Dataset and code for the manuscript: Persistence of human norovirus (GII) in surface water: Decay rate constants and inactivation mechanisms

This deposit contains three elements: 1. data analysis code (.ipynb files); 2. code input files (data); and 3. one code output file (data). The Jypyter notebook file and dataset reproduce analysis, figures, and tables for the manuscript titled "Persistence of human norovirus (GII) in surface water: Decay rate constants and inactivation mechanisms." The experiments are described in the manuscript.

1. The data analysis code "norovirus_persistence_data_analysis.ipynb" is a Jupyter Notebook in R and requires installation of an R kernel (installation instructions are available at: https://irkernel.github.io/installation/). To generate the figures and tables in the manuscript, place input files in a folder named "Data," create an empty folder named "Figures_and_tables", and execute the code in the same directory as the two created folders. These files are also available in github where the .ipynb file can be viewed directly (see "Links to related content" section).

2. The dataset includes five code input files: human norovirus infectivity quantified via human intestinal enteroid assay ("hunov.csv"), RT-qPCR standard curves for assay development ("assay_development_MK.csv", "assay_development_OL.csv"), RT-qPCR standard curves for experimental samples ("expt_1234_std.csv"), and human norovirus in experimental samples and experimental controls quantified via RT-qPCR as threshold cycle values ("expt_1234_unk_ntc.csv").

3. The dataset contains one code output file: human norovirus in experimental samples quantified via RT-qPCR and converted to units of gene copies per mL in the code ("hunov_qpcr_gcperml.csv").

Columns labeled "quantity" (RT-qPCR standard curve files) are in units of gene copies per reaction and columns labeled "CT" are unitless RT-qPCR threshold cycle values.