Near real-time tracking of the human neutralizing antibody landscape to influenza virus
Jesse Bloom
Fred Hutch Cancer Center / HHMI
These slides at https://slides.com/jbloom/flu-seqneut-2025
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 was 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 scenario with influenza like Panum's study of measles
In 1977, old H1N1 strain from ~1954 was inadvertently re-released and caused a global pandemic.
History offers scenario with influenza like Panum's study of measles
"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 durable immunity - but only if virus is evolutionarily frozen
Human neutralizing antibody landscape shapes influenza evolution and disease
Viral strains selected by evolution tend to be ones that are less neutralized by human antibodies.
People are more likely to be infected when they have low neutralizing titers to a strain to which they are exposed.
Immunity is heterogeneous across people: the median person never infected in a given year.
Vaccine is updated to try to track viral evolution.
How can we characterize human neutralizing antibody landscape at scale?
Traditional neutralization assays are low-throughput
Assays measure just one virus against one serum in each row (or column) of a 96-well plate
We developed new assay to measure 1000s of neutralization curves in a single plate
Our sequencing-based neutralization assay uses barcoded virions
Our sequencing-based neutralization assay uses barcoded virions
Full viral library assayed in each row of plate
Full viral library assayed in each row of plate
Full viral library assayed in each row of plate
Neutralization of all the different viruses is read out simultaneously be sequencing
Neutralization of all the different viruses is read out simultaneously be sequencing
Neutralization of all the different viruses is read out simultaneously be sequencing
Neutralization of all the different viruses is read out simultaneously be sequencing
Neutralization of all the different viruses is read out simultaneously be sequencing
Neutralization of all the different viruses is read out simultaneously be sequencing
different recent H3N2 viral strains
Each row of plate measures titers to many viruses. Below are titers for one child serum.
this child has low titers to these viral strains
Person-to-person variation in per-strain titers
Heterogeneity within and between age groups
How do these heterogeneous neutralization titers for different humans shape viral evolution?
We measured neutralization for a large set of sera in two ways
sera from 95 individuals of different ages
Measured neutralization by each individual serum
sera from 95 individuals of different ages
Measured neutralization by each individual serum
Measured neutralization by pool of all sera
We measured neutralization for a large set of sera in two ways
We calculated actual growth rates of different strains in human population
Growth rates of influenza strains correlate with fraction of sera with titer below cutoff
But viral growth rates do not correlate with titers of a pool of all serum
Can we measure human neutralizing antibody landscape in near real-time?
Timeline relative to Southern Hemisphere influenza vaccine strain selection
H3N2 strains in library vs global diversity
Strains in library mostly cover current diversity of human seasonal influenza
We measured neutralization titers of 188 human sera to 140 strains (~26,000 titers total)
We're still analyzing data to figure out how to best use them to inform evolutionary forecasts...
Exciting it is now possible to measure human influenza neutralizing antibody landscape in near real-time.
We're working to do the same for other viruses...
Lots of exciting experiments and analyses to come...
