SARS-CoV-2 IgG seroprevalence surveys in blood donors before the vaccination campaign, France 2020-2021

Covidonneur

Codes and Data for the paper “SARS-CoV-2 IgG seroprevalence surveys in blood donors before the vaccination campaign, France 2020-2021”.

Overview

This repository contains scripts to

• Read and format the serological data.
• Launch MCMC scripts to fit models of infection and antibody decay and estimate parameters of infection-hospitalisation ratio (IHR) and force of infection in each region.
• Infer prevalence and plot the output of the MCMC The first script to be launched is Setup_data.R; The model is launch with the script launch_analysis.

Data

The folder Data contains the seroneutralisation result for 32605 samples acquired from blood donors in 2020-2021 in metropolitan France (Covdon_v3.csv) corresponding to anti-S1 IgG samples and additional anti-N IgG samples (Etude antiN T3T4T6.csv). Data were aggregated in a format that maintains anonymity of the participants: For each individual, we provide the age group (in groups 18-30, 31-40, 41-50, 51-60, 61-70), department, survey period and median date of the survey. Additional necessary data are provided: the population size by age and region, the public daily hospital admissions.

Scripts

All analyses can be run from the main.R file, which calls scripts to run the analysis (contained in the scripts folder) and functions (contained in the R folder). The purpose of each R file is described below.

• main.R Launch all the necessary codes
• Setup_data.R Setup the data for further analysis
• functions.R Some usefuls functions
• launch_MCMC.R Launch the MCMC scripts. In the directory StanModels three models are provided.
• posthoc_analysis.R A script containing some posthoc analysis of the MCMC; It allows plotting the IHR by age and the decay of the assay capacity as a function of the time since seroconversion.
• IHR_Covidonneur.R Plot the IHR as estimated by the MCMC script. Here, a chain was uploaded (Model3b.rds and Model3f.rds).
• Seroprevalence_age.R This scripts plots the observed seroprevalence, the reconstructed number of infection, the inferred seroprevalence given by the exponential decay of the antibody response following infection.