amino-acid preference during deep mutational scanning

Growth/Fitness

Enrichment

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Illumina Sequencing , Deep Mutational Scanning , Viral Competition

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We used the deep mutational scanning approach in to estimate the effects of all single
amino-acid mutations to Env. We mutagenized amino acids 31±702 (throughout this paper, we
use the HXB2 numbering scheme [50]). We excluded the N-terminal signal peptide and the
C-terminal cytoplasmic tail, since mutations in these regions can alter Env expression in ways
that affect viral infectivity in cell culture [51±53]. The region of Env that we mutagenized
spanned 677 residues, meaning that there are 677 × 63 = 42,651 possible codon mutations, corresponding
to 677 × 19 = 12,863 possible amino-acid mutations. For each library, we passaged 5 × 105 infectious particles in order to maintain library diversity. We used Illumina deep sequencing to quantify the frequency of each mutation before and after passaging