To date, only the complete genome of one malva vein clearing virus (MVCV) has been sequenced worldwide. Here, for the first time, the genomic sequence of an isolate of MVCV affecting Malva sylvestris in Iran was determined, using RNA deep sequencing confirmed by reverse-transcription polymerase chain reaction and Sanger sequencing. The sequence of IR1 was 11,055 nucleotides in length and contained a single open reading frame of 10,527 nucleotides encoding a large polyprotein of 3,508 amino acids with predicted molecular weight of 395,08 KDa. The sequence contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. The P1 of the IR1 was 1236 nucleotides longer than that of the only recently reported sequence from China (MVCV-SX, MN116683). The complete genome sequence obtained from the study showed 81.24% and 91.93% identities to its Chinese counterpart at the nucleotide (nt) and deduced amino acid (aa) levels, respectively. The low nt and aa sequence identity with known MVCV isolate seems to indicate that IR1 is a novel strain. Phylogenetic analysis of the coat protein gene also showed that the Iranian isolate was most closely related to the Dutch isolate NAKT-NL (FJ539084), with identities of 94.06 (at nt level) and 96.04% (at aa level). The results of this study will be useful for understanding the global molecular epidemiology of MVCV.

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