*4.4. Antiretroviral Drugs*

RAL and EVG (repository references ARP980 and ARP991, respectively) were obtained from the National Institute for Biological Standards and Control.

## *4.5. Statistical Analyses*

Differences in EC50 values and replicative fitness were calculated using the Student's *t* test tool, available on www.graphpad.com (accessed on 10 June 2021). *p* values which were <0.05 were regarded as significant.

#### *4.6. Nucleotide Sequence Accession Numbers*

The single-genome sequences generated and used in this study have been submitted to GenBank and assigned the accession numbers MH663797-MH663975.

**Author Contributions:** Conceptualisation, P.A.C., D.P. and J.L.M.; data curation, S.A.M. and D.P.; formal analysis, S.A.M., P.A.C., D.P. and J.L.M.; funding acquisition, J.L.M.; investigation, S.A.M., P.A.C., D.P. and J.L.M.; methodology, S.A.M. and J.L.M.; project administration, J.L.M.; resources, D.P. and J.L.M.; supervision, P.A.C., D.P. and J.L.M.; writing—original draft, S.A.M. and J.L.M.; writing— review and editing, P.A.C., D.P. and J.L.M. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by a PHE PhD Studentship. The views expressed in this publication are those of the author(s) and not necessarily those of the NHS, the Department of Health and Social Care or PHE.

**Institutional Review Board Statement:** All experiments were performed in accordance with the "Guidance on Conducting Research in Public Health England" (Version 3, October 2015: Document code RD001A). This study uses samples and data collected as part of standard of care with informed consent, therefore specific approval was not necessary. The samples were anonymised by removal of any patient identifiable information and assignment of a non-specific project number prior to genetic characterization.

**Informed Consent Statement:** Informed consent was obtained in the context of routine resistance testing as a part of clinical protocol. Therefore, no ethical approval was required.

**Data Availability Statement:** Sequence data generated by the study is available through NCBI GenBank and assigned the accession numbers MH663797-MH663975.

**Acknowledgments:** We would like to thank Bridget Ferns of the University College London Hospitals (UCLH) NHS Foundation Trust and all members of the Antiviral Unit at Public Health England (PHE) for their support.

**Conflicts of Interest:** The authors declare no conflict of interest.
