Quasispecies analysis in hepatitis C virus infection by fluorescent single strand conformation polymorphism

Optimisation and sensitivity of single-stranded conformation polymorphism for the detection of hepatitis C virus quasi-species

Single-stranded conformation polymorphism (SSCP) is a technique used widely for the detection of differences in DNA sequence based on PCR technology. Developed by geneticists for the detection of mutations causing disease, it has been adopted more recently for the analysis of the quasi-species of viral genomes, such as hepatitis C virus (HCV). The rigorous standardisation and determination of the limit of detection of the technique has rarely been shown. Variants within the quasi-species of the hypervariable region of HCV were cloned into pUC119 and the resulting plasmids quantitated and used as templates to optimise SSCP. Variables studied included the number of variants detected, the sensitivity of detection of variants in the minority, the electrophoresis temperature, methods of generation of single-stranded DNA, effect of numbers of cycles of PCR and use of DNA polymerase with proof-reading ability. It was demonstrated that the optimised method could detect at least five variants within a quasi-species and that variants could be detected down to a level of 2% of the quasi-species. Electrophoresis at room temperature for 18 h was highly reproducible. Generation of single-stranded DNA using a single primer with Taq polymerase for 20 cycles gave an accurate reflection of the quasi-species make-up and use of Pfu polymerase reduced sensitivity of detection of minor bands. This SSCP method provides an accurate tool to evaluate HCV quasi-species.

Inferred hepatitis C virus quasispecies diversity is influenced by choice of DNA polymerase in reverse transcriptase-polymerase chain reactions

The hepatitis C virus (HCV) is known to circulate in vivo as a quasispecies, a population of closely related, but genetically nonidentical virions. HCV reverse transcriptase (RT)-(nested) polymerase chain reaction (PCR) strategies are used to study quasispecies diversity at certain important viral genetic loci, predominantly at hypervariable region 1 (HVR 1) of the E2 envelope gene, and the interferon sensitivity determining region (ISDR) of the nonstructural 5a (NS5a) gene. We have found that the choice of DNA polymerase employed in viral PCR has effects on the inferred viral diversity at two distinct loci on the HCV genome. Nested HVR 1 and ISDR PCR was performed with both proofreading (Pwo) and nonproofreading (Taq) DNA polymerases on identical cDNA derived from three separate HCV-positive sera. Amplicons were cloned and sequences determined for 18-20 individual clones per sample. Quasispecies diversity determined from HVR 1 and ISDR PCR products showed that there was a marked effect on the inferred diversity depending on which DNA polymerase was employed in the PCR. The deduced amino acid sequences of the major variants within each specimen were identical for both Taq and Pwo DNA polymerase-mediated PCRs. However, a greater number of minor variants were observed in the Taq-generated amplicons, 80% of which were not observed in the Pwo-generated amplicons. Primer editing in the Pwo-generated amplicons was observed in 19% (20/104) of clones examined. Single-strand conformational polymorphism analysis of multiple replicates of each amplicon revealed good intra-PCR reproducibility in terms of genetic heterogeneity, and that as such the observations were not due to poor PCR reproducibility. The use of nonproofreading DNA polymerases to assess viral diversity can yield an incorrect quasispecies spectrum and affect RT-PCR assay performance. The contribution of Taq-induced errors and lack of adaptability of primers to potentially heterologous template-binding sites indicate that proofreading DNA polymerases should be the enzyme of choice in these systems.

Apical hypertrophic cardiomyopathy and hepatitis C virus infection

The familial form of hypertrophic cardiomyopathy (HCM) is attributed to mutations in the genes for contractile proteins, but the etiology of non-familial form remains unknown. This study was designed to examine the clinical features, histopathologic changes, and hepatitis C virus (HCV) genomes in patients with HCM associated with HCV infection. Anti-HCV antibody was present in the sera of 9 of 65 patients (13.8%) with HCM versus 2.41% in a control population of voluntary blood donors in Japan, a statistically significant difference (p<0.0001). Among these 9 patients, 6 had ace-of-spades-shaped deformities of the left ventricle with apical hypertrophy. Myocardial fibrosis was found in all patients, and mild cellular infiltration was observed in 5 patients. Type 1b HCV RNA was present in the sera of 5 of the 9 patients. The copy number of HCV was 5.5x10(3)-8.6x10(5) genomes/ml serum, and multiple clones of HCV were detected in the sera of each patient by an analysis of the hypervariable regions using fluorescent single-strand conformation polymorphism. Positive strands of HCV were found in the hearts of 5 patients, and negative strands in the hearts of 2 patients. A high prevalence of HCV infection was found in patients with HCM, particularly of the apical variety, suggesting that HCV is an important causal agent in the pathogenesis of the disease.

Use of base excision sequence scanning for detection of genetic variations in St. Louis encephalitis virus isolates

Twenty-two isolates of St. Louis encephalitis (SLE) virus of various geographical origins (Brazil, Argentina, Panama, Texas, Missouri, Maryland, California, and Florida) were examined for genetic variation by the base excision sequence scanning (BESS T-scan) method. A fragment was amplified in the envelope gene with the forward primer labeled in the PCR. The BESS T-scan method determined different clusters according to the profiles generated for the isolates and successfully grouped the isolates according to their geographical origins. Two major clusters, the North American cluster (cluster A) and the South and Central American cluster (cluster B), were defined. Two subgroups, the Texas-California subgroup (subgroup A1) and the Missouri-Maryland-Florida subgroup (subgroup A2), were distinguished within group A. Similarly, group B strains were subclustered to a South American subgroup (subgroup B1) and a Central American subgroup (subgroup B2). These results were consistent with those obtained by DNA sequencing analysis. The ability of the BESS T-scan method to discriminate between strains that present with high degrees of nucleotide sequence similarity indicated that this method provides reliable results and multiple applications for other virus families. The method has proven to be suitable for phylogenetic comparison and molecular epidemiology studies and may be an alternative to DNA sequencing.