Resistance Testing by RT-PCR, Next Generation Sequencing and Mutation Database Analysis

Drug resistance testing of hepatitis C virus by reverse-transcription-PCR amplification of either the whole virus genome or the NS3-NS5B region followed by Next Generation Sequencing (NGS) and comparison of the sequences to a database of known drug resistance mutations.

• Hepatitis C

Serum or plasma sample.  Minimum volume required for serum or plasma – 1.0 mL. While not required, inclusion of a banked pre-treatment sample is valuable to differentiate between relapse and reinfection and to contribute information to the HCV resistance mutation database.

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.

HCV testing is primarily intended for patients who have failed a prior HCV therapy containing an NS3, NS5A and/or NS5B inhibitor. There are circumstances in which pre-treatment testing may be warranted. When in doubt, contact Dr. Mike Carpenter at the NML for further information. Patient samples with viral loads <103 IU/ml are not accepted at this time.

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. Where known, please include the viral load. If a banked pre-treatment sample is included, please include the same documentation for this specimen.

N/A

Depending on sample viral load and quality, one of two methods will be employed: i) Reverse transcription (RT) coupled to PCR amplification utilizing: i) genotype independent long-range PCR (near full-length amplification of the HCV genome) or targeted amplification of the NS3-NS5B region, or ii) random-primed RT-and PCR whole-genome amplification with or without capture probes. All samples are processed by next generation deep-sequencing. Resulting data is compared to a database of known resistance mutations. Detailed resistance associated substitutions (RAS) information and test metrics are noted in the final report. Test results are for research use only.

28 calendar days.

1. Shah H, Bilodeau M, Burak KW, Cooper C, Klein M, Ramji A, Smyth D and Feld J; for the Canadian Association for the Study of the Liver. 2018. The management of chronic hepatitis C: 2018 guideline update from the Canadian Association for the Study of the Liver. CMAJ 190 (22) E677-E687 (2018). DOI: https://doi.org/10.1503/cmaj.170453.
2.  Bradshaw D, Mbisa JL, Geretti AM et al. Consensus recommendations for resistance testing in the management of chronic hepatitis C virus infection: Public Health England HCV Resistance Group.J. Infect. 79(6):503-512 (2019). DOI: https://doi.org/10.1016/j.jinf.2019.10.007.
3.  AASLD-IDSA. HCV guidance: recommendations for testing, managing, and treating hepatitis C. Clin Infect Dis, 67 (10): 1477-1492 (2018) .See current update at: https://www.hcvguidelines.org.
4. Houldcroft, C, Beale, MA, Breuer, J. Clinical and biological insights from viral genome sequencing. Nature Reviews Microbiology 15: 183–192 (2017). https://www.nature.com/articles/nrmicro.2016.182

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