Genomic analysis of a recently identified virus (SEN virus) and genotypes D and H by polymerase chain reaction.
OBJECTIVE
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.
D000595:Amino Acid Sequence; D018136:Circoviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D018173:Circoviridae Infections / Q000175:diagnosis* / Q000821:virology; D004279:DNA, Viral / Q000097:blood / Q000737:chemistry / Q000302:isolation & purification; D014644:Genetic Variation; D005838:Genotype; D006521:Hepatitis, Chronic / Q000821:virology*; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D014764:Viral Proteins / Q000737:chemistry
D004279:DNA, Viral; D014764:Viral Proteins