Comparison of systems performance for TT virus detection using PCR primer sets located in non-coding and coding regions of the viral genome

• Published in: Journal of clinical virology 2001-08, Vol.22 (1), p.91-99
• Main Authors: Biagini, Philippe, Gallian, Pierre, Attoui, Houssam, Cantaloube, Jean-François, Touinssi, Mhammed, de Micco, Philippe, de Lamballerie, Xavier
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; 5' Untranslated Regions; Biological and medical sciences; DNA Primers; DNA Virus Infections - virology; DNA, Viral - analysis; Fundamental and applied biological sciences. Psychology; Genome, Viral; Humans; Microbiology; Molecular diagnosis; Polymerase chain reaction; Polymerase Chain Reaction - methods; Sequence Analysis, DNA; Torque teno virus - genetics; Torque teno virus - isolation & purification; TT virus
• ISSN: 1386-6532; 1873-5967
• DOI: 10.1016/S1386-6532(01)00179-2

Background: the heterogeneity of the TT virus (TTV) DNA prevalence values reported from comparable human cohorts suggests that diagnostic PCR protocols still require to be optimized. Objectives: to design TTV PCR primer sets with low genotype restriction and to compare their performances with commonly used amplification systems. Study design: we compared full length TTV genomic sequences and identified conserved nucleotide patterns in the 5′ and 3′ non-coding regions of the viral genome. This permitted to design two new primer sets usable for the PCR amplification of the most divergent human isolates of TTV described to date. The performances of these amplification systems were compared with those of three other PCR systems earlier used for prevalence studies. Results: the primer systems P5Bx and P3Bx exhibited higher PCR scores than the other systems tested; 14 to 34% improvement values were obtained, and divergent positive results of earlier described PCR systems were confirmed systematically by our new detection assays. Conclusions: an optimized detection of TT virus DNA is a pre-requisite for the accurate epidemiological survey of viral infection and for the realization of phylogenetic studies. Such PCR systems with low genotype restriction will be helpful in the future for a better knowledge of natural history of TT virus infection.