Periodic Reporting for period 3 - NaviFlu (Navigating the evolutionary routes of influenza viruses)
Reporting period: 2022-07-01 to 2023-12-31
Seasonal influenza viruses re-infect us repeatedly, escaping antibody recognition, due to the evolution of the virus itself. Being able to predict when and how the virus will evolve would be transformative for influenza virus control. Problematically, we have only observed one of the likely many possible routes of virus evolution and we do not know how many viable routes may have existed or about the repeatability of the observed evolution. These knowledge gaps limit the predictability of influenza virus evolution. This project seeks to fill these gaps by rigorously assessing the repeatability of influenza virus evolution and the diversity of routes the virus can explore and by better understanding the processes that drive and limit this evolution.
Recent work has shown that prolonged influenza virus infections can result in substantial virus evolution and occasionally portend virus mutational patterns on a global scale. However, observing large numbers of such infections is challenging. In this project we are using an innovative ex-vivo human airway epithelium culture system to artificially create and study prolonged human infections. Together with cutting-edge next generation sequencing and new analysis tools, we will quantify the evolutionary landscape of seasonal influenza viruses.
The project has three objectives, each building in complexity:
1–Quantify the evolutionary dynamics of seasonal influenza viruses in the absence of antibody-mediated selection to understand the fitness tradeoffs the virus makes in order to escape immunity.
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.
Through these objectives we will “play evolution forwards”, revealing the relative roles of different factors governing the mode and tempo of influenza virus evolution and quantify the predictability of virus evolution. This will improve the design of influenza vaccines, enhance prospects for influenza control, and lay new groundwork for exploring virus evolution.
Recent work has shown that prolonged influenza virus infections can result in substantial virus evolution and occasionally portend virus mutational patterns on a global scale. However, observing large numbers of such infections is challenging. In this project we are using an innovative ex-vivo human airway epithelium culture system to artificially create and study prolonged human infections. Together with cutting-edge next generation sequencing and new analysis tools, we will quantify the evolutionary landscape of seasonal influenza viruses.
The project has three objectives, each building in complexity:
1–Quantify the evolutionary dynamics of seasonal influenza viruses in the absence of antibody-mediated selection to understand the fitness tradeoffs the virus makes in order to escape immunity.
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.
Through these objectives we will “play evolution forwards”, revealing the relative roles of different factors governing the mode and tempo of influenza virus evolution and quantify the predictability of virus evolution. This will improve the design of influenza vaccines, enhance prospects for influenza control, and lay new groundwork for exploring virus evolution.
For the experimental portions of this work, we needed to develop a high through put experimental system that would allow us to simulate long term influenza infections in human tissue and virus genomic sequencing tools to quantify evolutionary dynamics is this system. Over the first year of the project, in spite of delays from the pandemic, we operationalised all of the wet tissue systems and next generation sequencing work and now have a long term evolution experiment of 12 independent virus populations in a near natural tissue system. This long term experiment will yield its primary outputs in ~18 months time. In addition to this long term work, we have also been using single cell RNA-seq to study how different cell types in our ex vivo tissue system respond to infections with different influenza virus types and subtypes to study how host, cell, and virus each contribute to infection dynamics.
In addition to the wet lab work, we have also pursued extensive modelling work to explore the conceptual basis of virus evolution both in our experimental system and in the real world. This vein of research has included four studies to date: 1. theoretical modelling to explore within- and between- host evolution; 2. modelling based on virus samples from children to explore how duration of infection shapes virus evolution; 3. modelling based on human serological samples and historical epidemiological data to explore the impact of the COVID-19 pandemic on influenza virus epidemics; 4. theoretical modelling to explore diagnostic testing and genomic sequencing resource allocation to monitor the emergence of new virus variants. Each of these projects had revealed new aspects of influenza virus evolution and epidemiology. The work on within and between host modelling revealed that typical short-term infections are unlikely to lead to the evolution of new variants due to the asynchrony between virus replication and the antibody response in infected individuals. This work highlighted the potential importance of the longer infections of children and/or immunocompromised people for virus evolution. As a direct followup to this project, we analysed the evolutionary dynamics of influenza viruses in young children where infections are typically much longer than in adults. We found important immunity driven evolution in most of the children in our study suggesting that children could be key for long term patterns of influenza virus evolution. In other work we explored the impact of the COVID-19 pandemic on the near term dynamics of influenza. Because there was little influenza virus circulation during the pandemic so far, there has been general concern that we are at risk for an unusually large and severe epidemic when control measures against Covid are relaxed. Our work showed that the expected amount of immune waning to influenza during the pandemic so far is likely to be negligible and that previous periods of low influenza virus circulation did not result in particularly large or severe epidemics. Instead, year-on-year effects that are likely to be driven by a complex mix of global virus spread, environmental factors, and yet to be described variables play a far more substantial role in shaping epidemic size and severity than small changes in population immunity. Finally, we performed modelling studies to investigate the levels of diagnostic testing required to meaningfully monitor virus evolution and the emergence of new virus variants. This work quantified the role diagnostic testing in the development of global infrastructure development for monitoring virus evolution and is being used widely the World Health Organization and its collaborative partners.
In addition to the wet lab work, we have also pursued extensive modelling work to explore the conceptual basis of virus evolution both in our experimental system and in the real world. This vein of research has included four studies to date: 1. theoretical modelling to explore within- and between- host evolution; 2. modelling based on virus samples from children to explore how duration of infection shapes virus evolution; 3. modelling based on human serological samples and historical epidemiological data to explore the impact of the COVID-19 pandemic on influenza virus epidemics; 4. theoretical modelling to explore diagnostic testing and genomic sequencing resource allocation to monitor the emergence of new virus variants. Each of these projects had revealed new aspects of influenza virus evolution and epidemiology. The work on within and between host modelling revealed that typical short-term infections are unlikely to lead to the evolution of new variants due to the asynchrony between virus replication and the antibody response in infected individuals. This work highlighted the potential importance of the longer infections of children and/or immunocompromised people for virus evolution. As a direct followup to this project, we analysed the evolutionary dynamics of influenza viruses in young children where infections are typically much longer than in adults. We found important immunity driven evolution in most of the children in our study suggesting that children could be key for long term patterns of influenza virus evolution. In other work we explored the impact of the COVID-19 pandemic on the near term dynamics of influenza. Because there was little influenza virus circulation during the pandemic so far, there has been general concern that we are at risk for an unusually large and severe epidemic when control measures against Covid are relaxed. Our work showed that the expected amount of immune waning to influenza during the pandemic so far is likely to be negligible and that previous periods of low influenza virus circulation did not result in particularly large or severe epidemics. Instead, year-on-year effects that are likely to be driven by a complex mix of global virus spread, environmental factors, and yet to be described variables play a far more substantial role in shaping epidemic size and severity than small changes in population immunity. Finally, we performed modelling studies to investigate the levels of diagnostic testing required to meaningfully monitor virus evolution and the emergence of new virus variants. This work quantified the role diagnostic testing in the development of global infrastructure development for monitoring virus evolution and is being used widely the World Health Organization and its collaborative partners.
All of the results described above have substantially moved forward the state of the art for understanding influenza virus evolution and out ability to monitor that evolution. That said, the results of the experimental components of this project (which are likely to be the most exciting) are still to come. In the next half of the project we will deliver the results of the influenza virus long term evolution experiment which should reveal the evolutionary "rules" that the virus uses to change its appearance to our immune system and the extent to which that evolution is predictable. From the single cell sequencing work we will get new insights into how influenza viruses interact differently with different cell types which should provide a further window into the molecular machinery and drivers of influenza virus evolution.