Introduction to Antigenic Evolution

Sidney M. Bell, PhD (@sidneymbell)

Chan Zuckerberg Initiative

 

Mini workshop: California Departments of Public Health

June 10, 2021

Outline

  • How do viruses evolve to escape the immune system?
     
  • What does this mean for vaccine escape?
     
  • How does genomic surveillance help with vaccine updates?
     
  • Discussion and questions

Grubaugh, Nature Micro, 2019

Viruses acquire mutations as they replicate and transmit from person to person.

SARS-CoV-2
(~7 day serial interval, ~25 subs/year)

ACTG

ACTT

AGTT

Antigenic variation

Genetic

variation

A very small minority of mutations may change the way the virus "looks" to the immune system

Antigenic variation is usually caused by a mutation in a "surface protein"

For some viruses, antigenic variation can help them escape from pre-existing immunity

Measles

Antigenically uniform

Flu

Antigenically

diverse

Lifelong protection

Temporary cross-protection

What does this mean for vaccine updates?

Influenza & SARS-CoV-2

Influenza evolves very rapidly

Clades don't stick around very long because they're constantly being outcompeted by new clades

Influenza evolves very rapidly

Flu

Dengue

Population susceptibility:

Previously circulating:

Population

immunity:

Clade growth:

Population immunity can influence viral evolution

**In flu, this is driven by natural infection, not vaccination

Wren, Bell et al., 2018

Population immunity drives flu evolution, necessitating a vaccine update every ~2 years

Influenza & SARS-CoV-2 have a similar number of substitutions per year in surface proteins

BUT! Need to consider...

  • Rate differences
    SARS-CoV-2 spike S1 gene is ~2x as long as Flu's HA1 gene
     
  • Is the last year typical for SARS-CoV-2?
    Not enough data to define "normal" for SARS-CoV-2
     
  • "Scariants are innocent until proven guilty"
    How much does each of these mutations actually
    matter for immune escape

Measuring antigenic change

Neutralization?

+

+

Replication

How much serum (neutralizing antibodies) is necessary to block replication?

Neutralizing flu requires about 2x as much serum after ~1 year's worth of antigenic change

+

Replication

Virus A

Antibodies from patient recovered from virus A

+

Replication

Virus B, which showed up ~1 year later

Antibodies from patient recovered from virus A

Neutralizing B.1.351 requires about 8x as much serum compared to the O.G.

+

Replication

O.G. SARS-CoV-2

Antibodies from patient recovered from O.G.
SARS-CoV-2

+

Replication

B.1.351

Antibodies from patient recovered from O.G. SARS-CoV-2

Some VoCs can escape antibodies from convalescent patients

Antigenic similarity = how much sera is required to neutralize viral replication?

Serum

Test viruses

1x

2x

4x

(relative to autologous)

X

X

X

X

X

X

--

Log2

0

1

2

Titer

Flu, per year

3

O.G. vs B1.351 SARS-CoV-2

Four reasons why we're not panicking about vaccine escape yet

  1. Immunity is broader after vaccination than after natural infection, especially for mRNA vaccines
     
  2. Antibodies aren't the whole story / immunity is a multi-layer defense system
     
  3. Usually requires a cluster of mutations to enable immune escape
     
  4. This has been a weird year for everyone -- host and virus alike
    • Adapting to a new host species
      (selective pressure for replication and transmission)
    • Totally naive population
      (selective pressure for immune escape is a new thing)

But, we will need to update the vaccines at some point

  • Likely a similar or slightly lower frequency than flu vaccine updates
     
  • Likely a simpler and faster process to update
    SARS-CoV-2 mRNA vaccines than to update the egg-grown flu vaccine

How genomic surveillance can inform eventual vaccine updates

So, which mutations matter? 

Starr et al, Cell Reports, 2021

Sequencing vaccine breakthrough cases helps us identify which [combinations of] mutations are important for vaccine escape, in the real world

Values from Juraska et al, PNAS 2018

Which clades / "variants" should we
vaccinate against?

\propto

John Huddleston

Antigenic change

Surface protein mutations

Recent clade expansion

Impact on protein function

+

+

+

Representative sampling helps us model and predict which clades ("variants") will become more common

Growth rate @

next year

Titers

Sequence

Trees

Sequence + modeling

Clade growth rates are well-predicted

John Huddleston

Clade growth vs decline is also well-predicted

John Huddleston

Representative sampling helps us model and predict which clades ("variants") will become more common

John Huddleston

Takehomes

  • SARS-CoV-2 will change antigenically, and we'll need to update our vaccines at some point, but we're not panicking
     
  • Individual mutations don't usually cause antigenic change on their own
     
  • Genomic surveillance is one of the best ways to ensure we're ready to update the vaccines when the time comes
     
  • SARS-CoV-2 is here to stay, but it won't ever sweep through a totally naive global population like this again. We're still learning what antigenic evolution "normally" looks like in this virus.

Questions?

@sidneymbell

Many thanks to the Bedford lab

& the Nextstrain team

Advanced methods reading

Antigenic cartography

Visualize antigenic space via a low-dimensional embedding

Smith et al, Science 2004
 

Evolution-based models

Assign antigenic change to branches or substitions, interpolate across dataset

Neher et al, PNAS 2016

 

Population dynamics

Antigenic fitness & clade turnover

Luksza and Lassig, Nature 2014