Prunus necrotic ringspot virus: incidence on stone and pome fruits and diversity analysis

Stone fruits and pome fruits are cultivated commercially worldwide. In India, they are grown in temperate regions, which mainly includes Jammu and Kashmir, Uttarakhand, Himachal Pradesh and some North-Eastern states. In this study, an attempt has been made to identify the Prunus necrotic ringspot virus (PNRSV) infecting stone and pome fruits in India and to characterise them on the molecular level. Surveys were conducted in the temperate fruit-growing areas and incidence of PNRSV was detected by serological and molecular means in almond, apple, cherry, nectarine, peach, plum and wild cherry. Further diversity analysis of PNRSV was performed using bioinformatics tools such as clustalW, DNA Data Bank of Japan, MultAlin and Recombination Detection Programme. PNRSV was detected in plum, peach, cherry, almond, nectarine, wild cherry and apple. In the diversity analysis study on the basis of coat protein gene, it was found that the isolates showed identity levels from 82 to 100%. In a plum isolate, a stretch of amino acids from 207 to 221 was found variable from Indian and other isolates. In one of the Indian apple isolates, “NR” repeats at 41–44 position (characteristic of PV-32 group, Group I) were identified. Phylogenetic analysis revealed that Indian isolates are falling in Group-I. Movement protein was also amplified from peach and multiple alignment studies showed that N-terminus was mostly conserved, whereas the C-terminal was highly variable.