Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates

Selinger, Christian; Tisoncik-Go, Jennifer; Menachery, Vineet D; Agnihothram, Sudhakar; Law, G Lynn; Chang, Jean; Kelly, Sara M; Sova, Pavel; Baric, Ralph S; Katze, Michael G

Differential expression was determined by comparing MERS-CoV SA 1-and MERS-CoV Eng 1-infected replicates to time-and data set-matched mock-infected controls, based on a linear model fit for each probe using the R package Limma [43] . The same method was applied to determine differential expression between strains using time-matched MERS-CoV SA 1-and MERS-CoV Eng 1-infected samples. Criteria for differential expression were an absolute log2 fold change of 1 and a q value of <0.05 calculated using a moderated t test with Benjamini-Hochberg correction. The cytokine Calu-3 treatment data sets were analyzed separately using the same methods and cut-offs as the virus-infected Calu-3 cells. Differentially expressed genes were determined to be statistically significant in at least on time point and for at least one treatment.