Table II.

Higher escape rates are observed in the first T cells of HIV-1 infection

PatientReferenceMutation/saAverage rate escape, kbt50cCD8 T cell epitopedConfirmed T cell response (HXB2 position)e
CH40a.Gag A120D0.1731nono
CH40b.Gag I401L, R403K0.1731yesyes (Gag389-406)
CH40d.Pol K76R0.015119yesnof
CH40h.Vif T167I0.3738yesno
CH40i.Vpr S84R0.1631yesno
CH40t.Nef S188R/N, R196Q0.2215yesyes, (Nef185-202)
CH77l.Tat I64TS0.428yesnog
CH77s.Env R355K/S/N,T358A0.369yesyes, (Env350-368)
CH77aa.Nef R21K/G, R22K/G/,TD23E/N, P25S0.3019yesyes, (Nef17-34)
CH77cc.Nef K82Q/T/P, A83G, L85H, L87I0.2924yesyes, (Nef81-98)
CH77b.Gag I147L0.063101yesyes, (Gag140-157) IW9
CH77c.Gag T242N,V247I, G248E/S0.035124yesyes, (Gag236-253) TW10
CH58e.Env Y586H0.1021yesyes, (Env576-596)
CH58g.Env F829V/S/L, I830M/L/F, A832T, V833I0.1227nono
CH58b.Gag I147L0.007430yesyes, (Gag140-157) IW9
CH58c.Gag T242N, G248E0.08560yesyes, (Gag236-253), TW10
SUMA0874Rev R48K, Q51H, Q53R, S54L, L55I0.3230yesyes, (Rev47-55)
Medianall demonstrated T cell epitopes0.17 (max. 0.42)0.14 (max. 0.36)
  • Summary of characteristics of several mutations that became fixed in the virus population within several weeks after the onset of symptoms.

  • a Note, that in the majority of cases, several different nonsynonymous mutations occurred in a given peptide in the model. All such escape variants are assumed not to be recognized by the corresponding CTL responses. Analysis of the extension of this model assumption will be presented elsewhere.

  • b The rate of escape, k, determines the mean rate at which mutations accumulated in the viral population.

  • c t50 is the predicted time of the mutant to reach 50% frequency in the viral population.

  • d The mutations occur in known CTL epitopes or in sites with CTL anchor binding motifs given the patient's HLA type (ELF software, LANL).

  • e A CD8 T cell response (as measured by ELISpot or ICS) to a peptide corresponding to the transmitted virus was detected at that site.

  • f This mutation is proximal to the Pol 80–97 epitope and may have had an impact on its processing. See also Fig. 5 H.

  • g This region partially overlaps with Rev in another reading frame. See paragraph three of the CH77 section of the Results for further discussion.