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A Novel H3N2 Influenza A Variant Emerges

By Amesh A. Adalja, MD, July 31, 2009

While the pandemic 2009 H1N1 influenza A virus continues to spread globally, it may not be the only significant influenza challenge we face this year. A new H3N2 variant has emerged that may be poorly matched to the 2009 seasonal influenza vaccine. This could pose a risk to the older population and to those who have been vaccinated against the pandemic strain.

Since 1968, H3N2 has been the dominant strain in most influenza seasons.1 It has been implicated in more severe annual flu outbreaks than seasonal H1N1, and it harbors almost universal resistance to the adamantane class of drugs.1,2 Over the past few months, the H3N2 virus has been accumulating genetic changes that may diminish the protectiveness of the seasonal influenza vaccine.3,4

Antigenic Drift Found in H3N2

A genetically drifted variant of the H3N2 strain of virus was uncovered in March. The mutated virus was first discovered in samples taken from an influenza outbreak within a nursing facility. It was found to have 3 mutations at 2 different antigenic sites when compared to the vaccine strain A/Brisbane/10/07 (H3N2), which was included in the current season's vaccine for both hemispheres. It is also  to be included in the 2009-2010 vaccine.3,4

The virus has been found to represent a minority of isolates in the current Southern Hemisphere flu season but has been deemed capable of becoming the dominant strain of H3N2. The WHO has been unable to assess the full potential of this new variant due to strain on resources from the concomitant H1N1 pandemic.3,4

The New Strain Could Complicate and Worsen the Flu Epidemic

While information on the clinical illness caused by the H3N2 variant and the amount of protection conferred by the seasonal vaccine is not yet available, the fact that a vaccine mismatch might exist is worrisome. While a mismatch to a single component of the trivalent influenza vaccine is not uncommon, for this coming season, it could mean a substantial increase in the number of flu victims. This is because H3N2 viruses have a penchant for disproportionately affecting the elderly,3,4 who have been largely spared by the pandemic strain now circulating. Also susceptible to the variant H3N2 virus would be those vaccinated against the pandemic strain. As a result, the coming flu season could be driven by a combination of these two viruses and could afflict a greater proportion of the population than would be vulnerable to either the novel H1N1 influenza A virus alone or to the seasonal flu alone. 

The emergence of this drifted variant of H3N2 underscores the vital need for continual surveillance of influenza isolates of all subtypes, as the propensity for this virus to alter its genetic components will also pose an obstacle to crafting efficacious vaccines.


  1. Simonsen L, Reichert TA, Viboud C. Impact of influenza vaccination on seasonal mortality in the US elderly population. Arch Intern Med. 2005;165:265-272

  2. ACIP. Prevention and control of influenza. MMWR 2008; 57(RR07):1-60. Accessed July 27, 2009

  3. ProMed mail. Seasonal influenza (H3N2) virus - potential vaccine mismatch. July 24, 2009. Accessed July 27, 2009.

  4. ProMed-mail. Influenza A (H1N1) - worldwide (11): coincident H3N2 variation. May 5, 2009. Accessed July 27, 2009.