Rstudio interface version 1

As previously performed specificity testing has shown no cross reactivity with N1, N2 primer set of the assay, a positive result was determined as either a positive N1 or N2 target. C_T values from SARS-CoV-2-specific targets, ORF1 a/b from NP specimens, and N2 (or in cases where N2 was negative N1 [n = 1]) from stool specimens where compared. For subjects who had multiple NP test results, the test closest to the date of stool testing was chosen. Cohen kappa coefficient was used to assess the agreement between stool and NP swab RT-PCR results. NP RT-PCR was considered the gold standard test based on previous work by our group showing high negative predictive value (100%) of NP RT-PCR when compared with unbiased metagenomic sequencing (14 (link)). Wilcoxon matched-pairs signed-rank 2-tailed test was used to compare the mean N1/N2 and ORF1 a/b C_T values. Negative predictive values were calculated using clinical specimens with known respiratory SARS-CoV-2 results. The performance of stool RT-PCR compared with NP RT-PCR was compared using a receiver operating characteristic curve analysis, and the area under the receiver operating characteristic curve was determined. Statistical analysis was performed using R version 4.0.2 (Vienna, Austria) and the RStudio interface version 1.3.1073 (Boston, MA).