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CDC Media Myths On trH3N2 Sequence Relationships
Recombinomics Commentary 11:30
September 12, 2011

Q: What's the story behind a new swine flu virus that health officials are concerned about?
A: The federal Centers for Disease Control and Prevention reported Sept. 2 on two cases of children infected with new swine flu viruses. One child was in Pennsylvania; the other was in Indiana.
A few days later, Pennsylvania health officials reported that they had identified two additional children in that state with the new swine flu virus, and that all three children had attended an agricultural fair in southwestern Pennsylvania during the week of Aug. 13-20.
The Indiana case was not linked to the others, and the flu-virus strain was slightly different.

The above Q&A is from a media report published today, which reflects the comments by the CDC in the week 34 FluView as well as the early release MMWR which noted drift variations between the isolate in from an Indiana patient (2M), A/Indiana/08/2011 (2M), and the Schuylkill patient (2F), A/Pennsylvania/09/2011, who visited the Washington County fair on August 16 and provided samples during an emergency department visit on August 20.

However, the PA Department of Health subsequently reported two addition confirmed cases (both 9F) and samples collected on August 25 and August 26 generated sequences (A/Pennsylvania/11/2011 and A/Pennsylvania/10/2011, respectively) which matched the Indiana sequence and did not have the drift variation sequences seen in the Schuylkill patient.  Thus, the constellation of the eight gene segments, including the M gene segment from pandemic H1N1 was the same for all four isolates, and the genetic drift was limited to the sequence from the Schuylkill isolate.  The two Washington County isolates matched each other and the Indiana sequence. 

The confusion created by the CDC report and failure to clarify after additional sequence data was generated from additional cases is similar to the confusion created by the WHO pager aler on trH3N2 in November, 2010.  The alert cited isolates from two cases (one from Illinois which was represented by the sample described by Wisconsin, A/Wisconsin/12/2010, and the other from Pennsylvania, A/Pennsylvania/14/2010 isolated from a patient who developed symptoms 6 weeks after the Illinois patient.  The two sequences were trH3N2 but distinct, especially in the NA gene, indocating they did not come from a common source.

However, in 2011 another Pennsylvania case, A/Pennsylvania/40/2010 was described, and that patient developed symptoms less than a week prior to the Illinois (Wisconsin) patient.  Moreover, the sequences were virtually identical.  Those cases were followed by a cluster from Minesota, and the sequences from the index case, A/Minnesota/11/2010, were virtually identical to the WI/12/10 and PA/40/10 sequences and five of the genes from those isolates (PB2, PA, HA, NP, NS) are in the recent 2011 isolates from Indianan and Pennsylvania.
Thus, in both cases the CDC cited differences between the common sequences and the exception, and ignored the identity between the dominant sequence identified in unrelated sequences and signaling human transmission.

These glaring omissions continue to increase pandemic concerns.

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