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Independent H1N1 D225G Introductions In California
Recombinomics Commentary 13:29
January 29, 2010

JCVI released 50 full sequences at Genbank and almost all were from California. Included was one sample with D225A, A/California/VRDL31/2009, (as mixture with wild type) as well as two D225G and 8 D225E.  These sequences were from isolates collected over the summer and early fall.  The two isolates with D225G are distinct from each other and the many recent examples from Ukraine and Russia, representing two additional independent introductions.

A/California/VRDL27/2009 has four recently acquire polymorphisms, including A716G, which codes for D225G.  The other three polymorphisms are in a California isolate, A/California/VDLR20/2009 and a Texas isolate, A/Texas/45101424/2009.

The first polymorphism, C437T, is in several other pandemic H1N1 sequences and many swine (see list here). Another polymorphism, A1280A is widespread and in Ukraine, Russia, and Norway isolates with D225G (see list here).  The third polymorphism, G1360A is only in the three pandemic H1N1 sequences (see list here), which are the ones listed above.  The Texas isolate only has the three polymorphisms listed above, so the California isolate is the Texas sequence plus D225G, representing an independent acquisition.  Like most of the polymorphism, the other California sequence is the Texas sequences plus two other polymorphisms that are share with additional sets of pandemic isolates.

In contrast, the other California sequence, A/California/VDLR7/2209, with D225G has a different set of polymorphisms. One, G79A, is in other California sequences (see list here) but not those sequences described above.  The second polymorphism, T598C, codes for S185P and is also in an isolate from Ankara (see list here).  The second California isolate is a second independent isolate acquisition of D225G, which is not linked to the other California sequence or the sequences in Russia and Ukraine.

The Russian and Ukraine sequences follow the same pattern, but at a much higher frequency.  There are examples of the same genetic background with wild type, D225G, D225N, or both new acquisitions.  Similarly the same polymorphism (D225G or D225N) is on multiple related but distinct backgrounds which includes isolate with a wild type HA receptor binding domain, which again requires separate independent acquisitions in the same are over a short time frame.  All of the Ukraine sequences were collected in late October or early November.  This clustering in time and space of related but distinct sequences that have acquired the same polymorphisms at position 225 are inconsistent with a random mutation mechanism, and is easily explained by recombination moving the polymorphism from one genetic background to another as was described for H274Y in seasonal H1N1 or a synonymous NA polymorphism, A743G ,in the H5N1 NA clade 2.2 sequence.

Similarly, the D225G polymorphism (A716G) has been added on D225E genetic backgrounds (with T717A and othere D225E markers), including the most recently released D225E sequence from Japan, A/Yamaguchi/247/2009, released today by NIID at GISAID, and earlier isolates in Europe.

The movement of polymorphisms from one genetic background to another via recombination is common, and readily explains the explosion of D225G on multiple H1N1 genetic backgrounds from fatal cases.

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