Interpreting the evolution

of SARS-CoV-2

 

Jesse Bloom

Fred Hutch Cancer Research Center / HHMI

 

Slides at https://slides.com/jbloom/ut-covid19

@jbloom_lab

Only sometimes does virus evolution lead to changes in antigenic phenotype

  • Measles virus: Does not evolve to escape immunity. People are infected at most once in their lives. A vaccine developed in the 1960s still works today.

 

  • Influenza virus: Evolves to escape immunity. People are infected every ~5 years. The vaccine needs to be updated annually.

We studied CoV-229E, a coronavirus that causes common colds and has been circulating in humans since at least the 1960s.

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

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. 

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.

Most mutations in RBD & NTD

Plot of sequence variability across CoV-229E spike taken from  Eguia, ..., Bloom, PLoS Pathogens (2021) . See also Wong, ..., Rini, Nature Communications (2017) and Li, ..., Rini, eLife (2019) for detailed structural studies of evolution in receptor-binding loops.

For SARS-CoV-2 RBD, want to prospectively map how each mutation affects phenotype

Impossible to measure true viral fitness in the lab, so we focus on three biochemical phenotypes that contribute to fitness:

 

1) Does RBD fold properly?

 

2) Does RBD bind ACE2 with high affinity?

 

3) Is RBD bound by anti-viral antibodies?

 

For SARS-CoV-2 RBD, want to prospectively map how each mutation affects phenotype

Impossible to measure true viral fitness in the lab, so we focus on three biochemical phenotypes that contribute to fitness:

 

1) Does RBD fold properly?

 

2) Does RBD bind ACE2 with high affinity?

 

3) Is RBD bound by anti-viral antibodies?

 

Evolutionary pressure is to maintain these two phenotypes...

 

 

... while changing this phenotype.

We use yeast display to enable high-throughput experiments

RBD

fluorescent ACE2

yeast

fluorescent tag on RBD

Importantly, we use ACE2 titrations to measure true affinities, not just relative FACS binding signal; see here for details.

Library of yeast, each expressing different RBD mutant with identifying 16 nt barcode

Click here for details on how library is made.

Phenotypic maps of how mutations affect RBD folding & ACE2 affinity

Escape map from a single antibody

Escape maps from lots of antibodies

Infection / vaccination elicit polyclonal antibodies that can bind many epitopes

Monoclonal antibodies bind one epitope, so can usually be escaped by single mutation

Polyclonal antibodies can bind many epitopes, so often more resistant to escape

Extent of focusing of polyclonal antibodies shapes antigenic evolution

  • For influenza virus, human polyclonal antibody immunity often highly focused, such that single mutations can reduce neutralization by >10 fold. (Lee et al, eLife, 2019)

 

  • For measles virus, polyclonal antibodies target many epitopes with similar potency, so no single mutation has a large effect. (Munoz-Alia, Cell Rep. Med., 2021)

RBD-binding antibodies are responsible for most neutralizing activty

Data from Greaney et al (2021a, 2021b) using lentiviral pseudotypes on ACE2-overexpressing cells. Similar results seen by Piccoli et al (2020). Neutralizing antibodies can target other spike regions such as NTD (e.g., McCallum et al, 2021).

RBD-binding antibodies are responsible for most neutralizing activty

Data from Greaney et al (2021a, 2021b) using lentiviral pseudotypes on ACE2-overexpressing cells. Similar results seen by Piccoli et al (2020). Neutralizing antibodies can target other spike regions such as NTD (e.g., McCallum et al, 2021).

RBD-binding antibodies are responsible for most neutralizing activty

Data from Greaney et al (2021a, 2021b) using lentiviral pseudotypes on ACE2-overexpressing cells. Similar results seen by Piccoli et al (2020). Neutralizing antibodies can target other spike regions such as NTD (e.g., McCallum et al, 2021).

How do different antibody classes contribute to polyclonal responses?

We use the Barnes antibody classification scheme from Barnes et al Nature (2020). The extension of these antibody classes to escape mapping is described in Greaney et al (2021), and escape maps are available here. Class 1, 2, and 3 antibodies are often potently neutralizing, while class 4 antibodies are often less neutralizing (see: Piccoli et al (2020), Dejnirattisai et al (2021), Liu et al (2020), Zost, et al (2020)).

A single antibody class makes the largest contribution to serum antibodies

Crowe lab (Vanderbilt): James Crowe, Seth Zost, Pavlo Gilchuk

Chu lab (Univ Wash): Helen Chu, Caitlin Wolf

Veesler lab (Univ Wash): David Veesler, Alexandra Walls, Ale Tortorici

King lab (Univ Wash): Neil King, Dan Ellis

Li lab (Brigham & Women's): Jonathan Li, Manish Choudhary

Whelan lab (Wash U)

Boeckh lab (Fred Hutch): Terry Stevens-Ayers

Alex Greninger (Univ Wash)

Janet Englund (Seattle Children's)

Adam Dingens

Will Hannon

Amin Addetia

Keara Malone

Tyler Starr

Allie Greaney

Rachel Eguia

Bloom lab (Fred Hutch)

Sarah Hilton

Kate Crawford

Andrea Loes

ut-covid19

By Jesse Bloom

ut-covid19

Interpreting the evolution of SARS-CoV-2

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