Supporting Information: Estimating HIV-1 Fitness Characteristics from Cross-sectional Genotype Data

Parameter Description Value λTU Synthesis of uninfected target T-cells 2·10 βT Infection of T-cells 8·10−12 ÑT = NTI +NTNI Viral production from infected T-cells 1000 δTU, δT1 Death of uninfected and early stage infected T-cells 0.02 δT2 Death of late stage infected T-cells 1 CLV Viral clearance 23 ρPR,φ Probability of successful assembly and maturation of viruses 0.67 ρrev,φ Probability of successful reverse transcription 0.33 μ Basal mutation 3.4 · 10−5 kT Integration of viral DNA in T-cells 0.35 δPIC,T Clearance of pre-integration complex in T-cells 0.35 α Activation of latent T-cells 10−3 λMU Synthesis of uninfected target macrophages 6.9 ·10 δMU, δM1 Death of uninfected and early stage infected macrophages 0.0069 δM2 Death of late stage infected macrophages 0.09 δTL Death of latent T-cells 10 −4