Development and Application of Full Genome Sequencing to Support Epidemiological Investigations During FMD Outbreaks

300 mi

O/BUL/1/2010 (Burgas 30/12/2010) O/TUR/926/2010* (Bursa 26/07/2010) Bulgaria O/TUR/1086/2010* (Antalya 16/08/2010) O/TUR/840/2010* (Agri 15/07/2010) Gümüşhane O/TUR/1094/2010* (Giresun 11/08/2010) Kastamonu O/TUR/868/2010* (Eskisehir 20/07/2010) O/TUR/1003/2010* (Sivas 10/08/2010) Bursa Eskişehir Sivas Ağrı O/TUR/18/2010 (Gumushane 09/07/2010) Turkey O/TUR/883/2010* (Kastamonu 23/07/2010) Antalya Iran O/TUR/35/2010 (Erzincan 13/08/2010) O/TUR/153/2010* (Gaziantep) O/TUR/154/2010* (Gaziantep) O/IRN/94/2010 (West Azerbaijan 15/04/2010) O/IRN/92/2010 (West Azerbaijan 14/04/2010) 100 O/AFG/59/2010 (Samangan 14/05/2010) 97 O/PAK/36/2010 (Gilgit-Baltistan 29/07/2010) O/TUR/36/2010 (Kocaeli 13/08/2010) O/UKG/12/2001 (AJ311724) O1/Manisa/TUR/69 (AJ251477)

0.01

Development and application of full genome sequencing to support epidemiological investigations during FMD outbreaks

Begoña Valdazo-Gonzalez, Nick J. Knowles, Donald P. King Molecular Characterisation and Diagnostics Group FMD programme Institute for Animal Health GU24 0NF Ash Road, Pirbright, Surrey UNITED KINGDOM Summary and Conclusion Aim • To develop FG sequencing protocols for FMDV • To apply FG sequencing data to discover the transmission pathways of FMDV in 2011 Bulgarian outbreak M&M • 7 epithelium from Bulgaria,5 from Middle East • Full genome sequencing based on 21 overlapping fragments • Statistical parsimony methods (TCS) Preliminary results • Same ancestor for FMDVs collected from: • Kosti; • Rezovo; • Cluster of outbreaks in April • Closer sequenced FMDV: • Wild boar near Kosti, 4nt changes (minimun) • Bursa, Turkey, 26/07/10, 31 nt changes (minimum) Discussion and conclusions • Independent spread in Bulgarian livestock and wildlife from single introduction (from Turkey, most likely) • Cluster of outbreaks in April are related • Existence of intermediary hosts (wild boar most likely) • Careful interpretation of VP1 results FMDV: VP1 molecular characterization

* putative functions Membrane-binding Genome-linked 5’UTR Carboxy-terminal (VPg) 3’UTR 2x VP2 Protease VP3 Capsid self-cleaving NTP binding* Protease Polymerase 5x VP1 5x VPG VP1 L 1A 1B 1C 1D 2B 2C 3A 3B 3C 3D VP4 VP2 VP3 VP1 2A VP2 VP3 VP1 AAA (n) 3x VP1 VP3 VP2 Poly(C) VP2 2x VP2 VP3 VP3 2x Primary cleavages L 2A 3C VP3 VP2 VP1 VP1 Secondary cleavages 1B/RNA? 3C 3C 3C 3C 3C 3C 5x Kilobases 0 1 2 3 4 5 6 7 8

VP1 region 640 nt

• FMDV is a rapidly evolving RNA virus

• VP1 phylogenetic analysis widely used for broad scale FMDV strain characterisation

• Useful for regional and country-level epidemiology (transboundary movements) © Daniel Dalet / d-maps.com

Bulgaria 2011 outbreak: VP1 molecular characterization

O/BUL/1/2010 (Burgas 30/12/2010) O/TUR/926/2010* (Bursa 26/07/2010) BulgariaBulgaria O/TUR/1086/2010* (Antalya 16/08/2010) O/TUR/840/2010* (Agri 15/07/2010) Gümüşhane O/TUR/1094/2010* (Giresun 11/08/2010) Kastamonu Kastamonu O/TUR/868/2010* (Eskisehir 20/07/2010) Bursa O/TUR/1003/2010* (Sivas 10/08/2010) Eskişehir Gümüşhane Bursa Sivas Ağrı O/TUR/18/2010 (Gumushane 09/07/2010) Eskişehir Turkey Sivas Ağrı O/TUR/883/2010* (Kastamonu 23/07/2010) Antalya Turkey IranIran O/TUR/35/2010 (Erzincan 13/08/2010) Antalya O/TUR/153/2010* (Gaziantep) O/TUR/154/2010* (Gaziantep) O/IRN/94/2010 (West Azerbaijan 15/04/2010) O/IRN/92/2010 (West Azerbaijan 14/04/2010) 100 O/AFG/59/2010 (Samangan 14/05/2010) 97 O/PAK/36/2010 (Gilgit-Baltistan 29/07/2010) O/TUR/36/2010 (Kocaeli 13/08/2010) O/UKG/12/2001 (AJ311724) O1/Manisa/TUR/69 (AJ251477)

0.01 • FMD viruses from Bulgaria characterized as belonging to ME-SA/PanAsia-2ANT-10 lineage • Closely related PanAsia-2 viruses have been recovered from the Middle East during 2010 • VP1 sequences cannot discrimminate between closely related FMDV field strains Use of complete genome sequences for high- resolution tracing:

• Uncertainty about precise source of infection for the majority of IPs during field outbreaks since FMDV is a rapidly evolving virus:

• Nucleotide changes accrue linearly with time and are inherited

• Can we use full genome sequence data to trace the spread of FMDV during an outbreak? Background: 2007 UK outbreak

IAH2 IP6b AY593815 IP1b(2) IP3c MAH IAH1 IP1b(1) IP3b IP8 IP4b IP2b IP7 Sampled virus IP2c IP5 Putative ancestor virus IP5 • Detected by sero-surveillance M4 Nt change • After IP3 and IP4 Aa change • Seropositive cattle and sheep WINDSOR HEATHROW His to Arg • No acute clinical signs Asp to Gly • Evidence of healed lesions 8 8 6 6 EGHAM 3b3b nd 3c • 2 phase of outbreaks (IP3 – IP8) 7 7 4 4 3c X 5 5 X shares all the unique changes X X common to 1st phase M3 Therefore outbreaks are linked WOKING X M25 X and not due to independent Pirbright

2b 2b sources 1b1b X 2c GUILDFORD • IP5 (farm with FMD serology ALDERSHOT 10 km positive cattle and sheep) bridges gap GODALMING between two phases of the outbreak X 1c KEY FMD confirmed Preclinical (lab only) X No evidence of infection Goals of complete genome sequence analysis

[1] to identify the most likely source of the FMD outbreaks in Bulgaria

[2] reconstruct the relationship between outbreaks within Bulgaria (build a transmission tree)

[3] assess whether there are gaps in the sampling of disease outbreaks (evidence for undisclosed infection) Full genome sequencing: material & methods

Original clinical sample One operator: 48 hours • Epithelium Two operators: 24 hours - suspension

BULGARIA – One per herd, higher CT value RNA extraction Wild boar – BUL1/2011 • RNeasy Mini Kit (QIAGEN) Starting point: Firat-Saraç, M. SAP, Turkey FAO/EuFMD (Project PR41764) 12LP1 – Kosti DTU Veterinary. National 12LPN3 – Rezovo Veterinary Institute Reverse Transcription BUL11/11 - Kirovo • Oligo-dT primer (Rev 6) (Ryan et al. 2008) BUL20/2011 – Golyamo Bukovo Negative controls~700b BUL26/2011 -Granichar cDNA clean up BUL30/2011 – Fakia ~700b PCR MIDDLE EAST – VP1 5UTR+P1 NSP+PoliA Backup ISR2/2011 cc DNA clean up 4 epithelium from Turkey Improved protocol Cycle sequencing reaction

Ethanol Precipitation Negative controls

ABI PRISM 3730 DNA Analyzer ~700b Data analysis:Statistical parsimony methods (TCS) 2-4 coverage /site 5UTR+P1 NSP+PoliA Backup Origins of the outbreaks in Bulgaria: Preliminary results: 7087 nt (most L-fragment )

ISR/02/2011 TUR/926/2010 2/2011 (Bursa) 26/07/10

10 nt changes 57 nt changes 30/12/2010

21 nt changes BUL/1/2010 (wild boar) 3 nt changes

21 nt changes 9 nt changes

12 nt changes

41 nt changes TUR/18/2010 (Gümüşhane) TUR/840/2010 09/07/2010 (Agri) TUR/36/2010 15/07/10 (Kocaeli) 13/08/2010 Putative common ancestor of the Turkish and Israeli viruses Putative common ancestor of Bulgarian viruses Relationship between Bulgarian field strains: TCS analysis - FG (First phase/wave)

Kosti village 11 nt changes 12LPN1 (IP 1)

4 nt changes TUR/18/2010 BUL/1/2010 35 nt changes (Gümüşhane) (wild boar) 09/07/2010 30/12/2010 12LPN3 (IP 4) 14 nt changes Rezovo village

putative common ancestor of the Bulgarian viruses

All nucleotide substitutions are unique

includes data from DTU, Lindholm Interpretation of data from first wave/phase

• The FMD outbreaks in Kosti and Rezovo villages are unlikely to be directly linked.

• Both have a common ancestor close to the virus from wild boar.

• The long branches between the putative common ancestor and each of the two outbreaks examined (IP1 and IP4) suggest possible intermediate hosts (either wildlife or domesticated animals). Full genome sequencing: TCS analysis Preliminary results (26/4/11): 7087 nt (most L-fragment )

30/12/2010 “TREE-LIKE” ≠ Linear pattern (UK2007) BUL/1/2010 02/2011 Wild boar 8 nt changes 12LPN1 Kosti 4 nt changes 02/2011 14 nt changes 12LPN3 Rezovo 6 nt changes BUL/11/11 Kirovo changes

(Bursa) 19/03/2011 26/07/2010 4 nt changes 31 nt 31 TUR/926/2010 28/03/2011

13 nt changes BUL/26/11 Granichar 28/03/2011 11 nt changes BUL/20/11 BUL/30/11 Golyamo Fakia Bukovo 01/04/2011

Putative common ancestor of Bulgarian wild board and first phase of the outbreaks Putative common ancestor of the second phase of the Bulgarian outbreaks Full genome sequencing: TCS analisys Preliminary results: 7087 nt (most L-fragment )

Secon Phase/wave March -April

Goliamo Black Sea Bukovo

Fakia Granichar Kirovo

Kosti

Wild boar First phase/wave January/February Rezovo

Turkey Future work • Keep sequencing  Gaps  TUR8/2011  Momina Tsarkva • Link genetic and epidemiological data • Further analysis:  Comparison with previous studies: 2001 and 2007 UK outbreaks  Molecular clock: BEAST Acknowledgements

Institute for Animal Health

Diagnosis of Vesicular disease group:Nigel Ferris and Geoff Hutchings

Molecular diagnostic and diagnostic group:Jemma Wadsworth, Miki Madi and Valerie Mioulet

SAP Foot-and-Mouth Disease Institute, Ulus, Ankara, TURKEY

Müge Firat-Saraç, Ünal Parlak and Fuat Ozyoruk

National Diagnostic and Research Veterinary Medical Institute

Lilyana Polyhronova and Georgi Kirilov Georgiev

National Veterinary Institute (DTU)

Graham Belsham

Food and Agriculture Organization of the United Nations/European Commission for the Control of Foot-and- Mouth Disease (Project PR41764)

Department for Environment, Food and Rural Affairs (SE2938)

Biotechnology and Biological Sciences Research Council Item 11 REPORT OF THE SESSION OF THE RESEARCH GROUP OF THE STANDING TECHNICAL COMMITTEE OF THE EUROPEAN COMMISSION FOR THE CONTROL OF FOOT-AND-MOUTH DISEASE (EUFMD) HELD AT Vienna (Austria) 29 September-1 OCTOBER 2010 (OPEN SESSION) 1 OCTOBER 2010 (CLOSED SESSION) FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS ROME, 2010 Table of Contents Acknowledgements ...... 3

Considerations and recommendations of the Open Session ...... 5

Report ...... 11

Open Session of the Research Group, 29 September-1 October ...... 11

Opening ...... 11

Frankel Lecture ...... 12

Control of FMD in Japan ...... 12

Session 1a: Progressive control of FMD - in practice ...... 12

Session 2a: FMD risk assessment, threat detection ...... 13

Session 1b: Vaccine Development ...... 13

Session 2b: Vaccine control ...... 13

Session 3a: Antigenic diversity, vaccine selection and monitoring ...... 13

Session 4a: The Progressive Control Pathway for FMD ; papers on lessons learnt from practise ...... 14

Session 6a: Monitoring Control and Vaccination Programmes Session and Panel ...... 14

Session 4b: FMD molecular characterization...... 14

Session 5a: Diagnostics ...... 14

Session 5b: FMD epidemiology – Eurasia and South America ...... 14

Session 6b: FMD epidemiology ...... 15

Africa ...... 15

Session 7a: Control of FMD in free countries ...... 15

Session 7b: Antivirals and other developments ...... 15

Session 8a: Surveillance technologies...... 15

Open session – FMD Real Time Training and Private Sector Platform ...... 16

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Acknowledgements The EuFMD Commission gratefully acknowledges the support of the European Commission, and the EuFMD Member States, for funding of the Committee meetings and Working Groups, and to the Chairman and Leaders of the Working groups for their guidance of the program.

The FMDWeek2010 is made possible through the outstanding efforts of Dr Ulrich Herzog, President of the EuFMD Commission, and Dr Polesney, AGES, and his team, to organize the facilities and hospitality throught the enthusiasm and interest of the participants, and the dedication and extraordinary efforts of the EuFMD Team – especially Nadia Rumich, Enrique Anton and Eleonora De Fea – and Claudia Ciarlantini, graphic designer, from FAO AGA.

We would also like to thank, for their hospitality, the Minister of Health, Alois STÖGER dipl. And the Mayor of Vienna, Dr. Dr. Micheal HÄUPL.

Organization of the 2010 Open Session Chairman of the EuFMD Standing Technical Committee: Dr. Aldo DEKKER

Leaders of the Working Groups: Dr. David Paton, IAH Pirbright, UK Dr. Giancarlo FERRARI, FAO Rome, Italy Dr. Emiliana BROCCHI, IZLER Brescia, Italy

Members of the EuFMD Standing Technical Committee: Dr. Bernd HAAS Dr. Dónal SAMMIN Dr. Emiliana BROCCHI Dr. Hagai YADIN Dr. Naci BULUT Dr. Stefan ZIENTARA Dr. Kris DE CLERCQ Dr. David PATON Dr. Jeff HAMMOND Dr. Georgi Kirilov GEORGIEV Dr. Helen HONDROKOUKI Dr. Fernando BOINAS Dr. Andrzej KESY Dr. Pascal HENDRIKX

The generous support of our sponsors has greatly assisted to reduce the costs of the event, enanbling us to widen participation, and is greatly appreciated.

DG-SANCO

EMPRES-Animal Health

Intervet International BV

Merial

Prionics

And special thanks to our Hosts and Local Organiser:

BUNDESMINISTERIUM FÜR GESUNDHEIT

AGES

Vetmeduni Vienna

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Considerations and recommendations of the Open Session Considering that:

1. There is a need to improve information flow between field, laboratory, and disease management teams, national and internationally, to enable each level to better identify the significance of disease and virological patterns; 2. Both free countries and those in endemic regions need to identify suitable vaccines/antigens for their emergency and preventive programs, but there is a lack of standardized framework or approach to deal with the uncertain incidence in endemic regions and risks of introduction, and to the level of cross-protection to be expected, and the duration of benefits of change in seed viruses; 3. In order to progress along the pathway, countries are required to provide evidence of application of activities involving monitoring and surveillance of FMD and on the application and impact of control programs. To generate such information, countries are challenged with the issue of designing complex surveys; 4. Value /market chain analysis methods are a means to identify critical FMD risk points in affected (and at risk) countries, building upon more traditional epidemiological and virological approaches; 5. In the last three years the PCP approach has been used in several parts of the world, and greater confidence in the results of Stage assessment could be achieved with further definition of the requirements in each stage, and to the system for verification of control activities (particularly the requirement for release of results). 6. There has been a focus on molecular diagnostics to explain the dynamics of FMD infection, but structured field investigation will provide a wider range of information and should not be overlooked; 7. There is need for collection of sufficient field samples, and even more important structured disease investigation accompanying sample collection and investigation of disease events. 8. Most countries in Subsaharan Africa are at PCP level 0; 9. Most countries have national reference laboratories for FMD but there are no Reference Centers (RCs) recognized by FAO or OIE within virus pools 4 and 5; 10. The economic and politic importance of FMD appears to be increasing, but the economic assessment of control options has yet to be systematically undertaken in most countries. 11. Prerequisites for efficient control include early warning and early detection, rapid and efficient response measures, and national capacity to inform and assist decision makers based on a well tested combination of local and national expertise and validated models.

Recommends that:

Regarding recommended antigen strains maintained in vaccine banks

1. Greater effort is placed by the international organizations to integrate the virological typing data such as generated by the World Reference Laboratory (WRL), with information from official and unofficial sources as a result of regional projects and programs; this effort should include greater integration and support for FMD networks and laboratories connecting National Reference Laboratories in each virus pool; 2. Continue development and evaluation of the model for ranking the risk posed by viral pools, but ensure that the limitations and assumptions are clearly identified and communicated with the results; both the ranking system and the results of virological assessments should be presented to the next EuFMD Commission Session; 3. More effort should be placed on integrating intra-regional animal movements information with other layers of risk information, to better assess risk associated with new virological findings; 4. Strain recommendations for inclusion in vaccines should be risk based, as well as taking account of international and regional vaccine availability and vaccine matching data; 5. To improve vaccine selection and stimulate the development of more cross-protective vaccines, research should be directed at understanding the repertoire and mechanism of action of the polyclonal antibody response as well as defining the protection associated with different paratopes; 6. International cooperation between vaccine producers and reference laboratories should be encouraged to help overcome problems in availability and access to vaccine matching reagents, i.e. vaccine strains, sequence data, field isolates and antisera; FAO and other vaccine purchasers should place conditions on suppliers to provide suitable reference reagents, or fund their production by independent laboratories, to ensure the vaccine matching system is sustainable; 7. Studies to better characterize and improve the reliability of vaccine matching methods should continue to be supported, not only for current vaccine selection but also for development of new in vitro and computer based (in silico) selection processes; 8. A fuller understanding is needed of the antigenic diversity within some serotypes and regions and of the significance that this has for vaccine induced protection. The EuFMD Research Group should assess the gaps in knowledge and their relative importance; 9. A more systematic approach should be developed and used to evaluate vaccine effectiveness in the field, and report made summarizing current studies and options, to the next Research Group Session.

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Regarding Vaccine control

10. In process control methods, for quantification of FMD-NSPs in vaccines should be further validated; if used by FMD vaccine producers, methods and results should be published when part of their claim for purity; 11. Indirect assessment of FMD vaccine potency and vaccine matching should be harmonized to obtain exchangeable / comparable results by close co-operation between vaccine producers and international FMD reference laboratories; 12. Antigen stability should be given greater priority in quality control, and standards and associated tests to measure stability should be further developed and validated by both vaccine producers and research laboratories.

Regarding : Antigenic diversity, vaccine selection and monitoring

13. Greater efficiency in the identification of significant variation in FMDV could be achieved through optimizing use of regional and world reference laboratories services; flowcharts describing sampling procedures could be agreed , covering sample selection, tests at national and regional level, and when to send samples to reference laboratories for advanced typing; 14. EuFMD/FAO should support initiatives that connect NRLs and International Reference Centres (IRCs) to achieve greater efficiency in application of molecular typing, using protocols which meet the quality standards of the FAO RCs; 15. More should be done to investigate the performance of vaccines in the field as this may differ from what was found at the point of manufacture for reasons such as vaccine stability. Greater application of vaccine effectiveness measurements are needed, comparing the risk of disease in vaccinated animals to the risk of disease in non-vaccinated animals. Different vaccination regimes could also be compared to identify optimal strategies.

Regarding: The Progressive Control Pathway for FMD in practice

16. That the EuFMD Working Group on the Progressive Control Pathway (PCP) Guidelines be further expanded to involve those epidemiologists with expertise in design of surveillance programs, and who are working on FAO or other PCP support projects, to learn the lessons from application, to further develop practical guidelines, and standards for surveys and analysis of data; 17. FAO is encouraged to further develop the market chain analysis approach and promote its use and integration in the framework of PCP/Roadmaps; 18. FAO and OIE are encouraged to further define requirements for each stage, make them verifiable and consider the possibility of some form of PCP status acceptance; 19. Support necessity of cooperation of EU, OIE and FAO on the PCP. Regarding : Diagnostics

Concerning pen-side tests

20. Information regarding performances of Lateral Flow Devices (LFD) for FMD antigen detection should be systematically collected, and guidelines developed for dealing with uncertainty (interpretation of weak results, false positive detected in the field, if any); 21. LFD for serotype-specific detection should be developed, and if the commercial market is uncertain, international organizations should consider taking the lead to commission LFD for field evaluation (EuFMD/FAO/EC ); 22. Research on development of other pen-side tests for antigen detection based on alternative methodologies, such as dry ELISA, is encouraged; 23. Continued development of high sensitivity (better than LFD) and high speed (similar to LFD) penside tests using genome amplification methods are recommended; 24. Guidance on the use of pen-side tests should be updated, particularly regarding use in countries without a national reference laboratory capable of alternative confirmation methods, should be established.

Concerning genome detection

25. Given the wide variation in protocols applied for RNA extraction and RT-PCR, it is recommended that countries make greater use of the protocols validated at the WRL (for both RealTime and classic RT-PCR); the SOPs on the WRL Web site should be used; 26. Diagnostic development priorities should be: i) the Development of ready-to-use kits for Real Time PCR, similar to those already commercially available for other TADs; ii) Development and validation of serotype-specific RT-PCR; iii) development and validation of multiplex RT-PCR appropriate for regional settings (as serotypes and strains differ).

Concerning Antigen detection and typing ELISA

27. Ready-to-use kits should be commercialized and the international organizations, representing buyers, should become early adopters for evaluation and to encourage sustainable supply.

Concerning immunoassays for Antibody detection

28. Ready-to-use kits for SP antibodies should be further developed, validated and made available; 29. The WRL should make available on demand a cost recovery basis, 1) international serological standards for Asia-1, SAT types, and for relevant antigenic variants (type A) and 2) proficiency panels for calibration and evaluation of in-house assays, and for batch control; 30. The EuFMD Research Group should work on guidance / recommendations for use of Solid Phase Competition ELISA compared to the Liquid Phase Blocking ELISA.

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Concerning QA/QC

31. FAO or the Research Group of the EuFMD should develop guidance on the minimum standards for QA/QC for laboratories performing services required for the different Stages of the PCP. 32. Diagnostic test producers should make available validation dossiers, for accreditation according to ISO17025.

Concerning new developments

33. Multiplex tests: priorities are a multiplex PCR with sufficient sensitivity, but also there should be attention to multiplex detection of FMD antigens and antibody, and greater use of recombinant antigens (VLP; universal ligands, etc).

Regarding FMD epidemiology – Eurasia and South America

34. Greater attention must be made to training in disciplines needed to rapidly assess “What is the impact on animal health, what are the possible routes of transmission and what are the socio- economical effects?” This information is necessary to identify and address the critical control points in the PCP, and is helpful to feed back to field veterinarians to support their activities in controlling FMD; 35. The time delay between disease event and results of molecular typing must be shortened to a few days, in order to support decision making in complex epidemic situations. Support should be given to use the power and throughput in high technology laboratories to test samples rapidly or transfer technologies to Regional RCs and NRLs in affected areas.

Regarding FMD epidemiology – Africa

36. International organizations should support countries in Sub-Saharan Africa to initiate PCP Stage 1 activities. Training of regional experts in PCP could assist to build confidence in design of activities, such as sero-surveillance and epidemiology and socioeconomic assessments needed to develop country strategies; 37. EuFMD or FAO should strengthen regional laboratories to support primary diagnosis in NRLs in West/Central and Eastern Africa.

Regarding Control of FMD in free countries

38. EuFMD reviews the use by countries of decision support systems, including models, in developing and testing their contingency plans for a variety of scenarios of disease introduction, and explore the impact of different control measures; 39. More research is conducted on the likely intra-community spread of FMD if introduced at different times and locations into the EU; 40. The continued development of expertise in FMD recognition and immediate response, but ensuring that laboratory veterinarians as well as field veterinarians are trained from each state, since they will need to work together to ensure rapid diagnosis and to establish surveillance; 41. Continued support for work to identify contact rates and critical points for transmission, with a view to develop practical methods for application in contingency planning or during the early epidemic response.

Regarding FMD training

42. Trainees from the Real Time training include, as far as possible, trainers in their own countries; 43. Better preparation for the training by the trainees would improve the team work and contribution to final output; 44. Refresher courses and workshops should be organized and update the trainees on developments; and that modules for additional FMD experience should be considered (outbreak management, use of decision support models…).

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Report

Open Session of the Research Group, 29 September-1 October

An Open Session of the Research Group of the Standing Technical Committee of the EuFMD was held in Vienna, Austria, between 29 September -1 October 2010, with the Theme “New tools and challenges for progressive control”. The Session was attended by over 240 participants from across the world, predominantly from Europe and Africa, but also with good participation from East Asia and South America. The program was organized into fourteen technical sessions were held, covering recent advances and ongoing technical constraints affecting progressive control of FMD. The Session considered six keynote papers and 82 presentations, relating to the 14 items. One evening debate was held, and forty two posters presented. Two panel discussions were included in the program, one concerning the control and monitoring of vaccination and another with private industry representatives.

The Agenda of the Session is found at (Appendix 1); the list of participants is found in (Appendix 2).

Opening

The Session was opened by Dr. Sonja Hammerschmid, Rector of the University of Veterinary Medicine, Vienna, who reminded the participants of the long history of the teaching and research in Vienna, from 1765. Control of infectious diseases had always been a major importance in Austria, being situated in the European landmass and at risk from sweeping epidemics arriving from far and near. Veterinary schools have an important role to ensure that the next generations of veterinarians have an understanding of their role, which can be crucial for early recognition and response.

Dr Ulrich Herzog, CVO Austria and Chairman of the EuFMD Executive Committee, welcomed participants to Vienna; he was glad to see that several networks and projects had used the opportunity to organize side meetings, and trusted that the Open Session would not only a great scientific success but assist experts to work together in new ways and with new ideas. He considered the Open Session of major International Importance and looked forward to receiving ideas and views on how the role as a forum and meeting point could assist in further international collaboration on FMD science. He declared the meeting Open.

Two Plenary presentations were then given, one being the Frenkel Lecture, and the other on the management of the recent type O incursion into Japan in 2010.

Frankel Lecture The Principal Plenary Lecture at the Open Session is named after the renowned Dutch scientist whose “Frenkel method” introduced the first possibility of mass vaccine production and application in the world.

The Lecture “Integrated procedures to assess FMD vaccine quality and herd immunity in Argentina” was presented by Dr Jose La Torre (Argentina). This paper described the development of the scientific basis for current control of vaccine quality and potency , and of vaccination programme monitoring, that has been a major part of the improvement in success of vaccination for the control of FMD in Argentina. The lessons learnt, he proposed, should be understood and applied in other regions where vaccination is to play the principal control measure in preventing virus circulation (Appendix 3).

Control of FMD in Japan Toshiyuki Tsutsui presented an paper on “The Foot and mouth disease epidemic in Japan, 2010”, which described the evolution and progression of this incursion which proved extremely challenging for control, and resulted in massive costs for the sector and Government, with stamping policy changed to vaccination during the crisis, which was followed by culling of vaccinated animals. Japan is a country that is usually FMD-free, and the area most affected was densely populated with pig, dairy and beef farms. He described some of the challenges encountered when implementing control in this area. (Appendix 4)

Session 1a: Progressive control of FMD - in practice The Session introduced the PCP for FMD, which was first developed by EuFMD together with FAO projects at a workshop in November 2008 for development of Long Term Regional approach to FMD control in West Eurasia. Issues considered: what have we learnt from applying the PCP approach in West Eurasia in 2008-10? After national sero-surveys for FMD, then what? Is there a smart alternative to national vaccination campaigns in all species? Are the guidelines for Monitoring and Surveillance, and for lab capacity in each country, appropriate? How do we identify critical control points, and bring in socio-economic assessments to identify how and what can be done better? This first session began with a keynote address by Keith Sumption, Secretary, EuFMD Commission (Appendix 5). Dr Kris de Clercq, representing the OIE, then described the work in progress on the relationship between PCP Stages and the OIE Standards (Appendix 6) Further presentations illustrated the experience of applying PCP to country situations, including design of surveys to achieve Stage 1 (Dr Ferrari :Appendix 7:), the monitoring of vaccination and control measures (Dr Yadin, Appendix 8) , the progress from zonal Stage 3 to official recognition of freedom under vaccination in Thrace (Dr Potzsch, Appendix 9) , and the activities needed to maintain freedom (Dr Füssel, Appendix 10).

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Session 2a: FMD risk assessment, threat detection Issues in this section were: how do we quantify/prioritise the threats from each virus pool, to Europe? How can we better use regional networks to give us “viral intelligence” on emerging threats? Can we predict epidemics within West Eurasia, based on long term monitoring and viral characteristics? What viral predictors could be used? How do we get closer to real-time information on FMD events? Does risk information change lead to any difference by national risk managers (e.g. to the Far-East type O epidemics in March/April 2010).

This session featured a keynote presentation from Dr Jef Hammond, Head of the FAO World Reference Laboratory for FMD, Pirbright (Appendix 11).This was followed by presentations considering if FMD epidemics can be predicted (Dr Bulut, Appendix 12) , on risk of FMD incursions from different regions to Europe (Dr McLaws, Appendix 13), on the genetic basis of the type A epidemic development in Turkey (Dr Ozyuruk, Appendix 14), and the further development of the FMD BioPortal (Dr Perez, Appendix 15).

Session 1b: Vaccine Development Developments in vaccine development and immune response to FMDV were presented with 6 presentations (Appendices 16-21). Four of these papers involved work with different approaches (reverse genetics and expression systems) to genetically engineer FMDV .

Session 2b: Vaccine control Seven papers were presented (Appendices 17-23), covering important developments in emergency vaccine formulation procedures, work to improve thermostability, indirect assessment of potency, serology for herd immunity, in process controls for NSP in vaccines, and effect of thiomersal on FMDV virions.

Session 3a: Antigenic diversity, vaccine selection and monitoring This Session was organised by the Antigenic diversity and Vaccine selection Working Group, under the EuFMD research group, led by Dr David Paton. The Issues: how can we improve the guidance (cross- protection, antigenic relevance) to Vaccine bank managers on which antigens to hold for the current risks? What do new approaches (such as Antigenic Cartography) offer? How will these methods change our working practises in Global Viral Threat identification and in countries using vaccination? Why do we seem to have a problem with type O vaccination, when type O is relatively antigenically stable?

This session opened with a keynote presentation by David Paton (Appendix 24), followed by 7 further presentations on antigenic diversity and methods to estimate antigenic relatedness and cross- protection, including progress to predict from sequence data, the use of serological data, including in antigenic cartography, and cross-protection studies between type O (Manisa and Campos). (Appendices 25-31). Session 4a: The Progressive Control Pathway for FMD ; papers on lessons learnt from practise Six papers were presented in this session that described approaches to surveillance, economic considerations and FMD control within the PCP framework. The first two (Dr Ferrari, FAO, and Dr Bartels, EuFMD) considered design of surveys needed for risk assessment (PCP Stage1) , followed by papers on methods for improving the identification of control measures in the market chain with socioeconomic assessments, and on implementing the PCP approach in Ethiopia and the TransCaucasus (Appendices 32 to 37).

Session 6a: Monitoring Control and Vaccination Programmes Session and Panel Two papers were presented in this session that described different approaches to evaluate vaccination at the herd level (Appendices 38-39) . This was followed by a panel discussion.

Session 4b: FMD molecular characterization This session comprised 6 presentations relating to advances in the molecular characterisation, starting with an overview on definitions and nomenclature given by Dr Nick Knowles (Appendix 40), followed by presentations on applications and advantages of full FMD genomic sequencing when applied to understanding big epidemics and localised spread between and within herds (Appendices 41-42). The potential of next generation sequencing was presented by Dr Caroline Wright (Appendix 43) and findings from Ethiopia and Pakistan/Afghanistan (Appendices 44-45).

Session 5a: Diagnostics This Session was organized by the Diagnostics Working Group of the EuFMD Research Group, led by Dr Emiliana Brocchi. Issues: FMDV nomenclature: proposal for new system. Test validation – what’s new, what are the gaps? What are the gaps in our diagnostic repertoire? Which diagnostic tests are needed at each PCP Stage, from endemic to near-freedom? (Guidelines). What are we gaining from Full-Genome sequencing to guide diagnostics? How do we rapidly type FMD to strain level, in affected West Eurasian countries? Can we profile herd infection using diagnostics, to identify how long infection has been in a herd? Carrier status of domestic buffalo. This large and important session considered a keynote presentation (Dr Wosloo, Appendix 46) and 12 papers concerning the detection of FMD virus, antigen and antibodies (Appendices 46-58). These papers covered important developments that could lead to preserved RNA rather than live virus being transported for reference centre typing, with use of transfection to recover live virus (project supported by EuFMD ); the development of simple ELISA for antigen detection, the evaluation of penside tests, and comparison of rapid one-step RT-PCR assays . Global and regional harmonisation and proficiency testing operated by WRL (for FAO and the EC) and Regional examples (for SADC) were presented.

Session 5b: FMD epidemiology – Eurasia and South America This Session consisted of 11 presentations on the epidemiology of FMD epidemiology in Eurasia and South America (Appendices 59-71). These papers highlighted the resurgence of interest in FMD epidemiology, and to the move beyond molecular studies into understanding contact networks and a Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

better description of the space and time dynamics of FMD. These studies fit well with requirements of PCP Stage 1 to define the risk populations and transmission risks.

Session 6b: FMD epidemiology Issues: what have we learnt, on why, when, how epidemics or outbreaks occur? Risk based surveillance: experience and guidance. Surveillance in vaccinated populations: still a problem with impure vaccines? What have we learnt from epidemics in free countries in 2010? Offered papers were invited from all regions.

Africa This session included 10 papers related to issues important to FMD in Africa, including results from sero- surveys and molecular and virological studies (Appendices 70-79).

Session 7a: Control of FMD in free countries This session included 6 scientific presentations concerning FMD preparedness and control in countries that are usually FMD-free (Appendices 80-88) , highlighting the importance of a using different rigorous testing procedures for evaluation of contingency plans for FMD incursions.

Session 7b: Antivirals and other developments Five papers were presented in this session (Appendices 89-93) concerning FMDV pathogenesis and recent advances in the development of antiviral drugs.

Session 8a: Surveillance technologies Issues: mobile phones and FMD: how do we communicate , quicker, smarter to those that need to know? Farmer-led reporting: can we rapidly scale up information flows during a crisis? iPhones and FMD. New diagnostics; theoretical or practical? What quality standard must novel FMD vaccines meet for international acceptance?

Two papers were presented in this session, concerning technological and diagnostic technologies relevant to FMD surveillance (Appendices 94-95) .

Open session – FMD Real Time Training and Private Sector Platform Issues: this Session reviewed lessons learnt from training of over 70 persons in FMD recognition and outbreak investigation practices, under the EuFMD/EC real-time FMD Training Program in 2009-10. How do we retain the experience and keep trainees up to date? Do we need refresher events/courses/online exercises, and to extend the experience to include FMD in pigs, etc? The program ended with an open session that included a description of FMD real-time training courses offered by EuFMD in 2010 (Appendix 96) and the platform was given to the private sector (representatives from Intervet and Merial).

Closure The EuFMD commission gratefully acknowledges the support of Dr Ulrich Herzog, CVO Austria and President of the EuFMD executive Committee, the local organizing agency AGES, as well as the companies who generously sponsored the meeting (

Open Session, Research Group, Vienna (Austria) 29 Sept- 1 October 2010

Vaccine Selection

Jef M. Hammond, Donald P. King, Nick J. Knowles, Jemma Wadsworth, Bob Statham, Yanmin Li, Phil Keel, Jo Stoner, Pip Hamblin, Ginette Wilsden, Geoff H. Hutchings, Nigel P. Ferris, Valerie Mioulet, Miki Madi, Begona Valdozo, Faiza Hamid and Elizabeth Wilson

Institute for Animal Health, Ash Road, Pirbright, Surrey, GU24 0NF, UNITED KINGDOM Vaccine Recommendations (Antigen Banks)

Vaccine recommendations for free countries included in each quarterly report How to: • Improve process for vaccine recommendations • Increase information made generally available • Provide a clearer understanding of risk • More of a systems approach The Importance of Networks

• OIE/FAO FMD Reference laboratory network

• FMD Vaccine Bank holders network

• PTS network laboratory diagnosis vaccine matching

• Global FMD Research Alliance WRLFMD • SEACFMD and other initiatives To make available accurate and timely global surveillance information – Value of sharing information – Developing trust and shared vision Enhanced Surveillance: OIE/FAO Lab network

• WRLFMD: Pirbright, UK • RRLSEA: Pakchong, Thailand • LVRI: Lanzhou, China • FGI ARRIAH: Vladimir, Russia • PDFMD: Mukteswar, India • RRLSSA: Gabarone, Botswana • FMD-Laboratory: Embakasi, Kenya • PANAFTOSA: Rio de Janeiro, Brazil Approximately ~2300 samples • LFADLCT: Argentina tested during 2010 • ARC-OVI: Onderstepoort, RSA • PIADC: Plum Island, USA • CODA-CERVA-VAR: Ukkel, Belgium

Institute for Animal Health Outputs

Current •Highly detailed analysis of virus •Serotype •Genotype/strain •Possible source •Vaccine matching by lab assay

•Average number of r1 values generated per week = 23.22 •Total number of r1 values generated in 2010 = 1209 •Animal experiments •Detailed reports Progress •Complete genome analysis •Epitope mapping •Antigenic cartography

•Combine data from all inputs to provide a more comprehensive analysis •Use of high potency vaccines Samples and virus isolates made by region in 2010.

In total 38 different countries submitted 2,338 samples to OIE/FAO FMD Network Laboratories

53% to WRLFMD 700

600 samples

500 isolates

400

300

200

100

0 Eastern Asia Southern Eur-Asia Eastern Western Southern South Asia Africa Africa Africa America Overview of serotyping results for 2010

2% 2.5% 7% 8.5%

O A SAT 1

80% SAT 2 Asia 1

80% of the samples characterised in 2010 were O serotype.

Note that serotypes C and SAT 3 were not detected. 300 Samples processed by WRLFMD

250 2010 2011

200

150

100

0 IRAN LAOS LIBYA NEPAL KENYA QATAR ZAMBIA ERITREA NIGERIA SENEGAL BAHRAIN ETHIOPIA VIETNAM ECUADOR EMIRATES BULGARIA THAILAND MALAYSIA TANZANIA MYANMAR CAMBODIA ZIMBABWE MONGOLIA BOTSWANA TURKEY**** HONG KONG HONG PAKISTAN*** UNITED ARAB SOUTH KOREA SOUTH MOZAMBIQUE SOUTH AFRICA SOUTH AFGHANISTAN**

Vaccine matching with O Manisa 2011 6

5 No Match 4 Match 3

-1

-2 Iran Pakistan Turkey Bulgaria Israel ROK

Asia1/PAK/32/2011 88 Asia1/PAK/38/2011

Asia1/PAK/109/2010

Asia1/PAK/50/2011 FMDV Asia 1 - 2011 Asia1/PAK/49/2011 Asia1/PAK/39/2011 Software: MEGA 5.0 Asia1/PAK/37/2011 Analysis Asia1/PAK/36/2011

Analysis ------Phylogeny Reconstruction Asia1/PAK/35/2011

Scope ------All Selected Taxa Asia1/PAK/16/2011

Statistical Method ------Neighbor-joining Asia1/PAK/15/2011

Phylogeny Test Asia1/PAK/14/2011

Test of Phylogeny ------Bootstrap method Asia1/PAK/13/2011

No. of Bootstrap Replications ------1000 Asia1/PAK/12/2011 Substitution Model Asia1/PAK/11/2011 Substitutions Type ------Nucleotide Asia1/PAK/8/2011 Model/Method ------Kimura 2-parameter model Asia1/PAK/7/2011 Substitutions to Include ------d: Transitions + Transversions Asia1/PAK/111/2010 Rates and Patterns Asia1/PAK/110/2010 Rates among Sites ------Uniform rates Asia1/PAK/108/2010 Pattern among Lineages ------Same (Homogeneous) Asia1/PAK/106/2010 Data Subset to Use Asia1/PAK/33/2011 Gaps/Missing Data Treatment ------Pairwise deletion Asia1/PAK/34/2011 Codons Included ------1st+2nd+3rd+Non-Coding Asia1/PAK/17/2011 No. of Sites : 635 100 Asia1/BAR/1/2011 Asia1/BAR/2/2011 No Of Bootstrap Reps = 1000 Asia1/BAR/3/2011 Only bootstrap values of 70% and above are shown Asia1/BAR/4/2011

Asia1/IRN/43/2011

*, not a WRLFMD Ref. No. Asia1/IRN/33/2011 100 Asia1/IRN/46/2011

Asia1/IRN/38/2011

N.J. Knowles & J. Wadsworth, 27 April 2011 Asia1/PAK/6/2011

Asia1/PAK/47/2011 99 © Institute for Animal Health Asia1/PAK/8/2008 Asia1/PAK/26/2009 99 Asia1/PAK/27/2009 100 Asia1/PAK/29/2009

Asia1/IRN/25/2004 (DQ121120)

Asia1/YNBS/CHA/58 (AY390432)

Asia1/CAM/9/80

Asia1/Shamir/ISR/89

100 Asia1/BAR/8/2009

Asia1/BAR/9/2009

100 Asia1/IND 32/08* (HQ224556) Asia1/IND 12/07* (HQ224553) 98 Asia1/IND 227/07* (HQ224555)

Asia1/IND 121/07* (HQ224554)

Asia1/IND 97/08* (HQ224560)

Asia1/IND 95/08* (HQ224558) 99 Asia1/IND 93/08* (HQ224557)

Asia1/IND 96/08* (HQ224559)

Asia1/IND 137/08* (HQ224561)

Asia1/Jiangsu/CHA/2005 (DQ156527)

85 Asia1/PAK/1/54

Vaccine matching with Asia 1 in 2011

Only based on 8 samples so far

Requirement for a challenge study 0

-0.5

-1

-1.5

-2 No Match -2.5 Match -3

-3.5

-4

-4.5 Bahrain Iran Pakistan What can we do to improve chances of matching field strains and vaccines?

PAUP* outgroup OMANISA Maximum Liklihood

0.07

Purple – Africa Green – Euro/S. America Blue - Asia What can we do to improve methods for matching field strains and vaccines?

PAUP* outgroup OMANISA Maximum Liklihood

0.07

Purple – Africa Green – Euro/S. America Blue - Asia Systems Approach Compiling Information Layers

For gathering information on FMD outbreaks and risk of spread

•3 areas of information layers

•Agricultural

•Climate

•Environmental

Plus FMD specific information Information layers What does WRLFMD and FMD network provide?

• Serotype • Sequence • Vaccine matching • Global Information • Global surveillance • Global early warning Can we obtain the other layers through OIE/FAO and other organisations?

Data gathered for FMD modelling Data gathered for other purposes 2010 FMD Epidemic West Eurasia

EuFMD/FAO/ Turkey and Iran Epi working group ("Ankara Working Group") Outline

1. Looking back: – What happened? – Why did it happen? 2. How can FMD control be improved to avoid large epidemics? 3. What is the current FMD situation in Iran and Turkey? • • Iran in endof June in Oct Turkey, in sharp decrease Lasteduntil and Iran in bothTurkey in March-April Increase started

Number of outbreaks Large surge in outbreaks in 2010 in surge inoutbreaks Large

100 200 300 400

w1/09 0 w13/09 2009 w26/09 Iranoutbreaks w40/09 w1/10 Week w13/10 2010 w26/10 Turkey Turkey outbreaks w40/10 w1/11 w13/11 100 20 40 60 80

12009 0 2009:181 outbreaks Epidemic Epidemic curve: Turkey 26 26 2009 O Serotype All outbreaks 12010 wy 2010:1613outbreaks Untyped Serotype A 26 26 2010 12011 Iran: FMD reports (epi-unit) 1388 1389

•2009: 2602 reports, •2010: 5242 reports •Biggest increase in reporting in the NE of country Looking back...what happened?

Turkey outbreaks

Anatolia serosurveillance>2010 Anatolia Samples Seroprevalence collected March/May 2010

Seroprevalence 0.27 - 0.75 0.16 - 0.27 0.08 - 0.16 0.06 - 0.08 0.03 - 0.06 0.01 - 0.03 No data FMDV O in Iran 2009 Slide from Nick Knowles, WRL

Turkey East84 54 North Azerbaijan 66 79 Khorasan 8085 6568 Zanjan 61 86 Mazandaran Qazvin 49 34 35Razavi38 51 Kordestan Tehran83 Semnan Khorasan52 81 Afghanistan Hamedan 60 42 Qom Kermanshah 62647071 Markazi 56 87 Lorestan 88 Esfahan South Yazd Chaharmahal 7 40 57 89 Khorasan and Bakhtiari Khuzestan Pakistan Kohgiluyeh and Boyer-Ahmad 75 76

31 41 43 72Kerman Fars PanAsia-2YAZ-09 14 FAR-09 PanAsia-2 Sistan and PanAsia-2ANT-10 Hormozgan Baluchistan PanAsia-2BAL-09 PanAsia-2SAN-09 Saudi Arabia Ind-2001

200 km Numbers represent WRLFMD Ref. Nos. (e.g. 88 = O/IRN/88/2009) 100 mi 7 © Daniel Dalet / d-maps.com FMDV O in Iran 2010

92 Locations unknown 90 28 34 40 160 161 162 170 172 173 Turkey 94 23 24 135 98 East 17 27 29 30 Azerbaijan 136 North 31 52 55 71 89 76 120 Khorasan 114 115 128 Zanjan126 127 142 Mazandaran 19 20 18 82 109 146 158Qazvin 148 149 60 61 Razavi64 66 69 Kordestan Tehran91 96 113 137 Semnan Khorasan Afghanistan Hamedan65 86 85 102 99 75 1 Qom133 Kermanshah67 100 101 140 143 Markazi 8 10 54 Lorestan78 79 88 37 38 3Esfahan4 35 44 51 62 81 93 95 104 105 South39 43 Yazd2 11 Chaharmahal 106 141 33 59 Khorasan 68 12 156 and Bakhtiari130 Khuzestan 41 157 Pakistan 83 Kohgiluyeh and Boyer-Ahmad 97 138 144 5 132 139 147 Kerman Fars 26 47 13 14 22 PanAsia-2YAZ-09 131 48 49 50 FAR-09 PanAsia-2 Sistan124 and129 15 150 PanAsia-2ANT-10 Hormozgan Baluchistan154 155 PanAsia-2BAL-09 PanAsia-2SAN-09 PanAsia-2PUN-10 United Arab 200 km Emirates Numbers represent WRLFMD Ref. Nos. (e.g. 8 = O/IRN/8/2010) 100 mi 8 © Daniel Dalet / d-maps.com Slide from Nick Knowles, WRL Why did it happen?

Factors: • Waning post-infection immunity • Antigenic drift: strain evolution, incursion(s) of new strain(s) – Vaccines available not protective – Strain more virulent • Vaccine effective but not applied optimally • Increased transmission opportunities: – Animal movements increased due to meat prices Factor: Waning post-infection immunity

– Post-infection immunity can last several years – After an epidemic, population immunity will decline: Population turnover, natural waning – Last type O epidemic in the region in 2007 – Outstanding Questions: – relative contribution to FMD control of natural immunity versus vaccine-induced immunity? – Would there be cross-immunity between 2007 & 2010 strains? Slide from SAP Institute Hypothesis: Available vaccines not protective Vaccine Matching 2009-2010 WRLFMD: Serotype O 1 1 figure from WRL

Match

NO Match

– Vaccines not protective in some samples – Samples not be representative of population Factor: Vaccine effective but not applied optimally • Policy: vaccinate large ruminants 2x (Turkey) 3x (Iran) per year and sheep 1/year • Vaccine provided free of charge • Huge task and resource intensive • Iran: 44.9 million doses in 2009 and 55.4 million in 2010 – 148% yearly coverage in LR – 55% yearly coverage in SR – 92% coverage reported within an epi-unit • Turkey: 51 million in 2010 (monovalent) Proportion of epi-units vaccinated per district in 2010 (Iranian year 1389) • 68% villages 1389 outbreak incidence vaccinated at least once, 36% vaccinated 3X • Regional variability • Coverage within-epi unit? Factor: Vaccine effective but not applied optimally: Role of unvaccinated sheep? Iran : Iran: reported FMD outbreaks 2009-2010 • 8 million cattle and 81.6 million sheep (2005 census) • Yearly vaccination coverage = 55%, so 44.9 million SR unvaccinated • Sheep and cattle curves rise at same time, sheep surpasses cattle Looking back...what caused the epidemic? Factor: Vaccine effective but not applied optimally: Role of unvaccinated sheep?

Anatolia 2010: – 17% overall NSP Proportion NSP seroconversion seroconversion, rate Age group LR SR Total SR/LR ~1.5 times higher than 4-12 mo 0.12 0.14 0.13 1.17 cattle – What risk do they pose? 12-18 mo 0.10 0.18 0.15 1.91 • Extent of transmission 18-24 mo 0.13 0.25 0.17 1.88 from SR to cattle? • Spread to other >24 mo 0.17 0.24 0.21 1.38 regions by SR? Total 0.11 0.17 0.14 1.45

Looking back...what caused the epidemic? Factor: Vaccine effective but not applied optimally – No booster to young animals • Immunity only last 1-2 months – Previous studies1 from Turkey concluded that: • High level of movement and trade in young animals • Young animals responsible for most FMDV transmission – Therefore effective immunization of young animals is critical

1 2007 project including outbreak investigation, serosurveillance and market chain analysis Factor: Increased transmission opportunities – Due to large scale animal movements – Leads to viral incursions, contact between infected and susceptibles – price differentials provide incentive for movements into Turkey & Iran – Difference heightened in 2010

Prices (in USD per kilo) for live cattle and beef (young male animals) Country Live Meat 2009 2010 2009 2010 Turkey 3.7 6.7 6.2 10.5 Iran 2.3 7 Georgia 1.5 2.0 4.2 4.3 Armenia 1.6 2.7 3.9 5,4 Azerbaijan 4 4,5 6,2 6,5 Outline

1. What happened? 2. Why did it happen? 3. How can disease control be improved to avoid large epidemics? 4. What is happening now? How can disease control be improved to avoid large epidemics?

1. Learn from the past 2. Improved data analysis to understand risk 3. Include other control measures: biosecurity 4. Maximise effectiveness of limited resources 5. Early warning, Regional cooperation: Learn from the past/ Understand risk • Use available data and epidemiological studies to develop understanding – Training in data management and epidemiology – Routine data analysis – Analysis of vaccination coverage and vaccine efficacy – Risk factors: – Further use of outbreak investigation – Multivariable statistical models: risk factors • Explore relative contribution of factors: – Waning post-infection immunity, available vaccines not protective, vaccine effective but not applied optimally, increased transmission potential 1. Understand risk (con’t) 2. Include other control measures 3. Maximise effectiveness of limited resources 1. Value chain analysis: identification of risk hotspots and critical control points – Targeting control measures based on risk – Emphasis on feasibility 2. Enhance biosecurity: increase awareness, movement controls, hygiene 3. Target control to high-risk groups – Young animals – Markets, border regions, ...?? 5. Early warning, Regional cooperation: Enable preparedness, early response through:  enhanced understanding of drivers of FMD transmission and regional cooperation Initiatives: • Data sharing – West Eurasia countries, starting with Iran and Turkey • Laboratory and epidemiology networks – Facilitate serotype and strain characterization • Routine data analysis and define triggers for alert Early warning: Development of data sharing protocol • Agreement in principle for Iran and Turkey to share outbreak data on monthly basis • using Empres-i platform • urgent notification of ‘significant epidemiological event’ (to be defined: eg new serotype detected) • Extend initiative to other interested countries in region Early warning: Define triggers for alert

Quantitative and qualitative criteria (under development) – Quantitative : • Plot cumulative sum of (observed-expected) over time (CuSum) • And/or technique to detect spatial clusters (SatScan) – Qualitative: • New serotype/strain in a province • Outbreaks in well vaccinated units/area (eg 80% of epi-units with > 80% of individuals, maximally 4 months before). • Other? Based on molecular epidemiology? Improving FMD control...

Early warning: Define triggers for alert

– Sensitivity/specificity Smoothed epidemic curves - Turkey 5 week rolling average

• Balance false- 60 positives and possibly missing situations 40

– Intended as trigger Outbreaks for closer look, not to 20 raise alarm instantly! 0

0 10 20 30 40 50 week

2009 2010 Early warning: Define triggers for alert

FMD outbreaks reported to OIE: Turkey 300 200 150 200 100 cusum3 Outbreaks 100 50 0 0

Jan 08 Jul 08 Jan 09 Jul 09 Jan 10 Jul 10 Date

Observed outbreaks CuSum Outline

1. What happened? 2. Why did it happen? 3. How can we improve for the future? 4. What is happening now? What is happening now? FMD infection • Type A may be on the rise • Asia-1 has been confirmed in Bahrain, Pakistan and Iran – Vaccine matching results Asia 1-Shamir vaccine not protective Serotype results from Iran, late 2010-early 2011 70 60 O 50 A neg 40 unsuitable 30 20 10 Number of samples Number 0 October November December January February Summary • Large type O epidemic in 2010 – due to multiple factors (virological change, waning natural immunity, increased animal movement) • Actions to improve FMD control – Early detection of conditions likely to lead to epidemic – Most effective use of limited resources: risk-based – Employ full complement of available of control measures: biosecurity, movement control, vaccination • Requires transdisciplinary approach – Incorporate virology, epidemiology and economics Proposed next steps • Support risk managers – Early detection of increased risk: • Data sharing initiative – Empres-i • Promote use of regional labs • facilitate sample submission from region to SAP Institute (strain characterization, vaccine seed strains) • Define triggers for alert/further investigation – Define risk in order to target control • Data collection and database management • Develop epidemiology capacity • Multivariable analysis • Value chain analysis – risk and feasible control measures • Outbreak investigation protocol