Introduction

The scripts and data attached in the folder june2022/ below represent revisions made for publication in PLOS Pathogens. Most notably, these revisions include expanding our sample size to approximately 30,000 SARS-CoV-2-positive PCR tests.

Scripts

The scripts included in june2022/scripts/ are:

1. dhs_data_filtering.R - A script that filters out uninformative or ambiguous rows from the full DHS dataset. Note the disclaimer at the top of the script. [Link]
2. dhs_data_testing.R - A script used to test the integrity of the filtering in the previous script. [Link]
3. additional_statistics.R - Statistics done on Ct_values_symptoms_culture.xlsx in R that were used in the manuscript [Link]
4. suppfig3_plotting.R - Script to plot days from symptom onset by vaccine status using Ct_values_symptoms_culture.xlsx (supplemental figure 3) [Link]
5. suppfig4_plotting.R - Script for plotting virus culture results by Ct value, grouped by vaccine status with Ct_values_symptoms_culture.xlsx [Link]

Data

The data included in june2022/data/ are:

1. 220615 datafile.xlsx - De-identified qPCR cycle threshold values for various groups compared in our study [Link]
2. dataFig1.txt - Ct values in our dataset at each month after full vaccination [Link]
3. dataFig2.txt - Ct values in our dataset at each month after full vaccination, binned by vaccine manufacturer [Link]
4. Ct_values_symptoms_culture.xlsx - Ct values with accompanying symptom data and virus culture results [Link]

Introduction

We are submitting the Medrxiv data to a peer-reviewed journal. This required us to revise the figures and the R script used to generate them. We are also adding culture data to the line list per a request from @vercheckt on Twitter.

We are also updating the Medrxiv article to harmonize with the journal submission and the journal's stylistic requirements.

Data

• Ct values, vaccine status, culture attempted, and symptom presence for specimens described in manuscript [link]
• Same data as above, with virus culture quantification from the same samples (after one additional freeze thaw) [offline because titration results from additional samples with one less freeze thaw are now available]
• Virus titration from an additional set of samples with a single freeze-thaw (added 30 Sept 2021) [link]

Workflow

• R code used to generate manuscript figures [link]

Introduction

This folder contains data from the manuscript "Shedding of Infectious SARS-CoV-2 Despite Vaccination when the Delta Variant is Prevalent - Wisconsin, July 2021."

These data are from the updated submission submitted to Medrxiv on August 10, 2021. The key changes in this revision are:

• Inclusion of more individuals dating to 31 July 2021
• Addition of verified vaccine statuses of some samples from official public health registries
• Addition of virus culture data from samples with a PCR Ct < 25
• Addition of information on testing timing
• Removal of Pango lineages and GISAID identifiers since we are now using an expanded dataset where delta was even more prevalent in Wisconsin

Data

Updated 16 August 2021 to include virus culture information

• Ct values, vaccine status, and symptom presence for specimens described in manuscript [link]

Workflow

Updated 16 August 2021 to include virus culture information

• R code used to generate manuscript figures [link]