Genotyping

Genotyping of hepatitis C virus specimens by: 1) random-primed or oligo d(A)-primed cDNA synthesis and PCR amplification followed by next generation sequencing (NGS) and/or 2) cDNA synthesis and PCR amplification using primers targeting conserved regions on the viral genome followed by NGS or Sanger sequencing

Serum or plasma sample. Minimum volume required for serum or plasma – 1.0 mL.

Collect blood in serum separator tubes (SST) or EDTA tubes.

Store samples frozen until shipped for testing. Ship frozen on dry ice.

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.

Suspected hepatitis C infection.  Serology results must show markers to the hepatitis C virus (anti-HCV (+)). If PCR was performed previously the result should be positive. If the viral load was previously determined, please include this information along with the request.

Completed Viral Hepatitis and Bloodborne Pathogens requisition including sender name, address and telephone number.  Patient name or identifier (referring specimen lab #), date of birth, suspected exposure, test(s) requested.  Type of specimen and date collected.  If possible, include the clinical history and lab results that have already been done at local or provincial laboratories. We would appreciate inclusion of viral load data for each specimen where available.

N/A

Testing is performed, in whole or in part, using a lab-developed test which has not been fully validated/verified due to a lack of well-characterized panel.

Conventional reverse transcription-PCR amplifying fragments of the Core, E1 and NS5B regions followed by Sanger sequencing or random-primed RT-PCR whole-genome amplification with or without capture probes. Sample libraries are processed for next generation deep-sequencing. For either method, sequences are evaluated by phylogenetic analysis in the context of HCV reference genomes to define genotypes and subgenotypes.

28 calendar days.

1. Kuiken C, Simmonds P. Nomenclature and numbering of the hepatitis C virus. Methods Mol Biol. 2009;510:33-53.
2. Simmonds P. Virology of hepatitis C virus. Clin Ther. 1996;18 Suppl B:9-36.
3. Bowden DS, Berzsenyi MD. Chronic hepatitis C virus infection: genotyping and its clinical role. Future Microbiol. 2006;1:103-12.