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CDC Urban Legend: H3N2pdm11 Not In Big Cities
Recombinomics Commentary 21:45
December 12, 2011

The most recent cases — the West Virginia case and a cluster of three children in Iowa a few weeks back — seem almost certainly to have been the result of viruses passing from person to person, not from pigs to people.
"We're not exactly sure how many generations these viruses are away from pigs. But it looks at least like those transmissions are person to person," Finelli said.

"(But) we haven't seen any cases in densely populated areas like in big cities in the U.S. And that makes us think there's not that many degrees of separation between pigs and people since these are all rural areas."

The above comments acknowledge the human to human transmission in the Iowa cluster and cases without swine contact, but invent an urban legend by citing a lack of cases in big cities, which is just an extension of the earlier testing bias of samples with “swine exposure” and claiming the detection of H3N2pdm11 in cases with “swine contact” indicated a swine origin of infections, rather than detection due to enhanced testing because of perceived swine exposure.

The first 10 cases in 2011 all shared the same constellation and lineage (H3N2pdm11) for all eight gene segments, which were in four states (Indiana, Pennsylvania, Maine, Iowa) involving multiple introductions in the absence of symptomatic swine.  The only link to symptomatic swine was the first cases in Maine, A/Maine/06/2011, but the symptomatic swine tested negative for SOIV’s.  The most recent “Have You Heard?” has indirectly acknowledged that the increased detection of H3N2pdm11 was due to increased testing by the CDC, because of technical difficulties in obtaining a trH3N2 profile (positive for H3 and NP) in samples with low RNA, which was the case for four of the first seven cases (A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011, A/Maine07/2011).  Thus most of the initial cases were identified as H3N2pdm11 because inconclusive samples were forwarded to the CDC because of the “swine contact”.

The CDC then reinforced this pseudo-linkage by citing jumps from swine to people, which increase awareness in rural areas, leading to increased testing, while urban areas had limited analysis (many of the samples are not sub-typed) and weak H3 positives are classified as seasonal H3N2.
The CDC has not released sequences from the “big cities” because this season there is only one seaonal H3N2 sequence, A/Indiana/09/2011, from a sample listed as under 10, in contrast to the seven most recent cases, all of which were novel influenza which either were of the trH3N2 lineage with H1N1pdm09 M gene or with a PB1 sequences with E618D.
The CDC has failed to link any of the novel cases with swine infected with any SOIV, and the only epidemiological link was two confirmed and suspect cases in Iowa, as well as a contact under investigation in Minnesota (linked to A/Minnesota/19/2011).

If the CDC has sequences showing that Influenza A positives samples for children under 10 from “big cities” are bot novel, they should public those sequences.

Without such data, the media myth of absence of H3N2pdm11 in big cities is in the same category as the “swine exposure” claim, which is well into the urban legend category.

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