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Fatally Flawed ECDC H3N2pdm11 Risk Assessment
Recombinomics Commentary 22:00
November 29, 2011

The public health importance of swine influenza is twofold. Firstly there is the direct risk of infection for those coming into close contact with pigs or through limited human-to-human transmission. Triple reassortant swine influenza viruses with avian, human and swine genes have been circulating in pigs in the US, and have been transmitted to humans. This is now also the case for the triple reassortant viruses with the additional A(H1N1) M-gene [1]. However, none of these reassortant viruses has been able to maintain themselves in the human population and, in addition, there have been no large clusters of infection. The second risk is of reassortment to produce a novel virus (possibly a strain with pandemic potential), either in the pig or in the human host, by co-infection with a human and a swine strain. The pandemic A(H1N1)pdm09 influenza virus is so far the only swine-origin virus that has shown the capacity to spread readily and extensively between humans. However, it demonstrates that this is a possibility.

The above comments are from the European (ECDC) risk assessment for “Swine-origin triple reassortant influenza (H3N2) viruses in North America, which is largely focused on swine.  It notes shortfalls in swine surveillance in North America and Europe and cites a need for more surveillance (European swine surveillance is beyond abysmal).

The report acknowledges the technical difficulties in the detection of H3N2pdm11 (trH3N2 with an H1N1 M gene), even with PCR detection kits that include H1N1pdm09 H1 and NP targets, and the need for sequence confirmation (which is conclusive even when partial sequences are generated).

However, the report is overly focused on the swine aspects of the pandemic and fails to note that the CDC has only published sequences for 12 patients under the age of 10 who tested as influenza A samples collected since July, 2011. 

Although the report notes the importance of testing children, since 9 of the 10 cases in the US are under 10 years of age, it fails to note that 9 of the 12 cases (75%) are H3N2pdm11 positive, signaling a serious surveillance failure that has created the illusion that the virus is not transmitting in a sustained manner.

The group appears to be seriously phylogenetically challenged because the sequence data is not a puzzle and clearly demonstrates sustained transmission of H3N2pdm11.

Therefore, the ECDC risk assessment for H3N2pdm11 is fatally flawed.

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