Navigating the evolutionary routes of influenza viruses

Each year 5-15% of the world*s human population is infected with seasonal
influenza viruses resulting in millions of hospitalizations and ~500,000
deaths. Vaccination is the primary strategy for reducing the public health
burden of influenza virus infection. Nearly everyone will be infected with
influenza viruses multiple times over the course of their lives. On average,
children are re-infected every 2-5 years and adults every 5-10 years. These
recurrent infections are possible because the virus*s antigenic phenotype
evolves allowing it to escape immunity induced by prior infection and
vaccination.

Influenza vaccine efficacy depends on the antigenic match between the viruses
in the vaccine and those circulating in the human population. The composition
of the seasonal influenza vaccines used worldwide is updated twice per year to
keep pace with the evolution of the virus. This composition is determined by
the World Health Organization (WHO), based on careful analysis of the viruses
that circulated over the preceding 6-12 months. If a new virus variant appears
in the months soon after the vaccine composition has been decided, manufactured
and distributed, seasonal vaccine efficacy suffers and a valuable public health
opportunity has been lost. Despite substantial effort by WHO and its
Collaborating Centers, the seasonal influenza virus vaccine mostly plays catch
up with the evolution of the virus. The ability to predict when and how
seasonal influenza viruses will evolve would enable us to base the seasonal
influenza vaccine composition decisions on the predicted evolutionary pathways
of the virus.

The objective of this study is to rigorously assess the repeatability and
predictability of influenza virus evolution by experimentally evolving human
seasonal influenza viruses in ex vivo human airway epithelium (HAE) cell
cultures.

We will use human airway epithelial cultures to serially passage seasonal
influenza viruses to mimic prolonged human infections. The study has three
objectives-

1-Quantify the evolutionary dynamics of seasonal influenza viruses in the
absence of antibody-mediated selection.
2-Determine how the antibody complexity of immune sera shape the evolutionary
trajectories of virus antigenic evolution.
3-Quantify the impact of differences in selection pressures by site of
infection and underlying host variation on virus evolution.

These experiments require the recruitment of human volunteers to obtain the
starting material for the HAE cultures. Obtaining the material required to
generate the HAE cultures involves taking direct nasal brushes from the middle
meatus of the nose. In rare cases this might result in local bleeding at the
biopsy site that would not require active intervention. These are routine
procedures and pose very low risk to the volunteer. After the brushes have been
performed, no further involvement of study participants is expected.

Seasonal influenza viruses will be serially passaged through the HAE cultures
and the viruses from these studies will be genetically sequenced and
phenotypically characterised to quantify the evolution of the viruses in each
experiment. Mathematical and statistical models will be applied to these data
to assess the repeatability and predictability of virus evolution.

This project requires human airway epithelial cells for the production of
cultures to simulate prolonged human infections. We will collect nasal
epithelial samples from patients of ENT department the Academic Medical Center
(AMC) in Amsterdam. Nasal brushes taken from the middle meatus of the nose, may
in rare cases result in local bleeding at the biopsy site that would not
require active intervention. These are routine procedures and pose very low
risk to the volunteer. The ENT department has extensive expertise in collecting
these airway mucosal samples in clinical and/or research settings.