ACE2 expression neuts
In this project we want to understand how Ace2 expression on target cell surface affects neutralization of SARS-CoV-2 virus by human sera and monoclonal antibodies.
We are using ACE2 expressing HEK-293T from Kenneth Matreyek. We have several clones of these cells ('high', 'medium', 'low', 'very low'), which have differential Ace2 surface expression due to modifications in Kozak sequence upstream of ACE2 gene.
In these experiments we use Wu-1-Hu-614G virus.
The experimental steps are as follows:
- test ability of this virus to infect different HEK-293T-Ace2 clones. Notebook: virus_titers.ipynb
- test ACE2 expression in different cell clones. Notebook: ACE2_expression_vs_infectivity.ipynb
- perform mock and RBD-binding antibody depletion on human sera. Notebook: rbd_depletions.ipynb
- perform virus neutralization experiments with RBD-binding antibody depleted and nondepleted sera. Notebook: virus_neutralization.ipynb
- perform virus neutralization experiments monoclonal antibodies targetting different Spike epitopes. Notebook: virus_neutralization_mAbs.ipynb
Sera that is used in these experiments comes from HAARVI study and is from individuals who have been infected with SARS-CoV-2 and subsequently received a two-dose vaccination.
To run the analysis using snakemake pipeline type:
sbatch run_Hutch_cluster.bash
After the run is finished analysis results are found in results folder.