A comprehensive map of evolutionary constraints across the enterovirus A genome

Insertions and deletions (InDels) are essential sources of novelty in protein evolution. In RNA viruses, InDels cause dramatic phenotypic changes that contribute to the emergence of viruses with altered immune profiles and host engagement. This work aims to comprehensively quantify the mutational tolerance of an RNA virus to insertion, deletion, and substitution. Using Enterovirus A71 (EV-A71) as a prototype for the Enterovirus A species (EV-A) of picornaviruses, we engineered approximately 45,000 insertions, 6,000 deletions, and 41,000 AA substitutions across the nearly 2,200 coding positions of the EV-A71 proteome, quantifying their effects on viral fitness. In contrast with AA changes, the vast majority of InDels are lethal to virus growth. Those that are tolerated primarily reside in a few hotspot regions. These tolerant sites highlight structurally flexible and mutationally plastic regions of EV-A71 proteins that avoid core structural and functional elements but often overlap with ..., These data were collected by sequencing the input and output libraries from deep mutational, insertional, and deletional scanning experiments. Data was processed by next-gen sequencing pipelines, in-house scripts, and published software to interpret the fitness effects of mutations engineered in the EV-A71 genome. Data was visualized using R packages, including ggplot2. All scripts for the analysis and generation and included here and also available through GitHub (see links in the Related Works section)., , # A comprehensive map of evolutionary constraints across the enterovirus A genome

[https://doi.org/10.5061/dryad.866t1g1xm](https://doi.org/10.5061/dryad.866t1g1xm)

**August 16, 2024 changes:** Changed relative paths in code to regenerate figures from paper.

## Description of the data and file structure

The files are organized in the following fashion: 

File directory tree:

```
.
├── 1_Molecular_Biology_Supp_Information
│   ├── SupplementalFile1_BB_Free_Assembly.fasta
│   ├── SupplementalFile2_Insertion_Capsid.fasta
│   ├── SupplementalFile3_Insertion_Replication.fasta
│   ├── SupplementalFile4_Deletion_Capsid.fasta
│   ├── SupplementalFile5_Deletion_Replication.fasta
│   ├── SupplementalFile6_DMS_Capsid.fasta
│   ├── SupplementalFile7_DMS_Replication.fasta
│   ├── SupplementalFile8_Chloramphenicol_Casette.fasta
│   └── SupplementalFile9_5AA_Oligopool.fasta
├── 2_Enrich2_Dataframes
│   ├── 5_AA_Insertion
│   │   ├── Capsid
│   │   │   ├── main_identifiers_scores_shared_full.tsv
│...