1. Western Institute for Neuroscience, Western University, London, ON, Canada, N6A 3K7
2. Department of Physiology and Pharmacology, Western University, London, ON, Canada, N6A 3K7
3. Department of Psychology, King's University College, Western University, London, ON, Canada, N6A 3K7
4. Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 2QQ
5. Faculty of Medicine, Department of Neurology, University of British Columbia, Vancouver, BC, Canada, V6T 2B5
6. Department of Medicine (Neurology), Hurvitz Brain Sciences Program, Sunnybrook HSC, University of Toronto, Toronto, ON, Canada, M4N 3M5
7. Department of Psychology, Western University, London, ON, Canada, N6A 3K7
8. Senior author
9. Lead contact
* Correspondence: [email protected], [email protected]

As COVID-19 cases exceed hundreds of millions globally, many survivors face cognitive challenges and prolonged symptoms. However, important questions about the cognitive impacts of COVID-19 remain unresolved. In this cross-sectional online study, 478 adult volunteers who self-reported a positive test for COVID-19 (M=30 days since most recent test) perform significantly worse than pre-pandemic norms on cognitive measures of processing speed, reasoning, verbal, and overall performance, but not short-term memory – suggesting domain-specific deficits. Cognitive differences are even observed in participants that did not require hospitalisation. Factor analysis of health- and COVID-related questionnaires reveals two clusters of symptoms: one that varies mostly with physical symptoms and illness severity, and one with mental health. Cognitive performance is positively correlated with the global measure encompassing physical symptoms, but not the one that broadly described mental health, suggesting that the subjective experience of “long COVID” relates to physical symptoms and cognitive deficits, especially executive dysfunction.

All anonymized data (i.e., cognitive testing and survey/questionnaire data) collected for this study are publicly available in the Scholar Portal Dataverse, as a part of this record (https://doi.org/10.5683/SP2/ZQR9QQ), and can be used to recreate all statistics, tables, and figures in this manuscript. See also Running This Analysis, below.

A viewable Python notebook of the entire analysis, including embedded images. It represents the most recent version of the analysis, including all tables, figures, and numbers. If you are unable to view the notebook in GitHub by clicking the file above (e.g., you get the "Sorry, something went wrong." message), trying opening it at nbviewer.

The executable analysis script used to generate the notebook.

A subpackage for loading data from this study. Download data files from the repository, and place them in this folder: ./cbs_data/data.

A subpackage that contains miscellaneous helpers and functions for performing statistics, generating figures, etc.

Contains the frozen list of python packages (and their versions) used in this data analysis; i.e., the supporting Python environment.

Contains PDF files of the manuscript preprint.

There are two options if you want to run this analysis on your local machine:

A prebuilt Docker image that contains this codebase, the supporting Python environment, and the actual data files, can be downloaded from the GitHub container registry at ghcr.io/theowenlab/2022-covid-cognition. Running this container will start a Jupyter notebook server that you can then access in your web browser. You can can run the entire analysis, tweak it, or add new cells of code. The only requirement is that you have Docker installed on your local computer. Give it a try!

docker run --rm -it -p 8888:8888 ghcr.io/theowenlab/2022-covid-cognition:latest

Then, in your web browser go to localhost:8888.

1. You must have a working Python (>v3.7) development environment, and probably a new (empty) virtual environment.
2. Clone this repository.
3. Install the required packages: pip3 install -r requirements.txt.
4. Download the data files and place them in the ./cbs_data/data/ folder.
5. Run the script ./covid_cognition.py.