title: Emergence and dynamics of influenza super-strains.
abstract: BACKGROUND
  Influenza super-strains can emerge through recombination of strains from birds, pigs, and humans. However, once a new recombinant strain emerges, it is not clear whether the strain is capable of sustaining an outbreak. In certain cases, such strains have caused major influenza pandemics.
  
  
  METHODS
  Here we develop a multi-host (i.e., birds, pigs, and humans) and multi-strain model of influenza to analyze the outcome of emergent strains. In the model, pigs act as "mixing vessels" for avian and human strains and can produce super-strains from genetic recombination.
  
  
  RESULTS
  We find that epidemiological outcomes are predicted by three factors: (i) contact between pigs and humans, (ii) transmissibility of the super-strain in humans, and (iii) transmissibility from pigs to humans. Specifically, outbreaks will reoccur when the super-strain infections are less frequent between humans (e.g., R0=1.4) but frequent from pigs to humans, and a large-scale outbreak followed by successively damping outbreaks will occur when human transmissibility is high (e.g., R0=2.3). The average time between the initial outbreak and the first resurgence varies from 41 to 82 years. We determine the largest outbreak will occur when 2.3 <R0 < 3.8 and the highest cumulative infections occur when 0 <R0 < 3.0 and is dependent on the frequency of pig-to-human infections for lower R0 values (0 <R0 < 1.9).
  
  
  CONCLUSIONS
  Our results provide insights on the effect of species interactions on the dynamics of influenza super-strains. Counter intuitively, epidemics may occur in humans even if the transmissibility of a super-strain is low. Surprisingly, our modeling shows strains that have generated past epidemics (e.g., H1N1) could resurge decades after they have apparently disappeared.
authors.affiliation: Center for Biomedical Modeling, Semel Institute of Neuroscience & Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, 10940 Wilshire Blvd, Suite 1450, Los Angeles, CA 90024, USA. bcoburn@mednet.ucla.edu
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Coburn
authors.forename: Chris
authors.initials: C
authors.lastname: Cosner
authors.forename: Shigui
authors.initials: S
authors.lastname: Ruan
mesh_terms: D000818:Animals; D001717:Birds; D021821:Communicable Diseases, Emerging / Q000635:transmission; D004196:Disease Outbreaks / Q000706:statistics & numerical data*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype; D009980:Influenza A virus / Q000235:genetics / Q000472:pathogenicity*; D005585:Influenza in Birds / Q000635:transmission; D007251:Influenza, Human / Q000453:epidemiology*; D009976:Orthomyxoviridae Infections / Q000635:transmission; D011995:Recombination, Genetic; D013552:Swine