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CDC Novel trH3N2 Swine Exposure Coupe De Grace
Recombinomics Commentary 01:00
November 28, 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. These viruses have been reported in swine in several states in the United States.

The CDC said several states have reported the novel virus in swine, but did not identify the states.

The virus has been isolated from pigs in the U.S. Midwest, says Dr. Nancy Cox, head of the CDC's influenza division, though she won't specify where.

The virus was previously isolated from pigs in the U.S. Midwest, says Dr. Nancy Cox, head of the CDC's influenza division, though she won't specify where.

The above comments represent the CDC’s latest attempt to maintain its swine exposure narrative on the trH3N2 pandemic.

The first quote in blue is from the November 22, “Have You Heard?” (HYH), which is on the Iowa cluster with no swine exposure.  HYH are media backgrounders put out by the CDC on topics of potential media interest.  The trH3N2 HYH frequency has increased significantly in the past few months, as it becomes increasingly clear that the trH3N2 pandemic is well underway.  However, the CDC has used HYH release to maintain its narrative on the linkage of “swine exposures” to trH3N2 cases and the associated "no sustained" human transmission..

The first HYH on trH3N2 was in 2010 (November 12) after WHO issued a pager alert on two trH3N2 cases (in Wisconsin and Pennsylvania).  However, the real story behind those two cases was a third case, which was not reported until 2011 because it was initially classified as seasonal H3N2,  The release of the sequence was delayed for 10 additional weeks and finally quietly released on a Sunday (April17), at a password protected database (GISAID).  This sequence (A/Pennsylvania/40/2010) was important because it was virtually identical to the Wisconsin sequence (A/Wisconsin/12/2010) signaling human adaptation and transmission at a high frequency between the two cases were not epidemiologically linked.

The second HYH was on December 17, 2010 on another trH3N2 case (from Minnesota), but once again the significant story came out in 2011 and not covered by a HYH.  The Minnesota case (A/Minnesota/11/2010) was part of a cluster of family members who were symptomatic but “under investigation” at the time of the HYH.  Six months later, the daughter of the index case was serologically trH3N2 confirmed and other cluster members were “inconclusive” confirming trH3N2 in two cluster members and strongly suggested additional contacts were trH3N2 infected.

The third HYH (September 6) followed an early release MMWR (September 2) which described the first two trH3N2 cases in 2011.  These cases were of concern because they were from two states (Indiana and Pennsylvania) but had the same novel constellation of flu genes, which include the M gene from H1N1pdm09.  The CDC offered some assurance against human transmission by noting sequence differences between the Indiana (A/Indiana/08/2011) and Pennsylvania (A/Pennsylvania/09/2011) sequences, but this assurance was eliminated by two additional Pennsylvania cases noted in the HYH.  These sequences (A/Pennsylvania/10/2011 and A/Pennsylvania/11/2011) matched each other and the Indiana sequence, once again signaling high levels of human transmission because none of the cases were epidemiologically linked.

The fourth HYH (October 21) was on a trH3N2 case in Maine  (A/Maine/06/2011), which had the same constellation of genes as the cases in Indiana and Pennsylvania, confirming that the novel trH3N2 was transmitting in humans, but the CDC maintained its "swine exposure” narrative by noting a visit to an agricultural fair, which had symptomatic swine, although the swine tested negative for swine influenza of any type.

The fifth HYH (November 4) cited two more trH3N2 cases (Maine, A/Maine/07/20911, and Indiana, A/Indiana/10/2011) which were not linked to prior cases, but had the same novel trH3N2 with an H1N1pdm09 M gene.  These cases left little doubt that these case represented a trH3N2 pandemic, but the CDC maintained that the loosely defined swine exposure indicated the trH3N2 was not transmitting in a sustained manner in humans.

However, the sixth HYH (November 22) was the coupe de grace for the CDC’s “swine exposure” narrative because the Iowa cluster involved three trH3N2 confirmed cases in two epidemiologically linked families, as well as two additional symptomatic family members, with no swine exposure for any of the confirmed cases or contacts.

The sequences confirmed that the trH3N2 matched those isolated from the seven earlier 2011 cases, which forced WHO to issue an alert and the CDC to publish another early release MMWR (November 23), yet the Nov 22 HYH included the comments quoted above.

The comments described the Iowa cluster, but then claimed that “these viruses” had been reported in swine, which was not true for the novel trH3N2 identified in all ten of the 2011 human cases.  Although the USDA had increased surveillance, and the agricultural departments in Indiana, Pennsylvania, and Maine had investigated the swine linked to the confirmed cases, none were found to be infected with any influenza virus, which was also true for all swine investigated in each state.  Moreover, the USDA failed to find the novel trH3N2 in any swine samples collected prior to the human cases.  The only example was from a Sept 13 collection for a pig in New York,

However, CIDRAP wrote a summary of the Iowa cluster, and used the information posted above (second blue quote) to reference a “CDC report” to claim that the “novel” trH3N2 had been found in swine in multiple undisclosed states.

The CIDRAP report was followed by a Helen Branswell story on WHO preparations for a trH3N2 pandemic.  She also cited trH3N2 in swine, but attributed the information to Nancy Cox, head of the CDC influenza program.  The information was similar to the CIDRAP comment, except the Branswell story (first red quote) indicated the swine were in undisclosed Midwestern state(s), which was curious because there were no reports of novel trH3N2 in Midwestern swine, and the New York swine was not mentioned, even though Nancy Cox would have been well aware of the New York match.

The Branswell quote was then modified to past tense (second red quote), suggesting that the Midwestern swine infected with trH3N2 were infections that were similar to the 2009 and initial 2010 trH3N2 cases (A/Kansas/13/2009, A/Iowa/16/2009. A/Minnesota/09/2010) which were from the Midwest but did not have the H1N1pdm09 M gene and were not closely related to the novel trH3N2 which did have the H1N1pdm09 M gene, which was also in all ten human cases in 2011.  However, this second version made little sense because the Midwestern location of the initial cases was contained in the names of each of the isolates.

A third version of the Branswell report was subsequently published without any reference to Nancy Cox or trH3N2 infections in swine.

Thus, the sixth HYH created significant confusion regarding the status of novel trH3N2 in swine.  The CDC has not acknowledged the failure of the USDA or the state agricultural department to find any swine infected with novel trH3N2, other than the recently released New York sequence for the only reported pig with the novel trH3N2. 

Similarly, CIDRAP and Helen Branswell have not addressed the confusion created by their reports, which have no factual basis with regard to reported novel trH3N2 in swine.

The CDC HYH and the associated media reports have created the false impression that the novel trH3N2 has been reported in swine in multiple states.

Therefore, all of the above should issue a retraction and clarification to end the CDC charade on swine exposure for the 2011 cases involving novel trH3N2 with a H1N1pdm09 M gene.

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