Structure and dynamics of enterovirus genotype networks

Like all biological populations, viral populations exist as networks of genotypes connected through mutation. Mapping the topology of these networks and quantifying population dynamics across them is crucial to understanding how populations adapt to changes in their selective environment. The influence of mutational networks is especially profound in viral populations which rapidly explore their mutational neighborhoods via high mutation rates. Using a novel single-cell sequencing method, scRNAseq-Enabled Acquisition of mRNA and Consensus Haplotypes Linking Individual Genotypes and Host Transcriptomes (SEARCHLIGHT), we captured and assembled viral haplotypes from hundreds of individual infected cells to reveal the complexity of viral populations. We obtained these genotypes in parallel with host cell transcriptome information, enabling us to link host cell transcriptional phenotypes to the genetic structures underlying virus adaptation. Our examination of these structures reveals the co..., These data were collected using 10x single-cell sequencing (10xgenomics.com). After collecting cDNA from the 10x process, the cDNA was processed for long-read sequencing. The resulting short- and long-read sequencing data was then processed through the anchovy script and associated R scripts to generate these outputs as described in the accompanying manuscript., , # Structure and dynamics of enterovirus genotypic networks

[https://doi.org/10.5061/dryad.6hdr7sr76](https://doi.org/10.5061/dryad.6hdr7sr76)

This data repository pertains to the publication \"Structure and Dynamics of Enterovirus Genotypic Networks\", by Nathânia Dábilla and Patrick Dolan. Currently in revision at *Science Advances.*

Descriptions of the data and file structure are below. ***Please note:*** Some CSV tables include blank values, consistent with how these files are produced by the Python and R scripts. These are left intentionally to ensure that these tables produce reproducible results. We included these files in their original form, without empty cells marked with 'N/A'. 

Correspondence can be sent to [[e-mail]](mailto:Patrick.Dolan@nih.g)

## Data Description

##### Genotype analysis of passaged EVA71 populations

1. EVA71_P3_annot_v2.csv    142.93 KB
2. EVA71_P5_annot_v2.csv    440.39 KB
3. EVA71_P1_annot_v2.csv    160.04 KB

Columns:

* *pos*: ge...