Kafkas Üniversitesi Veteriner Fakültesi Dergisi 2018 , Vol 24 , Issue 3
P1 Coding Region Diversity of Group VII (Sind-08) Serotype Asia-1 Foot-and-Mouth Disease Virus
Waqas ALI, Mudasser HABIB, Rai Shafqat Ali KHAN, Muhammad Ashir ZIA, Muhammad Usman MAZHAR, Asad JAVED, Muhammad FAROOQ, Muhammad Salah Ud Din SHAH
1Department of Biological Sciences, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, PAKISTAN DOI : 10.9775/kvfd.2017.18949 In this study, the capsid protein coding region of serotype Asia-1 viruses (n=131) were analyzed, giving importance to the viruses circulating since 2011 within the Group VII (Sind-08). The isolates recovered during 2011-2017 were found to group within the re-emerging cluster of Group VII (Sind-08). The time of the most recent common ancestor for this cluster was estimated to be approximately 2004. In comparison to the older isolates of Group VII (2001-2004), the re-emerging viruses showed variation at fourteen amino acid positions, including substitutions at the antigenically critical residues VP1140, VP1142 and VP277. In Group VII (Sind-08), all three major antigenic sites have mutations (Site I and II had four consensus changes at positions 140, 141 and 77, 79 respectively, while site IV had a replacement at position 59) relative to the internationally recommended vaccine strain (Shamir 89). This study also explains the development and optimization of a new RT-PCR method that may be employed to amplify and sequence a 2901 base pair (bp) section covering entire capsid coding region (P1) of the FMDV genome. This method offers a tool that can be employed for antigenic profiling and phylogenetic analyses of FMDV to help vaccine matching or strain selection in the episode of outbreaks. Keywords : Foot-and-mouth disease, Pakistan, Diagnosis, Vaccine