Interpreting the evolution of SARS-CoV-2
Jesse Bloom
Fred Hutch Cancer Center / HHMI
These slides at https://slides.com/jbloom/sars2-sinai
The Faroe Islands
"Measles had not prevailed on the Faroes since 1781, then it broke out early in April 1846."
"Of the 7782 inhabitants, about 6000 were taken with measles."
"Of the many aged people still living in the Faroes who had measles in 1781, not one was attacked the second time."
Panum is describing immune memory, which provides lifelong protection from measles.
But we are repeatedly infected by some other viruses. Typical person infected by influenza ~5 years. Why?
History offers natural experiment with influenza like Panum's study of measles
History offers natural experiment with influenza like Panum's study of measles
In 1977, old H1N1 strain from ~1954 was inadvertently re-released and caused pandemic. So re-introduction of identical virus after a few decades.
"One boy from Hong Kong had a transient febrile illness from 15 to 18 January. On Sunday 22 January, three boys were in the college infirmary… 512 boys (67%) spent between three and seven days away from class."
"Of about 130 adults who had some contact with the boys, only one, a house matron, developed similar symptoms."
Influenza infection also elicits multi-decade immunity, but only if virus is evolutionarily frozen
Some human RNA respiratory viruses evolve to escape immunity
Why some viruses evolve to escape immunity while others don't is a deep question outside scope of this talk. See here for some possible explanations.
Rate of viral antigenic evolution
Measles
Influenza
CoV-229E causes common colds and has been circulating in humans for a long time.
The typical person is infected every ~3 to 5 years.
How do other human coronaviruses evolve?
Evolution of CoV-229E spike
We experimentally generated CoV-229E spikes at ~8 year intervals so we could study them in the lab:
- 1984
- 1992
- 2001
- 2008
- 2016
Evolution of CoV-229E spike erodes neutralization by human serum antibodies
Evolution erodes CoV-229E neutralization by different sera at different rates
Ideally vaccines would elicit evolution-resistant neutralizing antibodies (like those naturally made by person at right) rather than evolution-sensitive antibodies (like those naturally made by person at left)
Strongest evolutionary selection is in RBD
Sites of evolutionary change in the spike of CoV-229E over the last four decades
Strongest evolutionary selection is in RBD
Sites of evolutionary change in the spike of CoV-229E over the last four decades
Sites of mutations in SARS-CoV-2 Omicron BQ.1.1 spike relative to Wuhan-Hu-1
RBD does not run out of evolutionary space
25 of 31 residues in CoV-229E RBD that contact receptor varied during virus's evolution in humans over last ~50 years (Li et al, 2019)
Phylogenetic tree shape & vaccine strategy
CoV-229E has ladder-like tree:
- new variants displace old ones
- new variants descend from recent successful ones
Human influenza A evolves this way too. It's theoretically possible to pick single well-matched vaccine strain.
Phylogenetic tree shape & vaccine strategy
CoV-229E has ladder-like tree:
- new variants displace old ones
- new variants descend from recent successful ones
Human influenza A evolves this way too. It's theoretically possible to pick single well-matched vaccine strain.
CoV-OC43 split into two ladder-like lineages. Influenza B evolves this way too. It's theoretically possible to pick well-matched bivalent vaccine.
Phylogenetic tree shape & vaccine strategy
CoV-229E has ladder-like tree:
- new variants displace old ones
- new variants descend from recent successful ones
Human influenza A evolves this way too. It's theoretically possible to pick single well-matched vaccine strain.
CoV-OC43 split into two ladder-like lineages. Influenza B evolves this way too. It's theoretically possible to pick well-matched bivalent vaccine.
In non-ladder-like tree, there can be high standing genetic variation. Makes picking vaccine strains difficult.
How did Omicron acquire so many mutations with no sampled evolutionary intermediates?
The molecular clock identifies unusual patterns in Omicron evolution
Excess antibody-escape mutations in spike are characteristic of viruses that evolve in chronic human infections
During typical acute infections, random transmission bottlenecks disrupt selection
But in chronic infections of 100+ days, selection can fix antibody-escape mutations without bottlenecks
If evolution is being driven by neutralizing antibody escape, what might be next?
First, some background on viral entry proteins and lentiviral pseudotyping
All enveloped viruses have one or more entry proteins that bind receptor and fuse the viral and cell membranes
- SARS-CoV-2 spike
- influenza hemagglutinin
- HIV envelope protein
- Lassa virus glycoprotein
- Nipah virus G and F proteins
- RSV G and F proteins
How can we rapidly and safely measure effects of mutations to viral entry proteins?
- General: can work for many viral entry proteins
- Comprehensive: measure mutations throughout the protein
- High-throughput: can be applied new variants and antibodies
- Safe: we want to avoid concerns with making novel replication-competent viruses
- Applicable directly to sera, to capture person-to-person heterogeneity
Lentiviral pseudotyping
- Many enveloped viruses have entry proteins amenable to lentiviral pseudotyping.
- Safe and well-established way to study cell entry function of these proteins
- However, traditional pseudotyping does not create genotype-phenotype link.
Two-step method to create genotype-phenotype linked pseudotype libraries
Two-step method to create genotype-phenotype linked spike-pseudotypes
Sequencing measures relative amounts, so include neutralization standard
Example: RBD antibody LY-CoV1404
Validates very well
Example: S2 antibody CC67.105
We mapped how all tolerated mutations to XBB.1.5 spike affect three key phenotypes
Cell entry: how well pseudovirus enters 293T-ACE2 cells
Sera escape: how pseudovirus is neutralized by human polyclonal serum
ACE2 binding: how pseudovirus is neutralized by soluble ACE2
Neutralization by soluble ACE2 is proportional to ACE2 binding affinity
How well do these spike phenotypes predict human SARS-CoV-2 clade growth?
change in clade growth
clade growth
Measured spike phenotypes correlate with changes in SARS-CoV-2 clade growth
Multiple linear regression combining spike phenotypes predicts clade growth well
Conclusions
Some viruses evolve to escape antibodies, and unfortunately SARS-CoV-2 is one of those viruses.
Patterns of substitution in the SARS-CoV-2 spike are similar to those in other human coronaviruses (eg, CoV-229E).
We can use deep mutational scanning to identify mutations that cause escape.
These data can be used to forecast with reasonable accuracy the relative clade growth of human SARS-CoV-2 clades
Bloom lab
Bernadeta Dadonaite
Kate Crawford
Caelan Radford
Tyler Starr
Allie Greaney
Rachel Eguia
rest of lab
University of Washington
Helen Chu and HAARVI cohort
David Veesler
Karolinska Institute
Ben Murrell
Thanks
