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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. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequence of an Indian isolate of Apple chlorotic leaf spot virus ( ACLSV) was determined and found to be 7,525 nt in length. The genome organization was similar to known isolates of ACLSV, encoding three ORFs. Comparisons indicated high sequence variability among known isolates with overall nucleotide sequence identities of 80 to 84%. A striking variable region was identified among the replicase protein upstream of the RNA-dependent RNA polymerase (aa 1510-1590), which showed a 41-43% match with the corresponding region in other isolates. Phylogenetic analysis at the nucleotide level clustered the isolates into three groups, without any relation to geographical origin. Recombination analysis showed that the isolate is a recombinant with recombination sites spread throughout the genome, especially in the polymerase gene region (nt 4700-5400). Most recombination sites were bordered by an upstream region (5′) of GC-rich and downstream region (3′) of AU-rich sequences of similar length. Correlation of recombination site with host type is discussed, and it was found that there were more interlineage recombinations in the apple host compared with intralineage recombinations. [ABSTRACT FROM AUTHOR]