Interpreting the evolution of SARS-CoV-2

Jesse Bloom

Fred Hutch Cancer Center / HHMI

These slides at https://slides.com/jbloom/sars2-keystone-2022

@jbloom_lab

Disclosures

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

My lab has unfunded research collaborations with Vir Biotechnology

Outline

• Conceptual principles of viral antigenic evolution

Outline

• Conceptual principles of viral antigenic evolution
• SARS-CoV-2 receptor-binding domain (RBD)

Outline

• Conceptual principles of viral antigenic evolution
• SARS-CoV-2 receptor-binding domain (RBD)
• Interpreting evolution of the SARS-CoV-2 RBD

Outline

• Conceptual principles of viral antigenic evolution
• SARS-CoV-2 receptor-binding domain (RBD)
• Interpreting evolution of the SARS-CoV-2 RBD

Panum, 1846

The Faroe Islands

Panum, 1846

"Measles had not prevailed on the Faroes since 1781, then it broke out early in April 1846."

Panum, 1846

"Of the 7782 inhabitants, about 6000 were taken with measles."

Panum, 1846

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

From 1918 to 1957, H1N1 influenza circulated in humans.

In 1957, H1N1 disappeared from humans due to new H2N2 pandemic.

In 1977, old H1N1 strain from ~1954 was accidentally released (probably during vaccine trial in China) and caused a global pandemic.

British Medical Journal (1978)

British Medical Journal (1978)

"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."

British Medical Journal (1978)

"Of about 130 adults who had some contact with the boys, only one, a house matron, developed similar symptoms."

Influenza infection elicits multi-decade immunity similar to measles - but only if virus is evolutionarily frozen

Only some human RNA respiratory viruses evolve to escape immunity

Rate of viral antigenic evolution

Measles

Influenza

Rate of viral antigenic evolution

Measles

Where do human coronaviruses fall on this spectrum?

Coronaviruses

Influenza

Rate of viral antigenic evolution

Measles

Coronaviruses

The Washington Post, March 4, 2020

Initially, people speculated SARS-CoV-2 would evolve slowly. But we weren't so sure...

Influenza

We decided to study another human coronavirus: CoV-229E causes common colds and has been circulating in humans for a long time.

Reconstructing 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

Note "ladder-like" shape of tree

Eguia, ..., Bloom (2021)

Evolution of CoV-229E spike erodes neutralization by human antibody immunity

Serum collected in 1985 neutralizes virus with spike from 1984, but less effective against more recent viruses. 

Eguia, ..., Bloom (2021)

Viral evolution erodes antibody immunity of different people at different rates

We are studying basis of these differences, as ideally vaccines would elicit more evolution-resistant sera as on the right.

Eguia, ..., Bloom (2021)

Rate of viral antigenic evolution

Measles

CoV-229E

CoV-OC43

SARS-CoV-2

Most human coronaviruses undergo rapid antigenic evolution

Influenza

Eguia, ..., Bloom (2021) and Kistler and Bedford (2021)

Outline

• Conceptual principles of viral antigenic evolution
• SARS-CoV-2 receptor-binding domain (RBD)
• Interpreting evolution of the SARS-CoV-2 RBD

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 mutations in SARS-CoV-2 Omicron (BA.1) spike relative to Wuhan-Hu-1

Main difference is SARS-CoV-2 also fixing transmissibility-enhancing spike mutations that affect proteolytic processing and stabilize defects cause by furin-cleavage site

Majority of neutralizing antibody response in vaccinated/infected humans targets RBD

Greaney et al, Science Translational Medicine (2021)

Importance of RBD

Human CoVs, which evolve to escape transmission-blocking immunity, show strongest selection in RBD.

So virus is telling us RBD antibodies matter most for blocking transmission. But other antibodies and T-cells still matter, and may reduce disease severity while putting less selection on virus.

Most neutralizing activity from RBD antibodies (although antibodies to other domains can also be neutralizing).​

SARS-CoV-2 variants like Omicron have a lot of mutations in RBD

RBD mutations in Omicron BA.1

RBD will 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)

There are lots of mutations to SARS-CoV-2 RBD that retain (and sometimes even enhance) ACE2 affinity (Starr et al, 2020; Starr et al, 2022)

Outline

• Principles of viral antigenic evolution and emergence of Omicron
• Importance of the SARS-CoV-2 receptor-binding domain (RBD)
• Mapping antibody escape to interpret viral evolution

We use deep mutational scanning to map all RBD mutations that escape antibody binding

Greaney*, Starr*, Gilchuk*, Zost*, ..., Crowe, Bloom. Cell Host & Microbe (2021)

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

For interactive escape map, see: https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_LY-CoV555/

Escape map from one antibody (LY-CoV555, ie bamlanivimab). Peaks indicate sites where mutations escape binding.

484

452

490

Infection / vaccination elicit polyclonal antibodies 

How do mutations affect polyclonal antibodies? First, consider an equal mix of three monoclonal antibodies.

Interactive version of this mini example is at https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/mini-example-escape-calc/

LY-CoV555 is escaped at both sites 484 and 490, so mutating either site has same overall effect

Average escape across all antibodies

Mutating site 484 or 490 eliminates neutralization by antibody LY-CoV555, as reflected in thick black line showing average

Interactive version of this mini example is at https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/mini-example-escape-calc/

Antibody-escape calculator extends this principle to deep mutational scanning data for ~1,500 different human antibodies

Escape calculator is described in Greaney et al (2022), and is available at https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/

36 antibodies mapped by Tyler Starr & Allie Greaney in Bloom lab, from early SARS-CoV-2 strains

Antibody-escape calculator extends this principle to deep mutational scanning data for ~1,500 different human antibodies

Escape calculator is described in Greaney et al (2022), and is available at https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/

36 antibodies mapped by Tyler Starr & Allie Greaney in Bloom lab, from early SARS-CoV-2 strains

1,522 (!) antibodies mapped by Sunney Xie, Richard Cao, Fanchong Jian, et al at Peking University. From early strains, BA.1, & patients with prior SARS-CoV-1 infection. See here.

What does escape calculator tell us about evolution that has already happened?

Antibodies elicited by early SARS-CoV-2 that neutralize Wuhan-Hu-1 heavily focus on sites like 484, 417, 446

417

446

484

417

446

484

490 not mutated, but antibodies that bind there are escaped by mutation at 484 which is in same epitope.

Note Omicron has additional escape not modeled here due to mutations that put RBD more in down conformation and cause N343 glycan displacement: Cao et al (2022), Gobeil et al (2022), and explanation here.

Omicron BA.1 is mutated at many of these sites, which is why it is neutralized substantially less well by current vaccines

Omicron BA.2 has some different RBD mutations than BA.1, but similar overall escape from antibodies from early SARS-CoV-2

Note Omicron has additional escape not modeled here due to mutations that put RBD more in down conformation and cause N343 glycan displacement: Cao et al (2022), Gobeil et al (2022), and explanation here.

Can identify mutations that mediate further escape. In Dec 2021 we predicted 486 as likely site of future evolution--in April 2022, mutation F486V was identified in Omicron BA.4 and BA.5.

486 is largest site of escape for antibodies not already escaped by mutations in BA.2

What are likely next steps in SARS-CoV-2's antigenic evolution?

Sites of escape from antibodies elicited by early (pre-Omicron) infection/vaccination that still neutralize Omicron BA.2

346

356

444-446

452

450

462

468

486

499

mutated in BA.4/BA.5

mutated in BA.2.75

Sites of escape are somewhat different for antibodies from people who had an Omicron BA.1 breakthrough infection 

346-348

444-446

468

356

490

Differences in antibody-escape mutations between people +/- BA.1 breakthrough infections is consistent with prior studies on other viruses showing that people with different exposure histories have different viral escape mutations.

452

486

mutated in BA.4/BA.5

mutated in BA.2.75

Explore yourself with online escape calculator: select antibodies by eliciting virus or strains they neutralize, click sites to mutate

https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/

Conclusions

• A subset of human respiratory viruses evolve to escape immunity
• Unfortunately, coronaviruses are among this subset
• The most important antigenic evolution occurs in the RBD
• We can use deep mutational scanning to identify antigenic mutations
• Sites to watch in SARS-CoV-2 RBD: 346-348, 444-446, 452, 468, 486

Crowe lab (Vanderbilt)

Chu lab (Univ Wash)

Veesler lab (Univ Wash)

King lab (Univ Wash)

Li lab (Brigham & Women's)

Boeckh lab (Fred Hutch)

Alex Greninger (Univ Wash)

Nussenzweig lab (Rockefeller)

Bjorkman lab (Caltech)

Tyler Starr

Allie Greaney

Rachel Eguia

Bloom lab (Fred Hutch)

Sarah Hilton

Kate Crawford

Andrea Loes

These slides at:

 https://slides.com/jbloom/sars2-keystone-2022