**10. Conclusions**

Next-generation sequencing-based viral genome sequencing is crucial to understanding the ever-changing dynamics of HIV and HCV. The ability to generate quality sequencing data from samples with low viral titre or samples with poor nucleic acid integrity is important. Target enrichment has emerged as a potential solution to the problems of sequencing difficult samples and can potentially enable complete viral genome sequence even for low-quality clinical specimens. Increased adoption of such technology in research and development fields for HIV, HCV, and other pathogens is foreseeable.

**Author Contributions:** Conceptualization, E.R.L. and H.J.; Methodology, C.M. and E.R.L.; Writing— Original Draft Preparation, C.M.; Writing—Review & Editing, C.M., H.J. and E.R.L.; Supervision, H.J.; Project Administration, E.R.L. All co-authors made substantial contributions to this work. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research received no external funding.

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** Not applicable.

**Acknowledgments:** This work is funded by the National Microbiology Laboratory branch of the Public Health Agency of Canada, to which all co-authors are affiliated.

**Conflicts of Interest:** The authors declare no conflict of interest. The funder played no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
