Genetic diversity and comparison of diagnostic tests for characterization of foot-and-mouth disease virus strains from Pakistan 2008-2012

Authors: AHMED, ZAHEER - Animal And Plant Health Inspection Service (APHIS); Pauszek, Steven; LUDI, ANNA - The Pirbright Institute; Larocco, Michael; KHAN, EHTISHAM - Food And Agriculture Organization Of The United Nations (FAO); AFZAL, MUHAMMAD - Food And Agriculture Organization Of The United Nations (FAO); ARSHED, M - Food And Agriculture Organization Of The United Nations (FAO); FAROOQ, UMER - National Agricultural Research Center - Pakistan; Arzt, Jonathan; BERTRAM, MIRANDA - Oak Ridge Institute For Science And Education (ORISE); BRITO, BARBARA - Oak Ridge Institute For Science And Education (ORISE); NAEEM, KHALID - National Agricultural Research Center - Pakistan; ABUBAKAR, MUHAMMAD - Ministry Of National Food Security & Research-National Veterinary Laboratory; Rodriguez, Luis

Submitted to: Transboundary and Emerging Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2017
Publication Date: 10/16/2017
Citation: Ahmed, Z., Pauszek, S.J., Ludi, A., Larocco, M.A., Khan, E., Afzal, M., Arshed, M.J., Farooq, U., Arzt, J., Bertram, M., Brito, B., Naeem, K., Abubakar, M., Rodriguez, L.L. 2017. Genetic diversity and comparison of diagnostic tests for characterization of foot-and-mouth disease virus strains from Pakistan 2008-2012. Transboundary and Emerging Diseases. 65(2):534-546. https://doi.org/10.1111/tbed.12737.
DOI: https://doi.org/10.1111/tbed.12737

Interpretive Summary: Foot-and-mouth disease (FMD), caused by FMD virus (FMDV), is an important livestock disease that causes substantial animal health problems in many countries in Africa, Asia, and the Middle East, including Pakistan. There are seven different types of FMDV, three of which are commonly found in Pakistan (types O, A, Asia1). Several different tests are available for identifying FMDV infection. This study investigated the strains of FMDV currently in Pakistan and compared the ability of different tests to detect those viruses. For this purpose, samples from cattle and buffalo from Pakistan were screened for the presence of FMDV using two different screening tests. Results of the two screening tests were the same for 98% of samples. The specific type of FMDV was determined by additional diagnostic tests which can identify specific viral proteins or genetic material. FMDV type Asia 1 was found most commonly, followed by type O; type A was also found in a fewer samples. Compared to genetic detection, the diagnostic protein test correctly identified 88% of type Asia 1 samples, 89% of type O, and 8% of type A. This study confirms earlier accounts of genetic diversity of FMDV in Pakistan and highlights the importance of checking that diagnostic tests for FMDV can detect current strains of the virus.

Technical Abstract: We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (kappa = 0.96). Samples that were VI-positive were serotyped by antigen-detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n=13), O (n=36), and Asia1 (n=41), including three samples from which both serotypes Asia1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11, and ESF-10. All serotype Asia1 were within Group VII (Sindh08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotype O were classified as PanAsia2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia1, and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia1, and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.