Biological and molecular characterization of two isolates of apple stem grooving virus revealed distinct properties and indicates virus emergence driven by recombination

Apple stem grooving virus (ASGV) is a highly variable RNA virus and recombination is one of the mechanisms that lead to variations in the viral genome. Here, we report the biological and molecular properties of two apple isolates of ASGV (p12 and MK) isolated from two different locations in India. Complete genome of both isolates consisted of 6493 nucleotides excluding the poly (A) tail and contained two open reading frames (ORFs). The isolates shared 97% sequence identity with each other. Phylogenetic analyses revealed neighbouring association of these isolates, but their infection on known herbaceous host, Phaseolus vulgaris, showed different phenotypes. Recombination analyses suggest isolate MK and p12 as non-recombinants, but recombination events increased with increasing host diversity. Two recombination hotspots were identified in the ORF1 region spanning nucleotides 4500–4800 and 6200–6500, which were designated as recombination hot spots I and II, respectively. The findings here also suggest that this virus is emerging with expanding host range breadth and diversified host adaptability driven by recombination.