) Asia1/ND/3/004* (PD-FMD) Asia1/ND/148/01* (PD-FMD) Asia1/ND/149/01* (PD-FMD) 93 Asia1/ND/160/01* (PD-FMD) Asia1/ND/114/004* (003)(DQ10139) Asia1/ND/147/004* (003)(PD-FMD) Asia1/ND/168/004* (PD-FMD) Asia1/ND/153/004* (003)(PD-FMD) Asia1/ND/150/004* (003)(PD-FMD) Asia1/ND/165/004* (DQ10138) Asia1/ND/158/004* (003)(PD-FMD) Asia1/ND/156/004* (003)(PD-FMD) Asia1/ND/3/004* (PD-FMD) Asia1/ND/68/004* (DQ10136) Asia1/ND/35/004* (PD-FMD) Asia1/ND/37/004* (PD-FMD) Asia1/ND/15/01* (PD-FMD) Asia1/ND/6/003* (DQ10141) Asia1/ND//003* (DQ10140) Asia1/ND/3/003* (PD-FMD) Asia1/ND 95/08* (HQ4558) Asia1/ND 137/08* (HQ4561) Asia1/ND /08* (HQ4559) Asia1/ND 93/08* (HQ4557) Asia1/ND /08* (HQ4560) Asia1/ND 11/07* (HQ4554) Asia1/ND 7/07* (HQ4555) Asia1/ND 3/08* (HQ4556) Asia1/ND 1/07* (HQ4553) Asia1/ND/155/010* (JN47565) Asia1/ND/509/010* (JN47566) Asia1/BAR/8/009 Asia1/ND/18/011* (JN47567) Asia1/ND/107/01* (PD-FMD) Asia1/ND/31/01* (AY6333) Asia1/ND/14/95* (AF3678) Asia1/RN/10/004 (DQ11119) Asia1/ND/367/00* (PD-FMD) Asia1/ND/3/00* (PD-FMD) Asia1/ND/48/01* (PD-FMD) Asia1/ND/383/00* (PD-FMD) Asia1/ND/384/00* (PD-FMD) Asia1/ND/379/00* (PD-FMD) Asia1/ND/378/00* (PD-FMD) Asia1/ND/374/00* (PD-FMD) Asia1/ND/377/00* (PD-FMD) Asia1/ND/51/01* (PD-FMD) Asia1/ND/5/01* (PD-FMD) Asia1/Shamir/SR/ Asia1/ND/8/79 (EU553910) Asia1/ND/4/004* (003)(PD-FMD) Asia1/WBN/117/ (EU553911) Asia1/HKN/19/74 Asia1/AFG/1/001 (DQ11109) Asia1/PAK/8/008 Asia1/ND// (14) Asia1/PAK/6/009 Asia1/RN/1/01 Asia1/TUR/1/01 Asia1/TUR/49/011 Asia1/AFG/39/011 Asia1/PAK/1/01 Asia1/PAK/106/010 Asia1/BAR/1/011 Asia1/RN/33/011 Asia1/PAK/6/011 Asia1/ND/63/* (AY3044) Asia1/YNBS/CHA/58 (AY343) Asia1/ND/16/ Asia1/ND/18/ (DQ11116) Asia1/ND/15/81 (DQ11117) Asia1/PAK/1/54 (AY593795) Group Group Sindh-08 Group V d nd-001 c a b -001 PanAsia Pak- 95 A/ND/18/08* (FJ6146) A/ND/18/008* (HQ17) A/ND/13/008* (HQ170) A/ND/14/08* (FJ6144) A/ND/14/008* (HQ171) A/ND/437/008* (HQ174) A/ND/437/008* (HQ83591) A/ND/438/008* (HQ175) A/ND/407/007* (HQ1) A/ND/6/010* (HQ6663) A/ND/413/007* (HQ177) A/ND/417/007* (HQ178) A/ND/45/007* (HQ174) A/ND/360/07* (FJ6143) A/ND/360/007* (HQ175) A/ND/45/007* (HQ835) A/ND/11/009* (008) (HQ177) A/ND/13/009* (008) (HQ178) A/ND/9/009* (008) (HQ176) A/ND/17/009* (008) (HQ179) A/ND/17/009* (HQ835) A/ND/447/005* (HQ1) A/ND/447/005* (HQ83583) A/ND/15/06* (FJ6147) A/ND/15/006* (HQ170) A/ND//006* (HQ1) A/ND/163/08* (FJ614) A/ND/163/008* (HQ173) A/ND/16/005* (HQ181) A/ND/PD//010* (HQ17) A/ND/136/010* (HQ6668) A/ND/PD/83/010* (HQ1) A/ND/PD/135/010* (HQ170) A/ND/63/010* (HQ6668) A/ND/PD/13/010* (HQ179) A/ND/61/010* (HQ666881) A/ND/1/010* (HQ1) A/ND/1/010* (HQ6668) A/ND/8/009* (HQ175) A/ND/749/009* (HQ174) A/ND/PD//010* (HQ178) A/ND/46/010* (HQ6669) A/ND/PD//010* (HQ177) A/ND/45/010* (HQ6668) A/ND/53/08* (FJ6141) A/ND/53/008* (HQ179) A/ND/88/006* (HQ83588) A/ND/109/006* (005) (HQ1) A/ND/109/006* (HQ835) A/APS/58/05* (ND)(EU10) A/APS/66/05* (ND)(EU1088) A/APS/59/05* (ND)(EU10) A/ND/174/005* (HQ184) A/ND//006* (HQ195) A/ND//006* (HQ1) A/ND/101/006* (HQ1) A/APS/44/05* (EF1040) A/APS/68/05* (EF10403) A/APR/51/05* (EF10400) A/APS/50/05/1* (ND)(EU1091) A/APS/45/05* (ND)(EU10) A/ND/59/006* (HQ193) A/ND/6/006* (HQ188) A/ND/7/006* (HQ1) A/ND/6/006* (HQ835) A/ND/8/006* (HQ1) A/ND/106/006* (HQ1) A/ND/43/006* (HQ191) A/ND/43/006* (HQ835) A/ND/15/005* (HQ183) A/ND/3/006* (005) (HQ1) A/ND//006* (005) (HQ1) A/ND//006* (HQ83584) A/ND//005* (HQ1) A/ND/50/006* (005) (HQ1) A/ND/50/006* (HQ835) A/ND/195/007* (HQ17) A/ND/1/007* (HQ1) A/ND/49/007* (HQ1) A/ND/1/010* (HQ6665) A/ND/0/010* (HQ6664) A/ND/1/010* (HQ6667) A/ND/1/010* (HQ6666) A/ND/33/009* (HQ1) A/ND/33/009* (HQ666884) A/ND/333/009* (HQ6668) A/ND/333/009* (HQ1) A/ND/744/009* (HQ17) A/ND/744/009* (HQ666883) A/ND/747/009* (HQ1) A/ND/747/009* (HQ6668) - A/RQ/64 (AY5933) A/RN// (EF0) Sea- Thai A15/Bangkok/TA/60 (AY593755) A3/Kitale/KEN/64 (AY5936) A11/GER/9 (AGB)(EU553) EUR-SA AFRCA ndia A - ASA Appendix 35 Serotype: Topotype: ndia Bangladesh ndia Bangladesh Nepal 008, (x1) TN 007 SRL 011 Sri Lanka? Southeast Asia SRL unnamed lineage possibly from Southeast Asia ndia 011 Serotype: A Topotype: ASA ndia ndia Bangladesh 010 Myanmar 18 Sri Lanka Type A has never been recorded in Sri Lanka Middle East Pool 3 Serotype: Topotype: ASA 0 km ndia Bangladesh, A,,,, (/PanAsia) (/) (/nd-001) A (ASA/-05) (ASA/Sindh-08) Sri Lanka Type has never been recorded in Sri Lanka Pool 3 & FAR-09 BAL-09 PUN-10 /RN/8/005 SAN Turkey Lebanon Syria srael Jordan raq Kuwait Saudi Arabia Georgia Azerbaijan Armenia Bahrain Qatar UAE Kazakhstan Kyrgyzstan - Tajikistan A--05 HER-10 Asia1-Sindh-08 /PanAsia Sub-lineages of TER-08 (/Erzincan/57/008) YAZ-09 (/RN/7/009) FAR-09 (/Agri//010) SAN-09 (/Sanliurfa/64/009) BAL-09 (/RN/18/010) ANT-10 (/Gaziantep/153/010) PUN-10 (/PAK/16/010) ANT-10 YAZ-09 /UKG/35/001 (AJ539141) /SRL/1/009 /BAN/3/009 /BAN/4/009 /BAN/5/009 /BAN/4/009 /NEP/10/009 /BAN/0/009 /NEP/6/009 /NEP/15/009 /NEP/14/009 /NEP/11/009 /NEP/13/009 /RN/61/001 (DQ1648) nd-001 PanAsia -001 Yemen A--05 /PAK/16/003 (DQ165068) /ND/53/79 (AF107) /ND/R/75* (AF04) 1/Manisa/TUR/69 (AY5933) EUR-SA Pak- pen Session of the EuFMD: 01, Jerez de la Frontera, Spain
3 FMDV sub-lineages Turkey East Azerbaijan 79 Zanjan 61 Qazvin Kordestan Kermanshah YAZ-09 FAR-09 ANT-10 BAL-09 SAN-09 nd-001 Hamedan Lorestan Khuzestan Saudi Arabia Numbers represent WRLFMD Ref. Nos. (e.g. 88 = /RN/88/009) Markazi Qom 88 Chaharmahal and Bakhtiari Kohgiluyeh and Boyer-Ahmad Mazandaran Tehran Esfahan 00 km mi Fars Semnan 4 7 Yazd North 75 Hormozgan Kerman Razavi South Sistan and Baluchistan N.J. Knowles, 5 May 010 (updated 09 August 010) Afghanistan Pakistan FMDV sub-lineages Turkey East Azerbaijan 136 North Zanjan Mazandaran Qazvin Kordestan Tehran Razavi Semnan Hamedan Kermanshah 1 Qom Markazi Lorestan Esfahan South Yazd 11 1 Chaharmahal and Bakhtiari Khuzestan Kohgiluyeh and Boyer-Ahmad Kerman Fars >15% animals affected (010) Sistan and 0 Mortalities observed (010) Hormozgan 150 Baluchistan YAZ-09 FAR-09 ANT-10 BAL-09 United Arab 00 km SAN-09 Emirates mi PUN-10 Location unknown Afghanistan Pakistan Virus Pools Africa n Africa there are currently three FMD virus pools loosely defined as covering East Africa (Pool 4), West Africa (Pool 5) and Southern Africa (). There is some overlap between Pools 4 and 5. t has been suggested to extend pool 4 southwards to include Tanzania and to contract to exclude that country. Thus contains only the SAT serotypes. n the countries of the Maghreb (except for Mauritania) FMD is normally absent, however, periodic incursions occur either from the Middle East (Pool 3), West Africa (Pool 5) or more recently from Pool 4. There is little or no information on FMD in Chad, the Central African Republic, Equitorial Guinea and Gabon. East Africa Pool 4 SAT, SAT, SAT SAT Eritrea Chad Sudan,, SAT SAT 1, Central South SAT Afr. Rep. Ethiopia Sudan,, Equatorial Uganda SAT 1, SAT 1, Guinea Gabon Congo SAT SAT DRC, Kenya SAT 1, SAT Tanzania Pool 4 East Africa (, SAT 1, SAT, SAT 3) Burundi, Democratic Republic of the Congo, Djibouti, Eritrea, Ethiopia, Kenya, Rwanda, Somalia, Sudan, South Sudan, Tanzania, Uganda (with periodic spill-over into Egypt, Libya, northern Malawi, northern Zambia and the Yemen Arab Republic). (EA-1, EA-,, EA-4) A (AFRCA/G-, G-, G-) SAT 1 (,, V,,, X) SAT (,,, X, X, X, X, X) SAT 3 (V) SAT 1 topotype is thought to have spread from southern Africa into Tanzania and Kenya (the only countries in East Africa where this topotype has been recorded) during the early 10 s. 0 km East Africa Pool 4 West Africa Pool 5 Pool 5 West Africa (, SAT ) G- G- Type EA-4 Type A G- EA-4 EA-4 EA-1 EA- EA- EA- G- G- G- G- EA- G- EA- G- V Type SAT 1 X Type SAT Type SAT 3 Uganda V X X X X, SAT 0 km A, SAT Chad A/G-: various,, SAT Central A, Afr. Rep. SAT Equatorial Guinea Gabon Congo Benin, Burkina Faso, Cameroon, Cote d'voire, The Gambia, Ghana, Guinea, Guinea-Bissau, Liberia, Mali, Mauritania, Niger, Nigeria, Senegal, Sierra Leone, Togo (with periodic spill-over into Sudan). Although FMDV type SAT 1 has occurred in West Africa, the serotype has not been isolated from the region for 30 years [what about serology?]. () A (AFRCA/G-V) SAT 1 (V, V) SAT (V, V, ) pen Session of the EuFMD: 01, Jerez de la Frontera, Spain 3
4 West Africa Pool 5 Southern Africa Type Type A G-V G-V G- G-V G-V G-V G- G- G-V G-V G- Southern Africa (SAT 1, SAT, SAT 3) Angola, Botswana, Lesotho, Malawi, Mozambique, Namibia, South Africa, Swaziland, Zambia, Topotypes/Lineages SAT 1 (,, ) SAT (,,, X) SAT 3 (,,, ) Type SAT 0 km Angola Angola Zambia Malawi Zambia Malawi Mozambique Mozambique Namibia Namibia Botswana Botswana Swaziland Swaziland South Africa Lesotho FMD hotspots South Africa Lesotho FMD hotspots South America Pool 7, C /EUR-SA A/EUR-SA C/EUR-SA (not since 004) 0 km pen Session of the EuFMD: 01, Jerez de la Frontera, Spain 4
5 Questions (1) What are the precise mechanisms which result in the generation and expansion of new FMDV variants in Western Asia? Are West African buffalo persistently infected with FMDV and if so with which serotypes? Does SAT 1 occur in West Africa (not recorded in that region since 11)? Which FMD viruses occur in Chad, Equatorial Guinea, Gabon and the Central African Republic? What role do African buffalo play in the maintenance of FMD in East African cattle? Questions () s FMDV SAT 3 widespread in buffalo herds outside of Southern Africa as serology suggests? Why do we see relatively few African-Asian virus transfers? No in Africa and few SAT outbreaks in Asia why? Regular transfer of type viruses from the Horn of Africa to Yemen, but not other serotypes why? Are there any reservoirs of FMDV type C (which has not caused an outbreak since 004)? Acknowledgements Jemma Wadsworth Begoña Valdazo-González Antonello Di Nardo Valerie Mioulet Claudia Doel Miki Madi Don King Jef Hammond David Paton Nigel Ferris (retired) Geoff Hutchings (retired) Keith Sumption Botswana Vaccine nstitute Lanzhou Veterinary Research nstitute nderstepoort Veterinary nstitute and many others SE 939 World rganisation for Animal Health The Pirbright campus is being redeveloped pen Session of the EuFMD: 01, Jerez de la Frontera, Spain 5
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