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ECDC Cites Serious trH3N2 and trH1N2 Testing Issues
Recombinomics Commentary 14:15
December 14, 2011

In the context of the swine-origin triple reassortant A(H3N2) viruses, since November 2010 ECDC has been collaborating with the Community Network of Reference Laboratories (CNRL) for Human Influenza in Europe and the WHO Collaborating Centre specifically to address the diagnostic aspects of these viruses. This year, the capability of European influenza reference laboratories to detect swine-origin triple reassortant viruses has been assessed. It was shown that there is good capacity to detect SOIVtrH3N2-M viruses as influenza A viruses but with restricted capability to subtype these viruses. Therefore it is important that all these viruses should be sent to the WHO Collaborating Centre in London.

Diagnostic RT-PCR for generic influenza A virus (targeted to the M-gene) will detect swine-origin triple reassortant A(H3N2) viruses as human influenza A. However, the subtype-specific RT-PCR for either H3 or N2 of human influenza A viruses will most probably have a decreased sensitivity or will result in no detection of the SO-A(H3N2) viruses. Probes directed against other genes, e.g. the nucleoprotein gene as was used during the early phase of the 2009 pandemic caused by the A(H1N1)pdm09 virus, will enable preliminary differentiation between human seasonal H3N2 viruses and these zoonotic H3N2 viruses.

Therefore, swine-origin specific subtype RT-PCR, antigenic characterisation, and partial or full genome sequencing are the most appropriate techniques to distinguish between the human and these new zoonotic-origin influenza viruses.

The European influenza reference laboratories (National Influenza Centres or NICs) are aware of the detection challenges and a number are updating their detection protocols to be able to make this distinction.

The above comments are from the ECDC Dec13 update on H3N2pdm11 risk.  The comments acknowledge the challenge of detection of these novel H3N2, but fails to mention trH1N2, which is even more challenging because labs are no longer testing for seasonal H1, so differential analysis is solely dependent on cross reactivity with H1N1pdm09 NP sequences.

Thus, most labs in the ECDC are not currently capable of distinguishing the novel triple reassortants from seasonal H3N2, and in many instance will either return a seasonal H3N2 pattern, or an anomalous unsubtypable result.

These testing issues led to the “swine exposure” linkage with earlier cases in the US (in Indiana, Pennsylvania, and Maine), but the ECDC ignores this relationship, and instead focuses on a recent swine sources, even though the five most recent cases, including the trH3N2 from West Virginia (A/West Virginia/06/2011) and trH1N2 from Minnesota (A/Minnesota/19/2011), have no reported swine exposure, and the five most recent cases, including the Iowa cluster, without such exposure are all 3 years of age of younger.

Thus, the absence of these cases in the EU, like the earlier “swine exposure” linkage in the United States, is strongly tied to testing issues, and not to swine.

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