Post-acute immunological and behavioral sequelae in mice after Omicron infection
Data files
Jun 09, 2023 version files 894.85 MB
-
BA1_1_Baseline.fcs
-
BA1_1_Sti.fcs
-
BA1_2_Baseline.fcs
-
BA1_2_Sti.fcs
-
BA1_3_Baseline.fcs
-
BA1_3_Sti.fcs
-
BA1_4_Baseline.fcs
-
BA1_4_Sti.fcs
-
BA1_5_Baseline.fcs
-
BA1_5_Sti.fcs
-
Mock_1_Baseline.fcs
-
Mock_1_Sti.fcs
-
Mock_2_Baseline.fcs
-
Mock_2_Sti.fcs
-
Mock_3_Baseline.fcs
-
Mock_3_Sti.fcs
-
Mock_4_Baseline.fcs
-
Mock_4_Sti.fcs
-
Mock_5_Baseline.fcs
-
Mock_5_Sti.fcs
-
README.md
-
Vac_1_Baseline.fcs
-
Vac_1_Sti.fcs
-
Vac_2_Baseline.fcs
-
Vac_2_Sti.fcs
-
Vac_3_Baseline.fcs
-
Vac_3_Sti.fcs
-
Vac_4_Baseline.fcs
-
Vac_4_Sti.fcs
-
Vac_5_Baseline.fcs
-
Vac_5_Sti.fcs
-
Vac_BA1_1_Baseline.fcs
-
Vac_BA1_1_Sti.fcs
-
Vac_BA1_2_Baseline.fcs
-
Vac_BA1_2_Sti.fcs
-
Vac_BA1_3_Baseline.fcs
-
Vac_BA1_3_Sti.fcs
-
Vac_BA1_4_Baseline.fcs
-
Vac_BA1_4_Sti.fcs
-
Vac_BA1_5_Baseline.fcs
-
Vac_BA1_5_Sti.fcs
Jun 09, 2023 version files 894.85 MB
-
BA1_1_Baseline.fcs
-
BA1_1_Sti.fcs
-
BA1_2_Baseline.fcs
-
BA1_2_Sti.fcs
-
BA1_3_Baseline.fcs
-
BA1_3_Sti.fcs
-
BA1_4_Baseline.fcs
-
BA1_4_Sti.fcs
-
BA1_5_Baseline.fcs
-
BA1_5_Sti.fcs
-
Mock_1_Baseline.fcs
-
Mock_1_Sti.fcs
-
Mock_2_Baseline.fcs
-
Mock_2_Sti.fcs
-
Mock_3_Baseline.fcs
-
Mock_3_Sti.fcs
-
Mock_4_Baseline.fcs
-
Mock_4_Sti.fcs
-
Mock_5_Baseline.fcs
-
Mock_5_Sti.fcs
-
README.md
-
Vac_1_Baseline.fcs
-
Vac_1_Sti.fcs
-
Vac_2_Baseline.fcs
-
Vac_2_Sti.fcs
-
Vac_3_Baseline.fcs
-
Vac_3_Sti.fcs
-
Vac_4_Baseline.fcs
-
Vac_4_Sti.fcs
-
Vac_5_Baseline.fcs
-
Vac_5_Sti.fcs
-
Vac_BA1_1_Baseline.fcs
-
Vac_BA1_1_Sti.fcs
-
Vac_BA1_2_Baseline.fcs
-
Vac_BA1_2_Sti.fcs
-
Vac_BA1_3_Baseline.fcs
-
Vac_BA1_3_Sti.fcs
-
Vac_BA1_4_Baseline.fcs
-
Vac_BA1_4_Sti.fcs
-
Vac_BA1_5_Baseline.fcs
-
Vac_BA1_5_Sti.fcs
Abstract
Progress in understanding long COVID and developing effective therapeutics is hampered in part by the lack of suitable animal models. Here we used ACE2-transgenic mice recovered from Omicron (BA.1) infection to test for pulmonary and behavioral post-acute sequelae. Through in-depth phenotyping by CyTOF, we demonstrate that naïve mice experiencing a first Omicron infection exhibit profound immune perturbations in the lung after resolving acute infection. This is not observed if mice were first vaccinated with spike-encoding mRNA. The protective effects of vaccination against post-acute sequelae were associated with a highly polyfunctional SARS-CoV-2-specific T cell response that was recalled upon BA.1 breakthrough infection but not seen with BA.1 infection alone. Without vaccination, the chemokine receptor CXCR4 was uniquely upregulated on multiple pulmonary immune subsets in the BA.1 convalescent mice, a process previously connected to severe COVID-19. Taking advantage of recent developments in AI-based assessments of murine behaviors, we demonstrate that BA.1 convalescent mice respond abnormally to a stimulus after repeated presentations (habituation). Collectively, our data identify immunological and behavioral post-acute sequelae after Omicron infection and uncover a protective effect of vaccination.
README
READ ME FILE
General Information
Title: Vaccination protects against persistence of pulmonary immunological perturbations in mouse model of long COVID
Contact:
Nadia Roan, PhD
Gladstone Institutes
University of California, San Francisco
Dates of collection:
4/1/2022 6/27/2022
Information about geographic location of data collection:
San Francisco Bay Area
Key Words:
COVID-19, SARS-CoV-2, Mouse Model, Long Covid, Post-Acute Sequelae of COVID-19 (PASC), T cells, CyTOF, CXCR4
Data and File Overview
Included are total 40 FCS files corresponding to CyTOF data generated from the murine lung. Data were generated from the following five groups of mice:
- Mock-treated (Mock)
- Vaccinated (Vac)
- BA.1 convalescent (BA1)
- Vaccinated, BA.1 convalescent (Vac_BA1)
Each experimental group had 5 mice. Each murine sample was analyzed at baseline, or following a 6 hour stimulation with SARS-CoV-2 peptides to characterize SARS-CoV-2-specific T cells.
Each FCS file name begins with the treatment group (shorthand names listed above in quotes), followed by a number (1-5) to identify the mouse. Of note, numbers identifying mice are shared between different experimental groups, but these do not correspond to the same mice; rather we arbitrarily numbered each mouse within each experimental group from 1-5. The last component of the file name was either Baseline or Sti (shorthand for stimulated) to indicate whether the sample was analyzed at baseline or after SARS-CoV-2 peptide stimulation.
All files were pre-gated on live, singlet CD45+ events.
Sharing and accessing information
No licenses or restrictions are placed on the data.
Methodological Information
Methods used for generating and analyzing the CyTOF datasets are similar to those recently described:
- https://www.nature.com/articles/s41586-022-04865-0
- https://doi.org/10.1016/j.xcrm.2020.100081
- https://doi.org/10.1016/j.celrep.2021.109414
- https://journals.aai.org/jimmunol/article/207/5/1344/234507/Protracted-yet-Coordinated-Differentiation-of-Long
- https://elifesciences.org/articles/72619
Data-specific information
Please see above information under data and file overview and methodological information.