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75% of US Sequenced Influenza A+ Under 10 Cases Are trH3N2
Recombinomics Commentary 22:45
November 23, 2011

Prior to the three cases in Iowa, most human infections with this virus were associated with exposure to swine. In Iowa, however, no swine exposure has been identified. At this time, it appears that unsustained human-to-human transmission may have occurred.

The above comments are from the November 22 “Have You Heard?”, a CDC backgrounder for the media.  The latest Iowa cluster leaves little doubt that the novel trH3N2 with the H1N1pdm09 M gene is transmitting in a sustained manner.  The CDC maintains its “unsustained” claim by limiting testing.

Since the trH3N2 virus has a human H3 and N2, it frequently tests positive for seasonal H3N2.  This mis-classification can be corrected in the newly approved CDC PCR test, which has two swine genes from H1N1pdm09, but low abundant RNA samples can test negative for these markers to produce a false positive for seasonal H3N2, as was reported for a case from 2010 (A/Pennsylvanai/40/2010), as well as the second case from Maine (A/Maine/07/2011).  Therefore sequencing is required to conclusively classify the H3N2 positive case as seasonal H3N2 or trH3N2.

The CDC has released 14 sequences collected from adolescent samples that were influenza A positive since July 20, 2011.  9 of the 10 confirmed trH3N2 cases in 2011 were from patients aged 1-9.  Thus, only 5 seasonal H3N2 sequences have been identified in public sequences which include the patients age and gender, as updated below.  trH3N2 cases are in bold.

As seen below, 64.2% of the US cases were trH3N2, and the percentage for those under 10 years-of-age is 75%.  Moreover, for cases in the four states where trH3N2 has been detected, 90% of the cases have been trH3N2 confirmed (all have the H1N1pdm09 M gene and all eight gene segments are from the same lineages). 

Other than the 9 cases from children, one novel trH3N2 case was from an adult, A/Indiana/10/2011, and one case was identified in swine, A/
swine/NY/A01104005/2011 .

Thus, trH3N2 is common and transmitting, and cases will explode if the CDC begins serious testing, including sequencing of influenza A positive samples from children under 10 years of age.

A/Iowa/09/2011                11/14 2M
A/Iowa/08/2011                11/14 1M
A/Iowa/07/2011                11/14 3F
A/Maine/07/2011              10/24 8M
A/Maine/06/2011              10/10 8M
A/Indiana/09/2011             10/03 1M
A/Washington/17/2011      09/14 10F
A/Pennsylvania/10/2011 08/26 9F
A/Florida/24/2011               08/25 1M
A/Pennsylvania/11/2011 08/25 9F
A/Pennsylvania/09/2011 08/20 2F
A/Louisiana/06/2011          08/16 13F
A/Florida/20/2011               08/05 8M
A/Indiana/08/2011              07/27 2M

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