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Table 2 Examples of possible transient early HLA-driven escape at HIV codons with stronger population-level signal in early versus chronic infection

From: Early immune adaptation in HIV-1 revealed by population-level approaches

HLA-associated HIV-1 polymorphism Patient HLA Days post-infection Bulk plasma seq. Adapted to HLA?
A*31:01-Gag-I401L A0301/3101 B4403/3503 C0401/0401 143 L yes
   226 L yes
   309 I no
   485 I/L partial
   563 I no
   683 I/L partial
B*57:01-Nef-x133I A2402/2902 B4403/5701 C0602/1601 30 I yes
   31 I yes
   60 I yes
   86 V no
   123 V no
   228 [I/V] partial
   361 [I/V] partial
   396 [I/V] partial
  1. A small number of HLA-associated polymorphisms, including A*31:01-Gag-I401L and B*57:01-Nef-x133I, showed stronger population-level escape signal in early versus chronic infection (see Table 1). Though these differences were not statistically significant (Table 1, last two columns), we nevertheless hypothesized that they could represent potential examples of transient escape. In support of this hypothesis, the above table provides examples of two cases where a patient harbored the HLA-associated adapted variant at a given HIV-1 codon at the earliest timepoint post-infection, that subsequently give way to a non-adapted form (and/or a mixture of the two), consistent with transient early escape at these positions in these patients.