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United States Department of Agriculture

Agricultural Research Service

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Research Project: Epidemiology, Vaccines and Control of Foot-and-Mouth Disease in Pakistan

Location: Foreign Animal Disease Research

2013 Annual Report


1a.Objectives (from AD-416):
This collaborative research project seeks to characterize the epidemiology of Foot-and-Mouth Disease Virus (FMDV) and the strains circulating in Pakistan in support of control strategies. The specific objectives of this research project include:

1. Identify current FMDV strains circulating in Pakistan. 2. Investigate the spatial and termporal distribution of FMDV and model the pattern of FMDV occurrence and transmission in Pakistan. 3. Carry out vaccine matching studies of the current circulating FMDV strains with vaccines to be used in control program. 4. Study the role of persistently infected cattle and Asian buffalo on the transmission of FMDV. 5. Characterize the anatomical pathology of persistence of FMDV in Asian buffalo and cattle. 6. If funding permits, carry out in vivo challenge studies to confirm in vitro vaccine matching.


1b.Approach (from AD-416):
To achieve our objective the following steps will be taken:

1. In close collaboration with the ongoing Foreign Agriculture Organization control project, the National Veterinary Laboratory (NVL) and the National Agriculture Research Center (NARC), sampling of FMDV will continue in Pakistan. The viruses will be isolated at either NVL or NARC and then shipped to ARS-PIADC for further molecular analysis. This will include sequencing and phylogenetic analysis.

2. At ARS-PIADC vaccine matching will be carried out using previously available vaccine sera and recent isolates. The assay carried out at ARS-PIADC will be harmonized with the World Reference Laboratory (WRL), Insitute for Animal Health (IAH) Pirbright, UK, to insure that the vaccine matching data is in agreement. If funding is available, a member from ARS-PIADC will travel to Pakistan to implement the vaccine matching protocol at NARC. If no funding is available alternative teaching methods, such as video conference calls, will be utilized.

3. In collaboration with the University of California-Davis, the Disease BioPortal will be used to display the spatial, temporal and phylogenetics of FMDV strains. The understanding of the patterns and dynamics of the disease will help to design appropriate control measures that might include other measures besides vaccine matching.

4. If funding is available, NARC will carry out in vivo challenge studies to verify the vaccine matching in vitro.

5. A number (20-40) of farms, with past history of FMDV and with at least 20 animals, will be selected for a prospective study. Blood, probang and nasal swabs will be collected from these animals. Blood will be tested for non-structural proteins (NSP) against FMDV using an ELISA. Probang and nasal swabs from all NSP positive animals will be processed by rRTPCR and virus isolation. Probang and nasal swab sampling from NSP positive animals will continue and will be collected after every 3-4 weeks day up to 90 days for determination of persistency and carrier animals. A comparison between probang data and nasal swabs will also be made.

6. Peri-urban farms which have Asian buffalo and cattle, age >6 months, for the market will be selected and registered. Both probang and blood samples will be collected for FMDV detection. All FMDV positive (NSP seropositive & probang rRT-PCR+) cases will be necropsied and various tissues will be collected, including roof of nasopharynx, dorsal soft palate, regional lymph nodes and tonsils. These samples will be screened by rRT-PCR, histopathology and immunomicrsoscopy at ARS PIADC.


3.Progress Report:

The fourth round of samples was completed to detect persistently infected buffaloes. More than 50% of the samples tested were found to be positive for FMDV. Samples were sent to ARS, PIADC for further analysis, including virus isolation and sequencing on positive isolates from these samples. FMD vaccine matching studies were done from locally available commercial FMDV vaccines using FMD isolates of serotypes A, O and Asia 1. Studies at NARC using liquid phase blocking ELISA technique were inconclusive. The sera was sent to ARS, PIADC for further analysis and vaccine matching studies. The preliminary results indicated that for serotype O, the vaccine is a good match to strains circulating in Pakistan whereas for serotypes A and Asia 1, the data suggests that the vaccine is not a good match against the strains circulating in Pakistan. FMDV isolation studies were conducted including typing and sequencing of the virus. This information was shared by FMD-FAO at the National Veterinary Laboratory.

In addition, a post-doctoral fellow from ARS, PIADC traveled to NARC and extended technical guidance for the establishment of a high containment animal facility and a molecular diagnostic laboratory and provided a training course to six laboratory personnel on rRTPCR and LAMP for FMDV diagnosis. The purpose of this exercise was to develop harmonization of rRTPCR protocol between the two labs.

In conjunction with this collaborative research project, two masters of philosophy and one post doctoral fellow completed their thesis in FY 2013. Their work focused on the role of buffalo as persistent carriers of FMDV. No technologies were transferred in FY 2013. Publications for the period include: 1) Brito, B., A. Perez, S. Pauszek, Z. Ahmed, E. Khan, K. Naeem, U. Farooq, and L. Rodriguez. Comparative analysis of Foot-and-Mouth Disease Virus serotype A positive selection in Pakistan, Afghanistan, Iran and Turkey. 2) Farooq, U., A. Ullah, A. Latif, A. B. Zahur, K. Naeem, F. Ashfaq, M. Afzal and A. U. Cheema. 2013. Sero-prevalence of foot and mouth disease (FMD) in large ruminants in peri urban dairy farms of Islamabad. Presentation accepted at Ninth International Biennial Conference of Pakistan Society of Microbiology. January 28-31, 2013. 3) Farooq, U., A. Ullah, A. Latif, K. Naeem, A. Bin Zahur, M. Hussain. 2013. Sero-prevalence of Foot-and-Mouth Disease in small ruminants of Pakistan, International Meeting on Infectious Diseases and Surveillance (IMED 2013) February 15-18 in Vienna. 4) Farooq, U., Serological survey of FMD in small ruminant population of Pakistan. 2012. 15th International Congress on Infectious Diseases (ICID), Bangkok, Thailand. June 13-16, 2012. 5) Foot-and-Mouth Disease Virus serotype O phylodynamics: genetic variability associated to epidemiological factors in Pakistan” to the Transboundary and Emerging Diseases” has been published (doi:10.1111/j.1865-11682.2012.01366.x). 6) Naveed, M. T., U. Farooq, N. Siddique, T. Kamal, A. B. Zahur, A. Ullah, K. Naeem, S. Raza, F. Rasheed and A. Latif. 2013. Evidence of Foot-and-Mouth Disease Viruses in apparently healthy buffaloes in abattoirs.. Presentation accepted at Ninth International Biennial Conference of Pakistan Society of Microbiology. January 28-31, 2013.


Last Modified: 9/22/2014
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