From subtyping to assessment of relapse and resistance


  • Sensitive, multi-target, sequence-based subtyping of HCV
  • Helps discriminate cases of "relapse vs reinfection" after therapy
  • Automatic detection of subtype-specific, resistance-encoding mutations
  • NGS pipeline provides quantitation of viral sub-populations and quasi-species

Current challenges in HCV patient management

Genotyping of HCV is standard practice before the initiation of therapy. New drugs and treatment paradigms reinforce the need for an in depth analysis of informative regions of the viral genome which is best accomplished by sequencing.

Analysis of HCV NS5b identifies viral subtypes and other genes, such as NS3 and NS5a, are useful for assessing drug resistance patterns for therapy monitoring. Furthermore, when a patient presents with detectable HCV following therapy with direct-acting antiviral (“DAA”) medications, an alignment of the historic and current viral sequences from the patient may discriminate cases of relapse versus re-infection with a different clade.

SmartGene provides Web-based applications for Sanger and NGS which manage and interpret HCV sequence data to precisely identify viral subtypes and drug resistance patterns. The modules benefit from a proprietary, up-to-date, curated database of subtype-specific, wild-type reference sequences which reflect the significant natural diversity of the virus, and are used to determine, automatically, and precisely subtype-specific amino acid mutations. Furthermore, the SmartGene HCV NGS Pipeline provides sensitive detection and relative quantitation of viral sub-populations elucidating minor populations of the virus which express amino acid mutations at resistance-relevant positions in the viral genome. Such minority mutations may, for example, explain the failure of DAA therapy in certain patients.

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