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Clarify CDC Confusion On Novel trH3N2 In US Swine
Recombinomics Commentary 16:00
November 27, 2011

Although reassortment between swine influenza and 2009 influenza A (H1N1) viruses has been reported in pigs in the United States (3), this particular genetic combination of swine influenza virus segments is unique and has not been reported previously in either swine or humans, based on a review of influenza genomic sequences publicly available in GenBank.† Analysis of data submitted to GenBank via the U.S. Department of Agriculture (USDA) Swine Influenza Virus Surveillance Program subsequent to this case identified two additional influenza A (H3N2) isolates from swine containing the M gene from the 2009 influenza A (H1N1) virus. Genome sequencing is underway to completely characterize the genetic composition of these two swine influenza isolates. (USDA Agricultural Research Service and USDA Animal and Plant Health Inspection Service, unpublished data, 2011).

The above comments are from the CDC’s September 2, 2011 early release MMWR on the first two cases with the novel trH3N2 that acquired the M gene from H1N1pdm09.  As noted, no such constellation had been previously reported, but two candidate isolates were mentioned.

Subsequently, two large series of sequences from US swine were published for isolates from samples collected between late 2010 and July 2011.  None of these isolates matched the novel trH3N2 that has been confirmed in ten human cases in 2011.

Recently, this expanded surveillance identified one swine in New York with the novel trH3N2, and this sequences was recently released at Genbank and was subsequently added to the database at GISAID.

The CDC has issued a new November 23, 2011 early release MMWR on the latest human cases infected with the novel trH3N2.  The virus was confirmed in three members of the cluster, and two additional family members were symptomatic but not tested, suggesting the size of the cluster was at least five.  None of these confirmed or suspect cases had a reported exposure to swine.  However, in spite of this absence of a swine exposure, and a failure to link any of the prior cases to swine infected with the novel trH3N2, the CDC requested samples from symptomatic patients with swine exposure.  The MMWR was silent on the failure to linked any of the prior cases to swine infected with trH3N2 or the failure of the USDA to identify any swine infected with the novel trH3N2 other than a Sept 13 collection from a New York swine,
A/swine/NY/A01104005/2011, not linked to any of the reported cases.

In spite of the failure to link any of the 2011 cases to any swine infected with novel trH3N2 or to identify the virus in any swine isolates from samples collected prior to the spread detected in the Indiana and Pennsylvania isolates in July and August, the CDC, in its November 22 “Have You Heard? on the Iowa cluster claimed that the novel virus had been reported in multiple states, which was then reported in multiple media reports.

CIDRAP noted that the CDC had reported the detection in multiple states, but failed to identify the sates.  Helen Branswell published multiple versions of a report on WHO pandemic plans which were brought into focus by the Iowa cluster.  The first report cited Nancy Cox, and attributed to her a claim of detection in multiple Midwestern states.  The second report changed the tense for the claim, implying that the detection was for earlier isolates, which did not match the 2011 human trH3N2 cases (this tense change also suggested that the CDC "Have Your Heard" was also referencing earlier trH3N2, causing the confusion in the subsequent media reports).  The third version removed all references to the presence of the novel virus in swine in the Midwest..

However, the failure to identify this novel trH3N2 in any of the four states reporting human cases (Indiana, Pennsylvania, Maine, Iowa) in spite of enhanced surveillance by the USDA and state department of agriculture investigations of the cases in Indiana, Pennsylvania, and Maine is significant, and the CDC as well as CIDRAP and Helen Barnswell should issue a retraction of the claim of novel trH3N2 in swine in multiple states, and instead describe the true status of these investigations and the failure to identify this novel trH3N2 in any swine anywhere in the world, other than the Sep 13 collection from the pig in New York.

Moreover, the CDC should aggressively test the influenza A positive samples, especially those from children under the age of 10, which account for 9 of the 10 confirmed trH3N2 cases in 2011 and request samples from children with influenza like illness who have NOT had a recent swine exposure, in contrast to the request in the Sept 2 and Nov 23 MMWRs.

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