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United States Department of Agriculture

Agricultural Research Service

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Location: Foreign Animal Disease Research

2013 Annual Report

1a.Objectives (from AD-416):
The Foot-and-Mouth Disease (FMD) lab within the CADMS (Center for Animal Disease Modelling Systems) is located at the University of California, Davis and along with ARS, is a member of the Global Foot-and-Mouth Disease Research Alliance (GFRA). CADMS is currently compiling extensive global disease surveillance data and is developing a global web-based disease surveillance system, which has resulted in the FMD BioPortal, a publically-available site. ARS is interested in leveraging CADMS capabilities with our offshore research efforts in countries like India, Pakistan as well as future research projects in South East Asia. The objectives of this collaboration are: 1. To expand the UC Davis FMD BioPortal and to provide epidemiological information to ARS, PIADC to aid in current offshore FMD research projects in India, Pakistan and other future related projects. 2. Incorporate FMD virus sequences and epidemiological data provided from ARS collaborators in India, Pakistan and other future collaborators in South East Asia, into the BioPortal system. 3. Identify relationships between the variation in number of different nucleotides within the P1 gene of FMD virus provided by ARS collaborators in India, Pakistan and other future collaborators in South East Asia or ARS, PIADC and features of the host population that were associated with changes in the virus sequences. Amendment 1: 4. Elucidate epidemiological aspects of FMD transmission and spread in Pakistan. 5. Provide epidemiological support and contribute to the coordination of the FMD control program conducted by the FAO and other instititutions in Pakistan. 6. Contribute to build technical capacity for the National Veterinary Laboratory (NVL) and other institutions in Pakistan related to strengthen the FMD control program in the country.

1b.Approach (from AD-416):
1. ARS, PIADC will provide sequencing data and analysis of field isolates of viruses made available through UC Davis. This data will be incorporated into the BioPortal. 2. UC Davis will provide epidemiological expertise to ARS, PIADC to further basic and applied research. 3. Epidemiological information and sequences provided by ARS, PIADC and ICAR will be incorporated to the FMD BioPortal and will be made available to research partners and the general public in near real time. 4. Data will be used to quantify the relation between nucleotide variation in the P1 sequences of the viruses provided by ICAR and ARS, PIADC and the epidemiological factors hypothesized to be associated with such variation. Amendment 1: 5. Data will be analyzed to: a. Quantify the geographical variation of FMD risk in Pakistan and its association with epidemiological factors. b. Identify areas to gather field samples of FMD in endemic regions of Pakistan for analysis and surveillance. c. Estimate the impact and effectiveness of alternative control strategies, including vaccination, in Pakistan. d. Elaborate and estimating indicators to measure the impact of FMD control strategies in the field, including the implementation of a surveillance program. 6. Results of analyses will be used to elaborate technical recommendations and help to coordinate the design and implementation of an FMD vaccination pilot program in Pakistan. 7. Scientists from the National Veterinary Laboratory in Islamabad, Pakistan, and other individuals in the field will be trained in epidemiological aspects of FMD control.

3.Progress Report:

Studies focused on samples obtained from collaborators in Pakistan. FMDV serotype O VP1 sequences were obtained from Pakistan and Afghanistan, Iran, and Turkey. These sequences were analyzed separately for each region for detection of evidence of positive selection by exploring the differences between synonymous and non-synonymous changes. Three different statistical methods were used. Tests indicated that the mean values of the viruses from Iran and Turkey were similar whereas they were higher for Pakistan/Afghanistan sequences. These results were presented at the EU FMD meeting in Spain. In addition, epidemiological and sequence data was compiled by ARS, PIADC from samples obtained from collaborators in Pakistan. This confidential information was uploaded in the BioPortal. A tutorial video was prepared so collaborators in Pakistan can access the BioPortal for the FMDV data generated in the future. This technology will be a useful epidemiological tool to generate reports, understand the virus location and genetics in time and to have a better understanding of the virus behavior and occurrence of the disease.

No publications were produced during this reporting period.

Last Modified: 10/22/2014
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