Predictable patterns of CTL escape and reversion across host populations and viral subtypes in HIV-1 evolution

TL;DR

This study investigates the rates of CTL escape and reversion in HIV-1 across different populations and finds consistent patterns linked to viral replicative capacity, highlighting the role of fitness costs in viral evolution.

Contribution

It provides a comparative analysis of escape and reversion rates across multiple populations and links these rates to viral replicative capacity, revealing consistent patterns and underlying mechanisms.

Findings

Escape rates are consistent across populations.

Reversion rates are similar between Canadian and South African cohorts.

Escape mutants with higher replicative capacity tend to revert more slowly.

Abstract

The twin processes of viral evolutionary escape and reversion in response to host immune pressure, in particular the cytotoxic T-lymphocyte (CTL) response, shape Human Immunodeficiency Virus-1 sequence evolution in infected host populations. The tempo of CTL escape and reversion is known to differ between CTL escape variants in a given host population. Here, we ask: are rates of escape and reversion comparable across infected host populations? For three cohorts taken from three continents, we estimate escape and reversion rates at 23 escape sites in optimally defined Gag epitopes. We find consistent escape rate estimates across the examined cohorts. Reversion rates are also consistent between a Canadian and South African infected host population. Certain Gag escape variants that incur a large replicative fitness cost are known to revert rapidly upon transmission. However, the relationship between escape/reversion rates and viral replicative capacity across a large number of epitopes has not been interrogated. We investigate this relationship by examining $in$ $vitro$ replicative capacities of viral sequences with minimal variation: point escape mutants induced in a lab strain. Remarkably, despite the complexities of epistatic effects exemplified by pathways to escape in famous epitopes, and the diversity of both hosts and viruses, CTL escape mutants which escape rapidly tend to be those with the highest replicative capacity when applied as a single point mutation. Similarly, mutants inducing the greatest costs to viral replicative capacity tend to revert more quickly. These data suggest that escape rates in Gag are consistent across host populations, and that in general these rates are dominated by site specific effects upon viral replicative capacity.