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Unsubtypables and trH3N2 Surveillance
Recombinomics Commentary 19:00
September 9, 2011

One case of human infection with a novel influenza A virus was reported by the Pennsylvania Department of Health. The patient was infected with a swine origin influenza A (H3N2) virus. The patient reported contact with pigs in the week preceding symptom onset on September 6, 2010, did not require hospitalization, and has since fully recovered. Initial testing of the specimen indicated a seasonal influenza A (H3N2) virus and the specimen was submitted to CDC as a routine surveillance sample. The delay from onset to detection occurred because attempts to culture the virus were unsuccessful. RT-PCR testing confirmed swine-origin influenza A (H3N2).

The above comments from the week 4 FluView describe an earlier isolate from Pennsylvania, A/Pennsylvania/40/2010 (PA/40/10), which is closely related to A/Wisconsin/12/2010 and A/Minnesota/11/2010, which are precursors to the four confirmed trH3N2 2011 cases.  As noted above, the PA/40/10 sample was initially classified as seasonal H3N2 and the announcement of trH3N2 was made 5 months after collection.

The H3 sequences from the latest trH3N2 isolates has evolved further from the 2010 sequences, and the unsubtypables listed for week 33 and week34 the week 35 report are likely A/Pennsylvania/09/2011 (PA/09/11) and A/Pennsylvania/11/2011 (PA/11/11) and suggests that the more 2011 trH3N2 isolates will register as influenza A positive, but H3 and H1 negative, which would facilitate detection by state labs who routinely determine sub-types. 

However, as seen in the week 35 report, many samples are not sub-typed, and the other two recent isolates may be in that category, but made be subsequently added after sub-type failure (and associated confirmation of trH3N2).

Thus, the comments posted above, coupled with the concentration of confirmed trH3n2 cases in Pennsylvania and prior reports of unsubtypable samples warrant a review / retesting of those samples via swine specific PCR analysis, as was done with PA/09/11.

This review should identify many additional prior trH3N2 cases in the 2010/2011 season and focus testing on influenza A positive cases, including those without linkage to swine.

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