George Charbonneau from South West Ontario Veterinary Services, IAV Diagnostics: They Did What???


At one time transmission of Influenza Type A from pigs to people was a very rare event. Transmission from live pigs to people is much more common today and exhibition swine are a known source for zoonotic transmission. Genomic analyses of IAV in swine are critical to understanding this risk, the types of viruses circulating in swine, and whether current vaccines developed for use in humans would be predicted to provide immune protection.

At this point in this story I need to provide a “Geezer Alert”. When I started in practice in 1981 we took diagnostic samples at the farm, packaged them up with a submission form and sent them off to the lab via courier or Canada Post. We then waited for a phone call from the lab or a report via the mail. No faxes and the internet of things was another decade away. Fortunately we were not frustrated as this was the technology of the day. This story demonstrates just how far diagnostic and communication technology has progressed.

The researchers in this story were working overnight at a swine exhibition and identified what looked clinically like an influenza A virus (IAV) outbreak in swine. They used Nanopore sequencing to identify 13 IAV genomes from samples and predicted in real time that these viruses posed a novel risk to humans due to genetic mismatches between the viruses and current prepandemic candidate vaccine viruses (CVVs). A portable IAV sequencing and analysis platform called Mia (Mobile Influenza Analysis) was used to complete and characterize the full-length consensus genomes approximately 18 hours after unpacking the mobile lab. The Mia system rapidly identified three genetically distinct swine IAV lineages from three subtypes, A (H1N1), A(H3N2), and A(H1N2). Analysis of the hemagglutinin (HA) sequences of the A(H1N2) viruses identified >30 amino acid differences between the HA1 of these viruses and the most closely related CVV.

As an exercise in pandemic preparedness, all sequences were emailed to CDC collaborators who initiated the development of a synthetically derived CVV. IMPORTANCE Swine are influenza virus reservoirs that have caused outbreaks and pandemics.

Take Home Messages

Instead of waiting for an IAV infection showing up in a sick human this process allowed for:

  • Identification of the 13 IAV virues involved in making the pigs cough.
  • Sequencing on site to determine that the viruses were different from human IAV seasonal vaccines coverage currently in use.
  • Sequences were emailed to the CDC collaborators who could then prepare a synthetically derived vaccine for the novel IAV.
  • Oh, and by the way, this novel IAV virus went on to cause 14 infections in humans and was the dominant U.S. variant virus in 2018.

Submitted by George Charbonneau, DVM

Ref: Neuhaus EB, Davis CT, Bowman AS, Wentworth DE, Barnes JR. Influenza A Virus Field Surveillance at a Swine-Human Interface. mSphere. 2020 Feb 5;5(1). pii: e00822-19. doi: 10.1128/ mSphere.00822-19.


Please enter your comment!
Please enter your name here