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Torque teno virus (TTV) has been found world-wide prevalent in healthy population and patients with various diseases, but its ethological role had not been determined yet. Using high throughput unbiased sequencing to screen viruses in serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV Virus (isolate rebel-1).The genome of TTV Hebel-1 is 3649bp, which encodes 4 putative open reading frames and has a G+C content of 49％. Genomic comparison and BLASTN search found that the assembled genome of the TTV-Hebel-1 represents a novel group with genome sequence highly heterologous to other reported TTV stains. Phylogenetic tree constructed with complete genome sequence Showed that TTV Hebel-1 arid an uncharacterized Taiwan Strain TW53A37 constitute a new TTV genotype. S1nGe the patient is high suspected of viral 1nfeGtlOn arid filed eventually without other known causes, and no virus other than the novel TTV is identified in his serum sample, we supposed that this virus might be the etiological agents of his disease. Although the direct causal link between the novel TTV genotype infection and the patients disease has not been confirmed yet, surveillance of the novel TTV genotype is advised and its role in disease deserves to be explored.