Comparative Sequence Analysis of Coat Protein Gene of Iranian Citrus tristeza virus Isolates

Twenty-two isolates of Citrus tristeza virus (CTV) collected from two different geographical regions of Iran were characterized based on coat protein (CP) gene sequences. Thirteen virus isolates were collected from northern parts of Iran with high distribution of CTV infection and nine isolates were obtained from southern regions where the presence and aphid transmission of CTV was previously reported. All isolates were recovered from field trees showing varied CTV symptoms such as decline in most citrus varieties on sour orange rootstock, inverse pitting on some sour orange rootstocks below bud union, mild-to-moderate stem pitting on the trunk of some sweet orange. Isolates F, G, MB1, MB7, MB2, MB8, MB9, MB11 and MB17 were recovered from healthy looking Miyagawa Satsuma on trifoliate rootstock originally infected with CTV imported from Japan in late- 1960s. The presence of virus in citrus samples was confirmed using polyclonal as well as monoclonal antibody. The CTV CP gene of all isolates was amplified by reverse transcriptase polymerase chain reaction (RT–PCR) using CP gene-specific primers yielding 672 bp amplicon. The restriction fragment length polymorphism (RFLP) profile, nucleotide and deduced amino acid sequences were analysed and compared with each other and also with some other exotic CP gene sequences of CTV isolates available in GenBank. Analysis of our data revealed that Iranian isolates have high similarity to California SY568 severe stem pitting and Japanese NUagA seedling yellows strains (up to 97%). The dendrogram generated from the deduced amino acid sequence could separate MB1, MB2, MB8, MB9, MB11 and MB17 isolates from others. However, no major dissociation between the isolates from northern and southern region could be obtained.