*3.5. HPV 16 Sub-Lineages and Overall Survival*

For the Kaplan-Meier estimator, overall survival was calculated by classifying HPV 16 sub-lineages into A1 presence or absence. No differences in overall survival were found between both sub-lineage groups (*p* = 0.57), Figure 2.

**Figure 2.** Kaplan-Meier survival curve stratified by HPV 16 sub-lineages (A1 vs. Non-A1). Survival time expressed in months from the diagnosis date. Data censored on 31 July 2020. **Figure 2.** Kaplan-Meier survival curve stratified by HPV 16 sub-lineages (A1 vs. Non-A1). Survival time expressed in months from the diagnosis date. Data censored on 31 July 2020.

Table 4 shows overall survival stratified by the clinical and demographic variables (age group, sex, cancer stage and response to treatment), with HPV 16 sub-lineages categorized into the two groups (A1 vs. non-A1) with A1 as the reference. Non-A1 (vs. A1) was not associated with improved overall survival in the univariate analysis, with a hazard ratio (HR) of 0.87 (0.37–2, *p* = 0.751). Variables associated with worse overall survival in the univariate model were stage IV vs. stage I with HR of 15.7 (3.38–72.8), *p* < 0.001 and response to treatment vs. no response to treatment with HR of 0.11 (0.05–0.25) *p* < 0.001. After adjustment for age, gender, stage and response to treatment, non-A1 sub-lineages did not significantly influence the overall survival compared to A1, with a HR 0.83 (0.28– 2.46, *p* = 0.743). Table 4 shows overall survival stratified by the clinical and demographic variables (age group, sex, cancer stage and response to treatment), with HPV 16 sub-lineages categorized into the two groups (A1 vs. non-A1) with A1 as the reference. Non-A1 (vs. A1) was not associated with improved overall survival in the univariate analysis, with a hazard ratio (HR) of 0.87 (0.37–2, *p* = 0.751). Variables associated with worse overall survival in the univariate model were stage IV vs. stage I with HR of 15.7 (3.38–72.8), *p* < 0.001 and response to treatment vs. no response to treatment with HR of 0.11 (0.05–0.25) *p* < 0.001. After adjustment for age, gender, stage and response to treatment, non-A1 sub-lineages did not significantly influence the overall survival compared to A1, with a HR 0.83 (0.28–2.46, *p* = 0.743).

**Table 4.** Hazard ratio of HPV 16 sub-lineages (univariate and multivariate) derived from Cox regression (*N* = 115) in anal cancer samples collected between 2009 to 2018 in the southeast of Scotland. **Table 4.** Hazard ratio of HPV 16 sub-lineages (univariate and multivariate) derived from Cox regression (*N* = 115) in anal cancer samples collected between 2009 to 2018 in the southeast of Scotland.

If only A1 and A2 samples were considered, no significant differences in HR were


found when using A1 as the reference (HR 0.74, 0.25–2.1, *p* = 0.575).

If only A1 and A2 samples were considered, no significant differences in HR were found when using A1 as the reference (HR 0.74, 0.25–2.1, *p* = 0.575).
