Sequence and phylogenetic analysis of the non-structural 3A and 3B protein-coding regions of foot-and-mouth disease virus subtype A Iran 05

Abstract

The A Iran 05 foot-and-mouth disease virus (FMDV) subtype was detected in Iran during 2005 and has proven to be highly virulent. This study was undertaken to focus on molecular and phylogenetic analysis of 3A and 3B coding-regions in the A Iran 05 field isolate. To assess the genetic relatedness of A Iran 05 isolate the nucleotide and predicted amino acid sequences of the 3AB region of type A FMDV isolates were compared with twenty previously described type A FMDV isolates. The phylogenetic tree based on the 672 bp 3AB gene sequences of type A FMDV from thirteen different locations clustered them into five distinct lineages. The A Iran 05 isolate clustered in lineage A along with four type A variants and was closely matched with viruses isolated in Turkey and Pakistan during 2005~2006. The number of protein sequence differences exhibited by each of the isolates revealed that A Iran 05 isolate contains three amino acid substitutions at positions 47 and 119 of 3A and 27 of the 3B coding region. The nucleotide identity between A Iran 05 and the other four isolates of lineage A was estimated to be 98%.

Fig. 1

(A) Alignment of the deduced amino acid sequences of the 3A gene. (B) Alignment of the deduced amino acid sequences of the 3B gene. Dot (.) indicates sequence identity in relation to the Iranian isolate (A Iran 05). Sequence dissimilarity is indicated in single letter code. Accession numbers are as detailed in the table.

Fig. 2

Nucleotide sequence similarity tree based on a comparison of A Iran 05 isolate to other type A isolates, established with 3AB coding sequences (672 bp).