Dataset for 'Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model'

Description

SARS-CoV-2’s transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. Primarily, the dataset contains (1) fastq files from next-generation sequencing of a small amplicon that contains the barcode of our barcoded viruses and (2) associated count matrices showing how many of each barcode are present in each sample. Secondarily, RT-qPCR results measuring viral titers in various respiratory tissues are also included.

Steps to reproduce

1. Description of methods used for collection/generation of data: Refer to the "Methods" section, subsections "Cells", "Recombinant barcoded SARS-CoV-2", "Hamster experiments", "Virus titration assays" of the manuscript. 2. Methods for processing the data: Refer to the "Methods" section, subsections "Barcode analysis", "Quantification and statistical analysis" of the manuscript. 3. Matlab (version R2024b) was used to analyze barcode distributions. BBTools suit (version 39.01) was used in NGS analysis. GraphPad Prism (version 10.1) was used for statistical analysis.

Institutions

Categories

Funding

Additional Metadata for Digital Commons Data@Becker

Related Links

Licence