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Retraction of Novel trH3N2 In US Swine Claim Overdue
Recombinomics Commentary 13:15
November 27, 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 above comments are from the CDC’s November 22 “Have You Heard?” (in blue) on the three trH3N2 cases in the Iowa cluster, which matched the prior seven 2011 cases, all of which matched in all eight genes, including the M gene, which was acquired from H1N1pdm09.  The “Have You Heard” reports put out for the CDC are backgrounders for media reports.  The second comment (in red) is from the CIDRAP report on this cluster, which used the CDC’s November 22 Have You Heard to claim that the novel trH3N2 in the had been reported in swine in several states, which was false.  There has only been one case of the novel trH3N2, which was in all ten human trH3N2 cases in 2011, reported in swine, which was the recent isolate
A/swine/NY/A01104005/2011, identified in New York.

This narrative of the novel trH3N2 in swine in several states, was then repeated in a Helen Branswell report on the WHO preparations for the trH3N2 pandemic.  Three versions of that report have been published. 

The first report quoted Nancy Cox, which, as noted in the CIDRAP report, clearly indicated that the novel trH3N2 in 2011 human cases had been isolated from swine in undisclosed Midwestern state(s) in the US.

The second version kept the quote, but added the word “previously” to raise the possibility that the isolates from swine were trH3N2, but NOT the version in 2011 cases (which was well known, but not as relevant to the novel trH3N2 in human cases, since efforts to find the virus in swine associated with the first seven cases failed).  The earlier cases were in Indiana, Pennsylvania, and Maine, but the sole novel trH3N2 in swine was a recently released sequence from a pig in New York. 

The latest version of the Helen Branswell report contains no quote from Nancy Cox and does not claim detection of the novel trH3N2, and qualified the earlier 2011 human cases as saying that the trH3N2 “appeared” to have originated in associated swine.
However, this “appearance” is linked to the detection of trH3N2 in these cases, because the appearance of a swine link leads to enhanced testing, including cases that initially tested as H3N2 seasonal flu.  Thus, the CDC heavily biases the testing and the “appearance” of a link between swine exposure and infection, when in fact the link is between swine exposure and testing.

In the Iowa cluster, testing used the newly approved CDC PCR kit, which includes two targets from H1N1pdm (H1 and NP).  The NP target from H1N1 can cross react with the swine NP in trH3N2 cases, so cases that are positive for seasonal H3 and swine NP are likely trH3N2 cases, which are confirmed by the CDC by sequencing, which is the history for the Iowa cluster.

However, many samples are not sub-typed with the newly approved CDC PCR kit, and samples with low abundant RNA from trH3N2 can still give the seasonal H3N2 profile (positive for seasonal H3 and negative for both swine markers), as was described for the second trH3N2 cases from Maine, A/Maine/07/2011.  However, that sample was forward to the CDC because of multiple swine exposures, and the sequence indicated the second trH3N2 case from Maine was virtually identical to the first trH3n2 case from Maine (A/Maine/06/2011), even though the cases were not epidemiologically linked and had disease onset dates separated by two weeks.

Thus, the ten reported 2011 trH3N2 cases all match in lineage, which includes the M gene from H1N1pdm09, and this virus has been identified in two Indiana cases separated by 3 months, two Maine cases separate by 2 weeks, three cases in Pennsylvania linked to the same Washington county fair, but not to each other or any other reported trH3n2 cases, and three cases from Iowa which were epidemiologically linked to each other, as well as two symptomatic but untested family members, which had no swine exposure.

Thus, the novel trH3N2 has been reported in 10 people in four states representing six separate instances, and reports of this novel trH3N2 in swine have been limited to one isolate in New York, from a sample collected Sept 13, 2011.

Therefore, the CDC, CIDRAP, and Helen Branswell should issue a retraction/clarification of the claim that the novel trH3N2 has been reported in swine in multiple states, which is clearly indicated in their reports on the Iowa cluster which had no swine exposure.  However, there are no reports supporting the claim of novel trH3N2 in swine in multiple states.

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