Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium

Satria P. Sajuthi; Peter DeFord; Nathan D. Jackson; Michael T. Montgomery; Jamie L. Everman; Cydney L. Rios; Elmar Pruesse; James D. Nolin; Elizabeth G. Plender; Michael E. Wechsler; Angel CY Mak; Celeste Eng; Sandra Salazar; Vivian Medina; Eric M. Wohlford; Scott Huntsman; Deborah A. Nickerson; Soren Germer; Michael C. Zody; Gonçalo Abecasis; Hyun Min Kang; Kenneth M. Rice; Rajesh Kumar; Sam Oh; Jose Rodriguez-Santana; Esteban G. Burchard; Max A. Seibold

CoV infection, we examined the distribution of viral reads for the 18 CoV + infected 723 subjects. We observed a clear break between the 7 subjects with the lowest viral read 724 counts (<3,000 reads) and 11 subjects with the highest viral read counts (>60,000 725 reads). Therefore, we selected these 11 highly infected subjects for analysis of host 726 responses to CoV infection. To generate a similar infection-control group, composed of 727 subjects highly infected with a different virus species, we examined the 67 HRV infected 728 subjects in GALA, enforcing a comparable lower bound of viral reads as with CoV, 729 adjusting for the smaller HRV genome size. Specifically, HRV genomes are ~7,000 730 base pairs, whereas CoV genomes are ~30,000 base pairs, making the HRV genome 731 ~25% of the size of the CoV genome. Therefore, we selected a cutoff of 15,000 viral 732 reads for subjects to be included in the HRV + highly infected group. Therefore, we 733 selected a cutoff of 15,000 viral reads for subjects to be included in the HRV + highly 734 infected group (n=37) analyzed in Figure 6 . All non-infected subjects (n=571), based on 735 the Virus Finder analysis described above, were used as comparison group for the 736 CoV + and HRV + groups. 737