Genetic diversity of the coat protein gene and biological variation of citrus yellow vein clearing virus infecting different citrus species

Abstract

Citrus is one of the most important fruit crops globally and rising incidence of citrus yellow vein clearing virus (CYVCV) in citrus orchards is an increasing concern in India. CYVCV and Indian citrus ringspot virus (ICRSV) are assigned to the only two known species in the genus Mandarivirus. Both viruses naturally infect several citrus plants. ICRSV produces ringspots symptoms in Kinnow mandarin, whereas CYVCV induces vein clearing symptoms on Etrog citron and lemon. Leaf samples and bud sticks of different citrus cultivars, exhibiting diverse symptoms were collected during 2012–2014 from 18 locations of India. The genetic variability was assessed through analysis of the coat protein (CP) gene sequences. Out of the 15 CP gene sequences, 13 sequences were of 978 nucleotides (nts) and showed 96–99% sequence identity with CYVCV-Y1 isolate (JX040635.1). However, sequences from the isolates HI and DLI shared only 78% and 73% nucleotide sequence identity with CYVCV and ICRSV, respectively, and that may represent distinct CYVCV isolates in the genus Mandarivirus. In phylogenetic analysis also HI and DLI isolates clustered neither with CYVCV nor with ICRSV isolates.