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Updated: Aug 30, 2026
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
Published on: May 26, 2013
Genomic analysis of a recently identified virus (SEN virus) and genotypes D and H by polymerase chain reaction
Hiroshige Kojima1, Kelly D E Kaita, Manna Zhang
1Department of Medicine, Liver Diseases Unit, Health Sciences Centre, John Buhler Research Centre, University of Manitoba, 803-715 McDermot Avenue, Winnipeg, Man., Canada MB R3E 3P4.
Background/Aims:
SEN virus (SENV) was discovered in 1999 as a DNA virus with hepatotropic properties. Nine genotypes (A-I) have been identified with genotypes D and H being more prevalent in cases of chronic hepatitis. Attempts to determine whether SENV causes liver disease have been hampered by limited diagnostic testing.
Methods:
In the present study, we developed two PCR based assays; a general SENV screening and genotype-specific assay.
Results:
By screening PCR, the specificity for all SENV genotypes and SENV-related sequences was 20/20 (100%) with confirmation of the results being provided by genomic sequencing. With the genotype-specific PCR, specificities for SENV-D and SENV-H were 7/7 (100%) and 7/11 (64%), respectively. All screening PCR products were cloned and sequenced. The results of sequencing showed high genetic diversity in representative SENV genotypes. Five of twenty patients (25%) had mixed infections with several SENV genotypes.
Conclusions:
The screening PCR was useful for identifying cases of SENV infection. However, because of high genetic divergence and mixed co-infection, it was difficult to establish a specific method for genotype distinction. Hence, sequencing is still required for further investigations of SENV as a potential cause of liver disease.
