Mild and Severe SARS-CoV-2 Infection Induces Respiratory and Intestinal Microbiome Changes in the K18-hACE2 Transgenic Mouse Model
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Abstract
The COVID-19 pandemic has resulted in millions of deaths. The host’s respiratory and intestinal microbiome can affect directly or indirectly the immune system during viral infections.
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SciScore for 10.1101/2021.04.20.440722: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IACUC: Ethics statement: Animal studies were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Georgia (Protocol A2019-03-032-Y1-A3) and performed following the IACUC Guidebook of the Office of Laboratory Animal Welfare and PHS policy on Humane Care and of Use of Laboratory Animals.
Field Sample Permit: Studies were performed in an animal Biosafety level 3 containment facility at the Animal Health Research Center (AHRC) at the University of Georgia. Cells and Virus: The SARS-CoV-2 (Isolate USA-WA1/2020) isolate, kindly provided by Dr. S. Mark Tompkins, Department of Infectious Diseases, University of Georgia, was used for virus challenge in the animal …SciScore for 10.1101/2021.04.20.440722: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IACUC: Ethics statement: Animal studies were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Georgia (Protocol A2019-03-032-Y1-A3) and performed following the IACUC Guidebook of the Office of Laboratory Animal Welfare and PHS policy on Humane Care and of Use of Laboratory Animals.
Field Sample Permit: Studies were performed in an animal Biosafety level 3 containment facility at the Animal Health Research Center (AHRC) at the University of Georgia. Cells and Virus: The SARS-CoV-2 (Isolate USA-WA1/2020) isolate, kindly provided by Dr. S. Mark Tompkins, Department of Infectious Diseases, University of Georgia, was used for virus challenge in the animal studies.Sex as a biological variable Mouse experiments: Female K18-hACE2 mice (6 weeks old) were randomly distributed into six groups (n=6/group for controls and n=9/group for challenged), anesthetized and challenged intranasally with 50 µL of phosphate buffer saline (PBS), 1×103 TCID50/mouse (Low virus dose) or 1×105 TCID50/mouse (High virus dose). Randomization Mouse experiments: Female K18-hACE2 mice (6 weeks old) were randomly distributed into six groups (n=6/group for controls and n=9/group for challenged), anesthetized and challenged intranasally with 50 µL of phosphate buffer saline (PBS), 1×103 TCID50/mouse (Low virus dose) or 1×105 TCID50/mouse (High virus dose). Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Briefly, the virus was grown in Vero E6 Pasteur cells provided by Maria Pinto (Center for Virus research, University of Glasgow, Scotland, UK), and maintained in Dulbecco’s Modified Eagles Medium (DMEM, Sigma-Aldrich, St Louis, MO) containing 10% fetal bovine serum (FBS, Sigma-Aldrich, St Louis, MO), 1% antibiotic/antimycotic (AB, Sigma-Aldrich, St Louis, MO) and 1% L-Glutamine (Sigma-Aldrich, St Louis, MO). Vero E6suggested: NoneExperimental Models: Organisms/Strains Sentences Resources Mouse experiments: Female K18-hACE2 mice (6 weeks old) were randomly distributed into six groups (n=6/group for controls and n=9/group for challenged), anesthetized and challenged intranasally with 50 µL of phosphate buffer saline (PBS), 1×103 TCID50/mouse (Low virus dose) or 1×105 TCID50/mouse (High virus dose). K18-hACE2suggested: RRID:IMSR_GPT:T037657)Software and Algorithms Sentences Resources Amplicon concentration was measured using the Qubit dsDNA HS Assay kit (ThermoFisher, Waltham, MA) on the Qubit 3.0 fluorometer (ThermoFisher, Waltham, MA). Ampliconsuggested: (Amplicon, RRID:SCR_003294)Fragment size distribution was analyzed on a subset of samples using the Agilent Bioanalyzer 2100 DNA-HS assay (Agilent, Santa Clara, CA, USA). Agilent Bioanalyzersuggested: NoneTaxonomy was assigned in ‘dada2’ using the native implementation of the naïve Bayesian classifier using Silva v. Silvasuggested: (SILVA, RRID:SCR_006423)Hierarchal cluster analysis of the Bray-Curtis distances was created using command hclust with agglomeration method “average” (UPGMA) producing a cophenetic correlation coefficient of 0.79. hclustsuggested: (HCLUST, RRID:SCR_009154)The dendrogram was created using the function plot and shading/group colors were added using Adobe Illustrator (Version 25.0.1) Adobe Illustratorsuggested: (Adobe Illustrator, RRID:SCR_010279)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Some limitations of this study must be noted. While the environment was stable and controlled, the sample size for each group at each time point was small and the potential contribution of cage effect on the microbiome was not analyzed. The high mortality observed in the high virus dose groups only allowed for collection of two time points (2 and 5 dpc, only one sample was collected at 14 dpc from the only survivor in the High/GC-376 group). As indicated above, ceca samples were only collected for mice not treated with GC-376. In contrast, lung samples from mock inoculation/vehicle treated control mice did not yield sufficient amplifiable microbial DNA for sequencing, so the comparison focused on SARS-CoV-2 dose-dependent responses in GC-376 treated mice. The microbiome of the cecum showed significant decreases in Shannon and Inv Simpson index comparing the control to the low-dose and high-dose infected groups (Fig. 2B and 2C). The low virus dose group shared a higher number of ASVs with the control group compared to the high virus dose group (Fig. 2D). These observations suggest a virus dose-dependent effect of the ceca microbial diversity in mice infected with SARS-CoV-2. While preparing the manuscript, a report was published that analyzed the small intestine microbiome of hACE2 mice among unvaccinated and vaccinated mice challenged with a high dose of SARS-CoV-2 (47). While we compare control mice to low and high doses of non-vaccinated mice challenged with SARS-CoV-2 in t...
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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
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