Evolution of human RNA viruses

Richard Neher
Biozentrum, University of Basel

slides at neherlab.org/202201_Thaler.html

Human seasonal influenza viruses

slide by Trevor Bedford

Positive tests for influenza in the USA by week

Data by the US CDC

  • Influenza viruses evolve to avoid human immunity
  • Vaccines need frequent updates

Do all eukaryotic viruses do this?

  • Many human RNA viruses show such patterns of rapid antigenic evolution
  • BUT: the same viruses evolve less rapidly in live-stock
    • Shorter generation time → less frequent re-infection
    • Selection is on transmission rather than re-infection
  • Human DNA viruses behave very differently

How do viruses achieve endemicity?

Endemicity requires
  • Waning immunity
  • Antigenic evolution/escape
  • Population turnover
  • Measles
    • Infection all naive as quickly as possible
    • Antigenically stable
    • Very high R0/transmissibility
  • Influenza and other respiratory viruses
    • Reinfection through antigenic evolution
    • Waning of immunity
    • Different viruses employ both strategies to different degrees
  • Plasticity/transmissibility trade-off
  • Eukaryotic vs prokaryotic viruses, RNA vs DNA viruses

    • Life-time of the host compared to the infection duration
      • long: HIV, Herpes Viruses, HPV
      • short: Influenza, common colds, enteroviruses, measles virus
    • Frequency of reinfections
      • common: Influenza viruses, enteroviruses,
      • rare: Herpes, HPV, Measles
    • Lytic vs lysogenic
      • maybe latent infections can be thought of as some sort of lysogeny? but no replication with the host
      • lytic would be more akin to a virus that kills its host