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Indiana DoH Detects trH3N2 With Newly Approved PCR Test
Recombinomics Commentary 09:00
November 17, 2011

• An adult male developed fever, cough, shortness of breath, nausea, vomiting and body aches on October 20, 2011. The patient was hospitalized, but has been discharged and is recovered from his illness.
• On October 22, 2011, a respiratory specimen was collected during hospital admission and after conflicting results were obtained at the hospital laboratory, the specimen was forwarded to the Indiana state public health laboratory.
• On October 28, 2011, testing at the Indiana public health laboratory indicated a likely swine-origin influenza A (H3) virus.
• The specimen was forwarded to CDC on October 29, 2011. On October 31, partial genome sequencing confirmed the virus as a swine-origin triple reassortant influenza A (H3N2) virus with the M gene from pH1N1.

The above detailed Louisiana Department of Health and Hospitals comments on the recent trH3N2 infection of a Indiana veterinarian (59M, A/Indiana/10/2011) indicates the “likely swine-origin influenza A(H3) virus” was determined using the newly approved CDC PCR test which includes a test for pdm NP.  Thus, trH3N2 samples return a positive for pdm NP, but a negative for pdm H1, as well as a positive for seasonal H3, leading to the above diagnosis by state labs, which is then confirmed in samples sent to the CDC, which are sequenced.

Thus, the three October trH3N2 originated from state labs in Maine and Indiana which used to the new PCR test which indirectly
(the test does not include a test for the H3 found in all seven of the 2011 human trH3N2 cases) detects trH3N2 .  However, the second case in Maine (8M, A/Maine/07/2011) was diagnosed with a sample that had a low level of RNA, so the testing was inconclusive (weak H3 positive) and sent to the CDC because the patient had attended the same state fair (Fryeburg) as the first case, participated in a swine scramble at the fair (video of Fryeburg scample filmed by coughing videographer), and had additional swine exposure after the fair.  Thus, the swine contact drove the additional testing, although the exposure at the fair was too early for the infection which had a disease onset date two weeks after the fair ended, the symptomatic swine at the fair have tested negative for SOIV’s (swine origin invluenza virus used for classification, not current origin), and the swine contacts after the fair were asymptomatic.

The detection of these cases in states using the new test raise concerns that samples without swine exposure are not being detected because many sites are not using the test and not sub-typing samples, as seen in samples reported sub-typing tables in weeks 43 and 44, or influenza samples from US Region 4 this season, where only one of thirty-two influenza A samples have been sub-typed.

Moreover, the detection of positives in Indiana and Maine has been limited.  Maine has only reported two cases identified in the PCR test, and both were trH3N2, while Indiana has only reported three influenza cases since July, and 2 of the 3 were trH3N2.

These high frequencies in states using the new PCR test raises concerns that the number of trH3N2 infections in recent influenza A positive samples is far higher than the seven reported since July, and these influenza A positive samples represent a tiny fraction of trH3N2 cases because most influenza infections are not reported, and most cases are not tested.

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