Scientist studying evolution of proteins and viruses.
Lentiviral pseudotype deep mutational scanning of SARS-CoV-2 spike
Fred Hutch Cancer Center / HHMI
I am on the scientific advisory boards of Apriori Bio and Oncorus
I have consulted on topics related to viral evolution for Moderna and Merck
I am an inventor on Fred Hutch licensed patents related to deep mutational scanning of viral proteins
Deep mutational scanning measures effects of many mutations to viral proteins
Limitations of RBD yeast-display deep mutational scanning
- Only examines mutations in RBD, which is just part of spike
- Measures antibody binding, not neutralization. They are unequal in polyclonal serum.
- Only works for viral entry proteins with domains amenable to yeast display.
Alternative: lentiviral pseudotyping
- Many viruses have entry proteins amenable to lentiviral pseudotyping.
- However, traditional pseudotyping does not create genotype-phenotype link.
Two-step method to create genotype-phenotype linked spike-pseudotypes
Sequencing only measures relative amounts, so include "absolute standard"
Example: RBD antibody LY-CoV1404
Validates very well
Also works for NTD antibodies
Also works for S2 antibodies
Method should be extensible to many other viral entry proteins
- System can provide safe way to do high-throughput mutational studies
- We need to be aware of information hazard
- We think hazard low for SARS-CoV-2 spike, which is already human adapted
- But maybe hazard of human-receptor adaptive mutations in potential pandemic viruses
- For such viruses, we propose to use natural host rather than human receptors
By Jesse Bloom