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Unsubtypables Dictate Widespread trH3N2 PCR Testing
Recombinomics Commentary 13:45
September 11, 2011

The latest CDC FluView (week 35) with two unsubtypables (unable to subtype) highlights the dramatic recent changes in the H3 sequences in the 2011 trH3N2 isolates, which include R50G, S107T, T117N, D133G, E142G, H156Y, A163E, L164Q, R189K, T203I, P274H, G276D, N277E, R299K, L427I, N444S, K452R, V489I, D492N. 

These changes create an “unsubtypable” result because the changes are too great for recognition by the reagents used to subtype human H3.  However, most of the above changes are also in the closely related 2010 trH3N2 isolates, like A/Pennsylvania/40/2010, which did initially type as human seasonal H3.  This variability raises concerns that some trH3N2 will sub-type as seasonal H3N2, while others will be usubtypable as seen with two of the four 2010 isolates which have H3 sequences that are virtually identical.

Most of those trH3N2 cases that type as seasonal H3N2 will not be further classified.  A small sub-set will be characterized furth in antigen characterization tests (which would identify such cases as LOW REACTORS) or sequencing, which would easily identify the above changes as well as a similar number of synonymous change.  Thus, even partial sequences will easily distinguish seasonal H3N2 from swine trH3N2.  However, these test generally rely on the isolation of virus and are done by the CDC, so the number of such identification will be low and may be significantly delayed, as seen in the 5 month delay for A/Pennsylvania/40/2010.  However, if the pandemic trH3N2 outcompetes the seasonal H3N2, these more complicated tests will clearly identify trH3N2, but the lag time may be significant.

PCR testing for the swine evolved sequences is very rapid and quickly identifies trH3N2, as was seen for the four 2011 sequences, and the PCR testing can be done by the state labs.  Therefore, such screening should be dramatically increased, as was done for pandemic H1N1.
The PCR testing would quickly identify the extent of the trH3N2 spread, which is likely to present in patients without swine exposure, as was seen in 3 of the 4 recent cases, as well as patients who do not live in areas with swine, who are rarely tested for trH3N2.

The identities between the isolates in Indiana and Pennsylvania strongly suggest this latest version of trH3N2 is spreading in humans since it has acquired the pandemic H1N1 M gene segment, and the H3 and other internal genes cluster in human trH3N2 cases, which is easily seen in phylogenetic analysis.

Release of results of widespread PCR testing on influenza A positive samples would be useful.

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