Table 2. Descriptions of the HPV16 natural history models included in predictions.
| Model acronym* | Clearance± | Natural immunity | Latency | Fractions that develop immunity or latency | Penile-to-anal transmissibility§ | Anal-to-penile transmissibility§ | Waning of natural immunity¶ | Reactivation of latent infections¶ |
|---|---|---|---|---|---|---|---|---|
| SIS | Exponential | No | No | Not applicable | 0.149 (0.116–0.191) | 0.015 (0.011–0.016) | Not applicable | Not applicable |
| SISPS | Biphasic | No | No | Not applicable | 0.115 (0.089–0.155) | 0.010 (0.007–0.011) | Not applicable | Not applicable |
| SIRS | Exponential | Systemic | No | 100% | 0.428 (0.225–0.999) | 0.040 (0.036–0.062) | 0.966/year | Not applicable |
| SIS33RS | Exponential | Systemic | No | 33% | 0.372 (0.200–0.999) | 0.032 (0.030–0.043) | 0.33/year¤ | Not applicable |
| SIS10RS | Exponential | Systemic | No | 10% | 0.330 (0.176–0.842) | 0.027 (0.023–0.036) | 0.10/year¤ | Not applicable |
| SISPminRS | Biphasic | Systemic | No | Only those that clear a persistent infection† | 0.179 (0.110–0.340) | 0.013 (0.009–0.035) | 0.819/year | Not applicable |
| SISPmaxRS | Biphasic | Systemic | No | Only those that clear a persistent infection†† | 0.191 (0.118–0.321) | 0.015 (0.011–0.035) | 0.886/year | Not applicable |
| SIR[local]S | Exponential | Local; both penile and anal | No | 100% | 0.379 (0.201–0.999) | 0.026 (0.022–0.033) | 0.989/year | Not applicable |
| SIS33R[local]S | Exponential | Local; both penile and anal | No | 33% | 0.367 (0.195–0.825) | 0.025 (0.020–0.032) | 0.33/year¤ | Not applicable |
| SIS10R[local]S | Exponential | Local; both penile and anal | No | 10% | 0.313 (0.175–0.628) | 0.022 (0.017–0.028) | 0.10/year¤ | Not applicable |
| SIR[penile]S | Exponential | Local; only penile | No | 100% upon clearing a penile infection | 0.156 (0.130–0.209) | 0.029 (0.021–0.228) | 0.710/year | Not applicable |
| SIS33R[penile]S | Exponential | Local; only penile | No | 33% upon clearing a penile infection | 0.150 (0.129–0.203) | 0.022 (0.018–0.032) | 0.319/year | Not applicable |
| SIS10R[penile]S | Exponential | Local; only penile | No | 10% upon clearing a penile infection | 0.152 (0.127–0.199) | 0.020 (0.016–0.025) | 0.10/year¤ | Not applicable |
| SIR[anal]S | Exponential | Local; only anal | No | 100% upon clearing an anal infection | 0.388 (0.180–0.994) | 0.018 (0.014–0.020) | 0.990/year | Not applicable |
| SIS33R[anal]S | Exponential | Local; only anal | No | 33% upon clearing an anal infection | 0.359 (0.176–0.839) | 0.018 (0.013–0.020) | 0.33/year¤ | Not applicable |
| SIS10R[anal]S | Exponential | Local; only anal | No | 10% upon clearing an anal infection | 0.351 (0.162–0.637) | 0.017 (0.013–0.019) | 0.10/year¤ | Not applicable |
| SIL | Exponential | No | Yes | 100% | 0.033 (0.020–0.070) | 0.002 (0.002–0.003) | Not applicable | 1.0/year¤ |
| SIS33L | Latent mixture | No | Yes | 33% | 0.115 (0.045–0.446) | 0.005 (0.003–0.006) | Not applicable | 0.546/year |
| SIS10L | Latent mixture | No | Yes | 10% | 0.446 (0.194–0.999) | 0.011 (0.004–0.018) | Not applicable | 0.341/year |
| SIR33L | Latent mixture | Systemic | Yes | Immunity: 67% Latency: 33% |
0.919 (0.262–0.999) | 0.031 (0.025–0.100) | 0 (no waning) | 0.845/year |
*Capital letters in model acronyms have the following meaning: S = susceptible; I = infected; P = persistently infected; R = resistant to infection; L = latently infected.
±Estimates of site-specific progression and clearance parameters are given in S3 Text.
§Median (minimum–maximum) per-partnership transmission probability across 18 settings of sexual contact structure.
¶Mean rate across 18 settings of sexual contact structure.
¤Upper bound of predefined estimation interval.
†In case of dual persistent infections, development of systemic immunity is determined by the anatomic site with slowest clearance.
††In case of dual persistent infections, development of systemic immunity is determined by the anatomic site with fastest clearance.
HPV16, human papillomavirus genotype 16.