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

Retrovirology

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

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

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.

ISSN: 1742-4690