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Background  Tobacco production in China has been affected by plant viruses with Milk vetch dwarf virus (MDV) as a recent invader posing serious concern. According to most of the studies, MDV mainly infects hosts from Fabaceae family but in our previous study we reported its infection in tobacco plant ( Nicotiana tabacum  L.) in Shandong province.    Findings  In current study (2016–2017), tobacco plants ( Nicotiana tabacum ) with severe stunting, yellowing and axillary bunch of new leaves were observed in Zhengning, Gansu province. Isolate GSZN yielded into eight genomic circular single-stranded DNA components while no alphasatellite DNA was obtained. High percent identity of this isolate was recorded in overall nucleotide and amino acid assembly with reported MDV isolates worldwide. Phylogenetic analysis fetched into a separate sub-clade comprising of new isolate along with other tobacco infecting isolates of MDV. While recombination was predicted in DNA-C encoding Clink protein and DNA-U1, which may attribute towards the potential host-shifting phenomenon and ability of this virus to expand its host range.    Conclusion  To our knowledge this is the first full genome annotation of a Nanovirus, infecting tobacco in natural field conditions, also this is the first extended analysis on host-shifting behavior of MDV.    Electronic supplementary material  The online version of this article (10.1186/s12985-019-1129-5) contains supplementary material, which is available to authorized users.

Full genome sequence analysis and putative host-shifting of Milk vetch dwarf virus infecting tobacco (Nicotiana tabacum) in China