SARS-CoV-2 infection leads to vastly divergent and heterogeneous clinical outcomes ranging from asymptomatic to fatal disease. Co-morbidities, sex, age, and host genetics together with vaccine status are known to affect disease severity. However, how the inflammatory milieu of the lung at the time of SARS-CoV-2 infection impacts control of the virus remains less well understood. Here, we identify key innate immune pathways required to limit viral replication, including the pro-inflammatory cytokine TNFα. Moreover, we demonstrate here that recent immune events in the lung proximal to the time of SARS-CoV-2 exposure can drastically impact viral control. A diverse set of pulmonary inflammatory stimuli, ranging from prior resolved respiratory infections of S. aureus or influenza, ongoing M. tuberculosis infection, or ovalbumin/alum-induced asthma to administration of defined TLR ligands and recombinant cytokines, resulted in an antiviral state that potently limited SARS-CoV-2 replication. In addition to type I interferons, the broadly inducible inflammatory cytokines TNFα and IL-1 very effectively conditioned the lung for enhanced viral control. Collectively, our work reveals that SARS-CoV-2 may benefit from an immunologically quiescent lung microenvironment and indicates that the recent and momentary pulmonary inflammatory tone during SARS-CoV-2 exposure may contribute to the population-wide variability in COVID-19 disease outcomes.
Overall design: Cryopreserved Bronchoalveolar lavage (BAL) cells from rhesus macaques infected with SARS-CoV-2 collected at days 0, 3, 7, 14 and 28-35 (necropsy) post-infection. This data is composed of 71 samples, whose general group distribution is as follows: aIFNg (n = 22), aIL10 (n = 24) and controls (n = 24).
Cryopreserved BAL cells from pre-infection (d0) and days 3, 7, 14, and 28-35 post infection (necropsy) were thawed and homogenized using Qiagen RLT buffer Plus (Cat # 1053393) and QIAShredder Columns (Cat # 79656). RNA was isolated using the Qiagen RNeasy Mini kit (Cat # 74134) according to manufacturer’s instructions and eluted in 25uL of RNase free water. RNA was concentrated to 25-50ng/uL using Eppendorf Vacufuge plus centrifuge concentrator. RNA quality was confirmed with Agilent TapeStation. RNA was sent to the National Cancer Institute (NCI) Center for Cancer Research Genomics Core at the Frederick National Laboratory. Digital mRNA gene expression analysis was performed with the Nanostring nCounter NHP Immunology panel V2 (Cat # 115000276). Raw read counts were obtained from RCC files using the nSolver 4.0 Data Analysis software and the NS_NHP_Immunology_V2.0 rlf file references included with the nCounter NHP Immunology panel V2 kit.
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