Impact of Viral Intra-Host Diversity on Transmission Dynamics and Antiviral Resistance

Influenza virus is a highly contagious virus that is typically transmitted person-to-person through sneezing and coughing. Critical gaps remain in our understanding of the evolutionary dynamics of IAV on both a global scale and at the level of intra-host dynamics and inter-host transmission. Similarly, resistance to the NA protein inhibitor, Oseltamivir, can be wide-spread among various subtypes of influenza viruses and has been reported for some highly pathogenic H5N1 influenza viruses. Resistance to the NA inhibitor, Zanamivir, has been documented as well, but it is less frequent than resistance to Oseltamivir.

The genetic variation of IAV within an individual is extensive and that both transmission between hosts and antiviral therapy act as bottlenecks that select for specific variants in the intra-host population. To understand the emergence and selection of viral subpopulations during respiratory droplet transmission in ferrets and humans, and the emergence of drug-resistant influenza virus variants using deep NGS of samples utilizing the following studies:

  • A household transmission study will be employed to address the dynamics of intra-host and inter-host virus populations in order to. To 1) define and compare the extent of intra-host genetic diversity in IAV- and IBV-infected humans, 2) determine if specific variants are consistently selected for during transmission or if this is host dependent, and 3) demonstrate how pre-existing immunity influences inter-host transmission.
  • A ferret transmission study will be utilized to address a number of critical questions, such as: 1) are certain, potentially mammalian-adapted mutations selected during avian H5 or H7 influenza virus replication in ferrets and are these mutations represented in low frequencies in the inoculum, or do they emerge de novo during replication in ferrets, and 2) is viral transmission a genetic bottleneck?
  • A human vaccine trial of subjects (18-64 years of age) who present with an influenza-like illness in participating U.S. hospitals without any risk factors for severe disease will be screened for NA mutations. This will address if NA resistance substitutions (e.g., H274Y in A/H3N2), are under positive selection. Also, this study will identify novel resistance mutations under positive selection and identify substitutions in the NA and/or other genes that potentiate or enhance Oseltamivir resistance, thereby elucidating epistatic interactions.


Research reported in this publication was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health under Award Number U19AI110819. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Principal Investigator


John Beigel
Leidos Biomedical Research, Inc.

Yoshihiro Kawaoka
University of Wisconsin-Madison

Aubree Gordon, PhD
University of Michigan


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