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CDC trH3N2 Mis-Match Myth Creates Confusion
Recombinomics Commentary 10:45
September 14, 2011

These viruses are genetically related, but different enough to suggest there was not a common source of infection.

The viruses are similar, but not identical to each other.

The two viruses are similar but not identical.

The viruses in the two children were similar but not identical

The Indiana case was not linked to the others, and the flu-virus strain was slightly different.

The above quotes are from the CDC’s week 34 FluView, the CDC’s MMWR (early release on Sept 2 and week 35 release on Sept 9) and media reports in the United States and China, as well as a Q&A for all four cases.

The comments in the CDC publications have led to the widespread belief that the trH3N2 isolated from Indiana (A/Indiana/08/2011) is distinct from the trH3N2 at the Washington County fair (although the same constellation of genes, including M from H1N1, is acknowledge for all four isolates).

However, the initial comments by the CDC were in reference to the Indiana isolate and the first isolate linked to the fair, A/Pennsylvania/09/2011, which was from a Schuylkill County resident (2F) who visited the fair on August 16, and is the only recent case with direct swine contact (although the nature of that contact remains unclear since the case was only 2 years of age, there were no events on the fair schedule that day that involved swine, no symptomatic swine from the fair have been identified or tested positive for trH3N2, and the positive sample from the patient was collected 4 days after the fair visit). 

The CDC subsequently acknowledged the two additional cases (both 9F) from the fair, and published sequences (at GISAID and Genbank) from samples collected August 25 (A/Pennsylvania/11/2011) and August 26 (A/Pennsylvania/10/2011), well after the end of the fair on August 20.  Sequences from these two patients, who had no swine contact, were virtually identical to each other and the Indiana sequence.

Thus, the widely cited “not identical” remarks (and no common source) only pertain to the sequence from the Schuylkill resident (PA/09/11), and the virtual identity between the sequence from Indiana (IN/08/1 and two independent isolates (PA/10/11 and PA/11/11) from Washington County (initially test by the PA Department of Health or the University of Pittsburgh diagnostic lab), signal human transmission because of the identity between the sequences, and the lack of direct swine contact by any of the three infected cases.

Moreover, the four isolates from two states represent four independent introductions, signaling efficient transmission of trH3N2 to humans, including the three of the four with no documented or stated swine contact.

The identity between patients unlinked to each other, in separate states, and in patients with no direct contact with swine, is remarkably similar to the first two pandemic H1N1 cases identified in southern California (in adjacent counties) in 2009, and why the CDC should be testing (by PCR for trH3N2)  all influenza A cases at this time,  which is a month prior to the start of the 2011/2012 flu season.

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