Grapevine fanleaf virus 2AHP gene shows more diversity at amino acid level rather than nucleotide level

Grapevine fanleaf virus (GFLV) has been reported from vineyards worldwide. The virus causes different symptoms categorized as three distinct syndromes including fanleaf degeneration, yellow mosaic, and vein banding. These variations in the symptoms can be addressed by analysis of genetic diversity of the virus. The aim of the present study was to estimate genetic diversity of the corresponding 2AHP gene in GFLV isolates especially the ones that are associated with the yellow mosaic syndrome. Accordingly, the grapevine samples were collected from vineyards in Bonab, Shir-Amin, Hossein-Abad, and Tabriz in East Azarbaijan Province of Iran. After amplification of GFLV 2AHP gene from the infected samples via RT-PCR, the products were cloned and sequenced. The sequenced GFLV 2AHP gene from 11 different isolates showed 0.8-27% and 0.8-35 % diversity at nucleotide and amino acid levels, respectively, denoting a higher diversity of 2AHP amino acid sequence than its nucleotide sequence. Likewise, presence of a hot spot for recombination events on 2AHP region was explored by the use of recombination analysis. Moreover, it was found that the selection pressure on 2AHP region is not uniformly distributed so that the ratio (dn/ds) for the N-terminus proximity, between the nucleotides 408-564, was more than one. Therefore, synonymus point mutations as well as recombination events might be reason for this evidence.