Abstract
HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIV’s most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIV’s replication in cell culture. We compare our experimental measurements of each site’s preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. Our data enable us to quantify the inherent mutational tolerance of each site in Env. We show that the epitopes of broadly neutralizing antibodies have a significantly reduced inherent capacity to tolerate mutations, rigorously validating a pervasive idea in the field. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Env’s evolution.
Highlights
HIV evolves rapidly: the envelope (Env) proteins of two viral strains within a single infected host diverge as much in a year as the typical human and chimpanzee ortholog has diverged over *5-million years [1,2,3,4]
HIV is infamous for the rapid evolution of its surface protein, Env
The ability to measure the effects of all mutations to Env under defined selection pressures in the lab would open the door to better understanding the factors that shape this evolution. This is a daunting experimental task since there are over 104 different single-amino acid mutations to Env
Summary
HIV evolves rapidly: the envelope (Env) proteins of two viral strains within a single infected host diverge as much in a year as the typical human and chimpanzee ortholog has diverged over *5-million years [1,2,3,4]. One strategy is experimental: numerous studies have used site-directed mutagenesis or alanine scanning to measure how specific mutations affect various aspects of Env’s function [8,9,10,11,12,13,14,15,16,17] These experiments have examined only a small fraction of the many possible mutations to Env. these experiments have examined only a small fraction of the many possible mutations to Env Another strategy is computational: under certain assumptions, the fitness effects of mutations can be estimated from their frequencies in global or intra-patient HIV sequences [18,19,20,21,22]. A more complete and direct delineation of how every mutation affects Env’s function would be of great value
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