Immediate myeloid depot for SARS-CoV-2 in the human lung
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Abstract
In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, considerable focus has been placed on a model of viral entry into host epithelial populations, with a separate focus upon the responding immune system dysfunction that exacerbates or causes disease. We developed a precision-cut lung slice model to investigate very early host-viral pathogenesis and found that SARS-CoV-2 had a rapid and specific tropism for myeloid populations in the human lung. Infection of alveolar macrophages was partially dependent upon their expression of ACE2, and the infections were productive for amplifying virus, both findings which were in contrast with their neutralization of another pandemic virus, Influenza A virus (IAV). Compared to IAV, SARS-CoV-2 was extremely poor at inducing interferon-stimulated genes in infected myeloid cells, providing a window of opportunity for modest titers to amplify within these cells. Endotracheal aspirate samples from humans with the acute respiratory distress syndrome (ARDS) from COVID-19 confirmed the lung slice findings, revealing a persistent myeloid depot. In the early phase of SARS-CoV-2 infection, myeloid cells may provide a safe harbor for the virus with minimal immune stimulatory cues being generated, resulting in effective viral colonization and quenching of the immune system.
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SciScore for 10.1101/2022.04.28.489942: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: , Zuckerberg San Francisco General Hospital) under research protocol 20-30497 approved by the University of California San Francisco Institutional Review Board. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources For selected experiments, BAL cells were treated for 2h before infection with an ACE2 blocking antibody at 10 µg/ml (AF933, R&D systems). ACE2suggested: NoneExperimental Models: Cell Lines Sentences Resources SARS-CoV-2 infections: Vero E6 and Vero-TMPRSS2 cells (gift from Dr. Melanie Ott) were cultured in DMEM supplemented with 10% FBS, … SciScore for 10.1101/2022.04.28.489942: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: , Zuckerberg San Francisco General Hospital) under research protocol 20-30497 approved by the University of California San Francisco Institutional Review Board. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources For selected experiments, BAL cells were treated for 2h before infection with an ACE2 blocking antibody at 10 µg/ml (AF933, R&D systems). ACE2suggested: NoneExperimental Models: Cell Lines Sentences Resources SARS-CoV-2 infections: Vero E6 and Vero-TMPRSS2 cells (gift from Dr. Melanie Ott) were cultured in DMEM supplemented with 10% FBS, penicillin/streptomycin, and L-glutamine (Corning) in a humidified incubator at 37°C and 5% CO2. Vero E6suggested: NoneVero-TMPRSS2suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)Briefly, 10-fold dilutions of the virus stock were added to Vero cells in a 12-well plate for 1 hour, after which an overlay of 1.2% Avicel RC-581 in DMEM was added. Verosuggested: NoneThis solution was used as inoculum for Vero E6 cells (SARS-CoV-2) or MDCK cells (IAV-Venus). MDCKsuggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)Experimental Models: Organisms/Strains Sentences Resources SARS-CoV-2 B.1.617.2 (delta) variant was acquired from the California Department of Public Health, cultured in Vero-TMPRSS2 cells. SARS-CoV-2 B.1.617.2suggested: NoneSoftware and Algorithms Sentences Resources Confocal imaging was performed using a Nikon A1R laser scanning confocal microscope with NIS-Elements software and a 16X LWD water dipping objective. NIS-Elementssuggested: None50 – 100 µm-thick images with a z-step of 1.5 µm were taken and analyzed using Imaris (Bitplane). Imarissuggested: NoneData were collected using the BD LSRII Cytometer and analyzed using FlowJo version 10 (BD Biosciences). FlowJosuggested: (FlowJo, RRID:SCR_008520)Briefly, raw gene-expression fastqs were aligned to the GRCh38 reference genome annotated with Ensembl v85, and Lipid Hashtag fastqs were processed to count the incidences of each expected index per cell. Ensemblsuggested: NoneData quality control and normalization: The gene expression count matrices were normalized, and variance stabilized using negative binomial regression using the scTransform algorithm21 in the Seurat package. Seuratsuggested: (SEURAT, RRID:SCR_007322)Statistical analyses: Statistical analysis was performed using GraphPad Prism v7.0e. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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