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Rapid H1N1 Evolution in Beijing Raises Concerns
Recombinomics Commentary 13:25
December 15, 2009

The Beijing Institute for Microbiology and Epidemiology has released sequences from a recent isolates collected in Beijing.  All eight were nasal swabs collected in November.  Although MP and NS sequences were deposited for all eight samples, these sequences match the pandemic H1N1 consensus and therefore were not informative.  However, NP sequences from five isolates had a number of polymorphic markers and all five sequences were virtually identical, These markers were found in other H1N1 sequences, but had a wide geographic distribution matching sequences from Texas (see list here) , Spain (here), and China (here), as well as H5N1 (here) or swine (here) signaling extensive recombination.

Similar analysis for other genes showed the the Beijing sequences were closely related to each other, but the newly acquired polymorphisms traced back to H1N1 in a number of geographic locations.

However, most striking were the three HA sequences which had a clustering of polymorphisms flanking the HA cleavage site.  Several of these polymorphisms were non-synonymous and signaled rapid evolution of the HA gene.

Two of the non-synonymous polymorphisms (S131P and A337T) were in all three isolates (A/Beijing/718/2009. A/Beijing/720/2009, A/Beijing/721/2009).  Three were in 720 and 721 (T314P, L322M, S327F).  One was in 718 and 720 (S330Y).  Unique changes were in 718 (A319T), 720 (L5R), 721 (T320S, G342E, Y354F).

The large number of changes, and the combinations of shared polymorphisms, suggest significant recombination and rapid evolution, which may be heralding a new wave.

Full sequences on all eight isolates would be useful, as would more timely release of sequences from other countries.

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