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. 2022 Jun 7:eabq3059. doi: 10.1126/scitranslmed.abq3059

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Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works

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Fig. 5. — Persistent inflammation in the olfactory bulb and epithelium is observed in response to SARS-CoV-2 infection in hamsters. (A) A heat map is shown denoting differential expression analysis conducted on RNA-seq derived from olfactory bulbs of 3dpi and 31dpi IAV- and SARS-CoV-2-infected hamsters compared to mock-infected hamsters. Log2 fold-change of IFN-I response genes are displayed. (B to F) Expression of key IFN-I response associated genes (B) Isg15, (C) Mx2, and (D) Irf7; chemokines (E) Cxcl10, and (F) Ccl5 were quantified by qRT-PCR (n=4 to 5 per treatment and time point group). Error bars display standard deviation, and significance was determined by independent tests on samples from 3dpi and 31dpi for each gene using one-way ANOVA with Tukey’s multiple comparisons test; *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. (G) Differential expression data derived from olfactory bulbs of hamsters 31dpi was analyzed by GSEA analysis to deconvolute specific cellular identity signatures. Top positive enrichments are denoted by lollipop chart based on their NES (magnitude of line) and significance (-log10(FDR q-val)) (dot size). (CTX: Cortex; PFC: Prefrontal Cortex) (H) Expression of Aif-1 (also known as Iba1) was quantified by qRT-PCR (n=4 to 5 per treatment and time point group). Error bars display standard deviation, and significance was determined by independent tests on samples from 3dpi and 31dpi for each gene using one-way ANOVA with Tukey’s multiple comparisons test; **p<0.01, ***p<0.001. (I) Concentrations of IAV or SARS-CoV-2 RNA in the olfactory bulbs were measured by qRT-PCR with primers for IAV nucleoprotein (IAV NP) or SARS-CoV-2 subgenomic nucleocapsid protein (SARS-CoV-2 sgN), respectively (n=4 per treatment and time point group). Error bars display standard deviation. (J) Olfactory epithelium samples from mock-, IAV-, or SARS-CoV-2-infected hamsters were harvested and transcriptionally profiled using RNA-seq. Differential expression analysis was conducted on infected groups compared to mock. Log2 Fold Change for expression of individual genes relevant to ontologies concerning IFN-I, chemokine, and T cell activation are presented in the graph for both IAV and SARS-CoV-2 compared to mock; error bars denote standard error.