Interpreting the evolution of SARS-CoV-2

 

Jesse Bloom

Fred Hutch Cancer Center / HHMI

 

These slides at https://slides.com/jbloom/stanford2023

 

Disclosures

I am on the scientific advisory boards of Apriori Bio, Aerium Therapeutics, Invivyd, and the Vaccine Company. 

 

I am an inventor on Fred Hutch licensed patents related to deep mutational scanning of viral proteins

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 H3N2 influenza ~5 years. Why?

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 a global pandemic.

"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?

Deep mutational scanning to map RBD mutations that escape antibody binding

RBD

fluorescently labeled antibody

yeast

fluorescent tag on RBD

Experiments combine flow cytometry and deep sequencing of a library of yeast expressing all RBD mutants

These measurements can be made on ~10,000 to ~100,000 mutants all at once 

Escape map from one antibody (LY-CoV555, ie bamlanivimab)

484

452

490

This turned out be an unfortunate choice of an antibody for Eli Lilly to develop as drug, as mutations at sites 484 and 452 were prevalent by early to mid 2021

Infection / vaccination elicit polyclonal antibodies 

Deep mutational scanning has now been applied to many antibodies

36 antibodies mapped by Tyler Starr & Allie Greaney in Bloom lab.

36 antibodies mapped by Tyler Starr & Allie Greaney in Bloom lab.

>4,000 (!) antibodies mapped by Yunlong Cao et al at Peking University. See here and here.

Deep mutational scanning has now been applied to many antibodies

Sites of likely future escape in XBB

Generalizing deep mutational scanning to other viral entry proteins

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 measures relative amounts, so include neutralization standard

Example: RBD antibody LY-CoV1404

Validates very well

Example: S2 antibody CC67.105

Using this system, we mapped how all XBB.1.5 spike mutations affect serum antibody escape, spike-mediated infection, and ACE2 affinity

We can also apply method to emerging viruses that may pose a future risk

Prospective maps of antigenic and functional effects of mutations to H5N1 HA

Enables real-time interpretation of viral antigenic evolution

In addition, knowing effects of all mutations to H5N1 hemagglutinin can help:

  • Identify conserved sites that can be targeted by antibodies
  • Map escape mutations for candidate antibodies
  • Inform design of immunogens and candidate vaccines

Method should be extensible to many other viral entry proteins

  • System provides safe way to do mutational studies using pseudotyped lentivirions
  • We have completely or partially implemented this system for:
    • SARS-CoV-2 spike
    • HIV Env
    • H5 influenza hemagglutinin
    • Nipah virus RBP
    • Lassa virus GP
    • Rabies virus GP
  • It could likely be applied to many other viruses, including:
    • RSV
    • human parainfluenza virus
    • Ebola virus
    • other human and potential pandemic coronaviruses and influenza viruses

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

Alex Greninger and UW Lab Medicine

 

Thanks

stanford2023

By Jesse Bloom

stanford2023

Interpreting the evolution of SARS-CoV-2

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