Distribution and phylogenetic analysis of the 3′UTR and coat protein gene of Iranian Beet black scorch virus

Abstract

Beet black scorch virus (BBSV) was surveyed in major sugar beet cultivation areas in Iran in 2008–2013 growing seasons. A total of 148 out of 308 samples (48%) collected in seven Iranian provinces were BBSV-infected, as shown by RT-PCR. To investigate the genetic diversity of Iranian BBSV isolates, sequences of the coat protein (CP) gene and of the 3′ untranslated region (3′UTR) were compared to corresponding sequences in GenBank. The CP nucleotide sequence identity among Iranian isolates was 87.9–99.9%. They shared nucleotide sequence identities of 88–89.8% with those of other BBSV isolates available at GenBank. Phylogenetic analyses of CP sequences demonstrated that Iranian isolates were distant from Chinese and US isolates at both nucleotide and amino acid levels. Three isolates from western provinces of the country showed independent divergent lineage compared with other Iranian isolates. Comparison of 3′UTR region of BBSV indicated that all Iranian isolates, except four isolates from the west of the country, were distinct from European, Chinese, and US isolates. Population genetic analyses revealed that BBSV populations from west of Iran had distinct evolutionary divergence and differentiated from eastern BBSV isolates. Our results indicated that purifying selection might have contributed to evolution of the isolates belonging to the four identified BBSV subgroups with infrequent genetic exchanges occurring between them. Phylogenetic analyses and estimation of genetic distance indicated that Iranian isolates in both CP and 3′UTR genomic regions had wider genetic diversity than isolates from other parts of the world. Based on the result of phylogenetic and population analyses, we suggest discriminating two different groups, namely BBSV western and BBSV eastern strains.