Statistical analysis
In NH 4 (Table S1), blood sampling was not possible, and residents’ data were used only to assess the link between vaccination status and SARS-CoV-2 infection and severe Covid-19 incidence. Due to the very low number of missing data in the 6 NHs in which blood was collected, and to the fact that residents who did ou did not contribute to blood collection did not differ for age, gender, and comorbidity status, no assumptions were made for missing data et missing data were not replaced.
Categorical variables were described with frequency and proportions for each category. The description of continuous variables was performed using mean and standard deviation and/or median, with interquartiles, according to the distribution.
The statistical analysis plan was pre-specified according to previous studies from our group. 6,7, with the following primary, secondary, and exploratory outcomes
The primary outcome (incidence of positive RT-PCR) was estimated in the entire cohort with 95% confidence interval (CI), and compared according to the residents’ vaccination status (non-vaccinated, one vaccine dose, or two vaccine doses) using the Chi-2 test. Death was not considered as a competing risk as all deaths were related to Covid-19 during the study period. Covid-19-related deaths were considered as incident cases.
Secondary outcomes were compared in the whole cohort according to the vaccination status using the Fisher exact test for deaths and the Kruskal-Wallis (KW) test for RBD-IgG levels.
Other secondary outcomes according to the vaccination status were analyzed in RT-PCR-positive residents: Covid-19 symptom severity using the Fisher exact test, RBD-IgG and N-Ag using the KW test. The relationship between levels of RBD-IgG and risk of incident SARS-CoV-2 was analyzed using the Fisher exact test.
Exploratory analyzes on the relationship between RBD IgG levels and serum neutralization in RT-PCR-positive residents of one NH were performed using Fisher’s exact test. Wilcoxon–Mann–Whitney 2-sided tests were used to compare N-Ag in asymptomatic, mild, and severe Covid-19 residents.
Holm’s correction was applied for the post-hoc comparisons for each outcome. The statistical significance threshold was set at 5%.
We displayed the positive predicted values (PPVs) and negative predictive values (NPVs) of a positive RT-PCR testing for the accepted thresholds of IgG-RBD values (positive threshold set at 50 AU/mL, significant threshold set at 1,050 AU/mL, and 4,160 AU/mL, indication a high neutralizing effect). 26,27
Analyses were performed and illustrated using SAS Enterprise Guide, v7.3 (SAS Institute Inc) and GraphPad Prism 9.1.1 (GraphPad Software, Inc., San Diego, CA).