FMDV belongs to the family Picornaviridae with seven serotypes around the world. Nevertheless, serotypes prevalent in Asia includes A, O and Asia-1. Because of evolution in genomic sequence of FMDV, it is becoming difficult to control the problem through conventional methods. Changes in the genome can be detected using software through sequence analysis. In the software, evolutionary models are used to measure the evolutionary change for the identification of new sub lineages.
In current study genomes sequence data (1998 - 2011) of bovine FMD serotypes (A, O and Asia 1) was collected through NCBI in FASTA format. This data was converted into PHYLIP format. On Dell workstation, with Microsoft Windows 8.1 operating system, BioEdit, TipDate V.1.2 was deployed. Sequence data was aligned through CLUSTAL W algorithm of Multiple Sequence Alignment using BioEdit. Using TipDate, genome sequence data was analyzed using three evolutionary models (F84, HKY and REV) and phylogenetic trees were produced showing evolutionary rate and likelihood ratio of FMDV serotypes O, A and Asia-1..
Results of the current study showed higher values of evolutionary rate in bovine FMD virus which was estimated 7.49 x 10-4 with likelihood value -1429.507680 in serotype A, 2.418 x 10-3 with likelihood -3707.168484 in serotype O and2.16 x 10-3 with likelihood value -3723.344884 in serotype Asia-1, respectively. Markove Reversible Model showed higher rates of evolution in all three serotype with best likelihood values. Phylogenetic results showed higher rate of evolution or substitution in viruses. Furthermore serotypes A, O and Asia-1are mutating with passage of time and new variants are being observed. It was also observed that this evolutionary process is continued in these three serotypes during 1998-2011.
This study confirmed the evolutionary changes in FMDV serotypes prevalent in Pakistan during the period 1998 – 2011. This study showed that isolate are evolving with increasing rate. High rate of mutation in Asia-1 was observed than serotype A and serotype O. F84 and HKY85 models produced close results
but these models are not identical works on equal and unequal base frequencies. Markove model estimated average base substitution with mutation and depicts good phylogenetic trees of sequence data.