A New Flu Reassortant: H3N2 Meets H1N1 in an Idaho Teenager, 2019

On February 17, 2019, a 13-year-old boy with no underlying conditions came to an Idaho hospital emergency department after a day of fever (103°F/39.4°C), dry cough, sore throat, headache and weakness. A rapid test showed influenza A. He was treated at home with oseltamivir and recovered. Randi Pedersen of the Idaho Department of Health and Welfare and colleagues, with CDC, reported what his virus turned out to be — the first detection by CDC of this kind of reassortant.

An unexpected result

As part of routine surveillance, a second sample went to the Idaho Bureau of Laboratories. CDC's flu PCR panel found markers for both pandemic influenza A and H3, suggesting a swine-origin H3N2 variant virus. The sample was sent to CDC, and the boy was interviewed.

In the week before he got sick he had not traveled and had no contact with animals; he had not had the 2018–19 flu vaccine. One household member developed respiratory symptoms on February 23 and tested positive for influenza A by rapid test, but no sample was kept for further testing. No other household members got sick, and no other exposures were found.

What sequencing showed

Next-generation sequencing at CDC showed not a swine variant but a new reassortant of two human seasonal viruses: influenza A(H3N2) and A(H1N1)pdm09.

Reassortment happens when two flu viruses infect the same cell and swap gene segments, creating a new virus.

• The data suggested the boy was not infected with both viruses at once; the swap probably happened in someone else.
• No genetic markers of reduced susceptibility to oseltamivir, peramivir or zanamivir were found.
• Viruses in H3 subclade 3C.3a react poorly with antisera raised against the 2018–19 Northern Hemisphere vaccine strain, so that season's vaccine might not have protected against this virus.

Influenza in Idaho around the time of the case. Credit: CDC, MMWR.

Looking for more

The hospital sent 45 more rapid-test-positive samples collected from January 1 to April 27, 2019. PCR found 23 (51.1%) were A(H1N1)pdm09, 13 (28.9%) A(H3N2), and nine (20.0%) had no detectable flu. Seventeen were sequenced at CDC, and no other reassortants turned up. At the time the boy fell ill, A(H1N1)pdm09 and A(H3) were both circulating in Idaho.

The virus was identified and investigated in March 2019; the authors stressed that continued surveillance for emerging influenza viruses remained especially relevant.

Sources

Based on Pedersen R, Barton V, Tripp J, Blanton L, Barnes J, Hahn C, "Notes from the Field: Seasonal Human Influenza A(H3N2) and Influenza A(H1N1)pdm09 Reassortant Infection — Idaho, 2019," MMWR, Centers for Disease Control and Prevention; a work of the United States government in the public domain.