Early prediction of antigenic transitions for influenza A/H3N2

PLoS Comput Biol. 2020 Feb 18;16(2):e1007683. doi: 10.1371/journal.pcbi.1007683. eCollection 2020 Feb.

Abstract

Influenza A/H3N2 is a rapidly evolving virus which experiences major antigenic transitions every two to eight years. Anticipating the timing and outcome of transitions is critical to developing effective seasonal influenza vaccines. Using a published phylodynamic model of influenza transmission, we identified indicators of future evolutionary success for an emerging antigenic cluster and quantified fundamental trade-offs in our ability to make such predictions. The eventual fate of a new cluster depends on its initial epidemiological growth rate--which is a function of mutational load and population susceptibility to the cluster--along with the variance in growth rate across co-circulating viruses. Logistic regression can predict whether a cluster at 5% relative frequency will eventually succeed with ~80% sensitivity, providing up to eight months advance warning. As a cluster expands, the predictions improve while the lead-time for vaccine development and other interventions decreases. However, attempts to make comparable predictions from 12 years of empirical influenza surveillance data, which are far sparser and more coarse-grained, achieve only 56% sensitivity. By expanding influenza surveillance to obtain more granular estimates of the frequencies of and population-wide susceptibility to emerging viruses, we can better anticipate major antigenic transitions. This provides added incentives for accelerating the vaccine production cycle to reduce the lead time required for strain selection.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Viral / chemistry*
  • Antigens, Viral / immunology
  • Area Under Curve
  • Biological Evolution
  • Cluster Analysis
  • Computational Biology*
  • Computer Simulation
  • Epitopes
  • Hemagglutinin Glycoproteins, Influenza Virus / chemistry
  • Hemagglutinin Glycoproteins, Influenza Virus / immunology
  • Humans
  • Influenza A Virus, H3N2 Subtype / chemistry*
  • Influenza A Virus, H3N2 Subtype / immunology*
  • Influenza Vaccines / immunology
  • Influenza, Human / immunology
  • Influenza, Human / virology*
  • Phylogeny
  • Sequence Analysis, DNA
  • Stochastic Processes

Substances

  • Antigens, Viral
  • Epitopes
  • Hemagglutinin Glycoproteins, Influenza Virus
  • Influenza Vaccines