Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms.

"rna-seq data processing and reference mapping were done with custom analysis scripts combining publicly available tools as previously described 15 with modifications as follows and reads were mapped to a custom reference that combined the human hg38 reference genome (release 34 grch38 p13) and the sars-cov-2 genome (refseq nc_045512) for simultaneous quantification of host and virus transcripts."

"Conflicts of interest These authors disclose the following: Girish Nadkarni reports employment with, consultancy agreements with, and ownership interest in Pensieve Health and Renalytix AI; has received consulting fees from AstraZeneca, BioVie, GLG Consulting, and Reata; and has served as a scientific advisor or member of Pensieve Health and Renalytix AI. Jeremiah J. Faith has served on the scientific advisor board of Vedanta Biosciences and has received grants from Janssen (unrelated to this work). Jean-Frederic Colombel has served as a consultant for AbbVie, Amgen, Arena Pharmaceuticals, Boehringer Ingelheim, Celgene Corporations, Celltrion, Eli Lilly, and Enterome (all unrelated to this work). Sacha Gnjatic has received research grants from Bristol Myers Squibb, Genentech, Immune Design, Agenus, and Janssen and has served as a consultant for Merck, OncoMed, and Neon Therapeutics. Noam Harpaz has served as a consultant for Lilly USA and has received a pathology service contract with AbbVie and Celgene. Silvio Danese has served as a consultant for Ely Lilly, Enthera, Ferring Pharmaceuticals, Gilead, Hospira, Inotrem, Janssen, Johnson & Johnson, Merck Sharp & Dohme Mundipharma, Mylan, Pfizer, Roche, Sandoz, Sublimity Therapeutics, Takeda, TiGenix, UCB, and Vifor. Robert E. Schwartz has served on the scientific advisory board of Miromatrix Inc and is a consultant and speaker for Alnylam Inc. Nikhil A. Kumta has served as a consultant for Apollo Endosurgery, Boston Scientific, Gyrus AMCI, and Olympus. The remaining authors disclose no conflicts."

"Funding This research was partly funded by 10.13039/100000002National Institutes of Health (NIH)/ 10.13039/100000062National Institute of Diabetes and Digestive and Kidney Diseases 123749 0S1 (to Saurabh Mehandru). Additional support was provided by the Center for Research for Influenza Pathogenesis, a 10.13039/100000060National Institute of Allergy and Infectious Diseases (NIAID)–supported Center of Excellence for Influenza Research and Surveillance (contract no. HHSN272201400008C), and NIAID R01AI113186 (to Harm van Bakel). Additionally, the work was supported by the generous support of the 10.13039/100007457JPB Foundation , the 10.13039/100014895Open Philanthropy Project (research grant 2020-215611 [5384]), the 10.13039/100000185Defense Advanced Research Projects Agency , and anonymous donors to Adolfo Garcia-Sastre. Minami Tokuyama was funded by the Digestive Disease 10.13039/100005930Research Foundation . Ana S. Gonzalez-Reiche is supported in part by a Robin Chemers Neustein Postdoctoral Fellowship Award. The research carried out by Harm van Bakel and Ana S. Gonzalez-Reiche was supported by the Office of Research Infrastructure of the NIH under awards S10OD018522 and S10OD026880. Robert E. Schwartz is funded by NCI R01CA234614, NIAID 2R01AI107301, and NIDDK R01DK121072 and is supported as an Irma Hirschl Trust Research Award Scholar. Emily A. Bruce is supported by NIH grant P20GM125498 (awarded to University of Vermont Translational Global Infectious Disease Research Center). Pamela J. Bjorkman and Mark S. Ladinsky are supported by 10.13039/100006369George Mason University Fast Grants. Steven T. Chen is supported by grant F30CA243210. Graham J. Britton is supported by a Research Fellowship Award from the Crohn’s and Colitis Foundation of America. Matthew P. Spindler is supported by NIH T32 5T32AI007605. Sacha Gnjatic is supported by grants U24 CA224319, U01 DK124165, and P01 CA190174."