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Pipeline publication

[…] PLICOR HCV Monitor version 2.0; Roche Molecular Systems). This assay has a lower limit of quantitation of 2.8 log10 IU/ml. When HCV RNA was not detected by using this assay, the sample was retested using the Roche qualitative test., Genotype was determined by performing phylogenetic analysis on Core-E1 region sequences of HCV that was obtained from the first viremic specimen. For most specimens, sequences were obtained from cDNA clones that were generated with a long amplicon RT-PCR method that was described previously (). For other specimens, genotype was determined by direct sequencing of RT-PCR products from the same Core-E1 region as described previously (). Sequences were aligned using ClustalX (), and trimmed to equal length using BioEdit (). The GTR+I+G analytical model (parameters available on request from the authors) was selected using the Akaike information criterion as implemented in ModelTest version 3.06 () and PAUP* version 4b10 (Sinauer Associates). Phylogenetic trees were estimated using the neighbor-joining algorithm implemented in PAUP*, and robustness of clustering was tested by using bootstrap analysis ()., HCV clearance was defined as the presence of anti-HCV with HCV RNA undetectable by the COBAS AMPLICOR qualitative assay in serum or plasma specimens from at least two consecutive visits that were obtained at least 300 d after the initial detection of viremia. Persistence was defined as the persistent presence of anti-HCV with HCV RNA detectable by the qualitative or quantitative COBAS AMPLICOR assay in serum or plasma specimens that were obtained at least 300 d after initial viremia ()., The 5.2-kb region from the 5′ UTR to the NS3/NS4A junction was cloned from 140–280 μL of serum or plasma as described previousl […]

Pipeline specifications

Software tools Clustal W, BioEdit, PAUP*
Organisms Homo sapiens
Diseases Hepatitis, Flaviviridae Infections, Hepatitis C, Viremia, Inflammation