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All Oct/Nov H1N1 US Sequences Have S186P or S188T
Recombinomics Commentary 13:20
January 19, 2011

The recently released HA sequences from Iran and the UK have focused attention on two emerging sub-clades which have S186P or S188T.  The most recent sequences are from Iran and were collected in mid-December, 2010.  All four have one of the two changes including three with S188T.  Three earlier sequences, from October or early December also had the same two markers.  Similarly, all December sequences from the UK had S188T, and 16/17 November sequences have one of the markers including ten with S188T.

The CDC has recently released a small series of sequences from the United States and although none are from December, six are from October or November and all six have one of the two markers.  The two most recent sequences are from the fatal cases in Lehigh, Pennsylvania.  Both sequences (A/Pennsylvania/16/2010 and A/Pennsylvania/17/2010) are identical and have S186P.  The other November isolate, A/Kentucky/09/2010 has S188T.  Similarly, two of the October isolates, A/Kentucky/08/2010 and A/Wisconsin/10/2010, have S188T, while the third October isolate, A/New Hampshire/03/2010, has S186P.

The emergence of these two sub-clades is supported by the most recent isolates from Russia and Japan, which have S188T.  The Russia isolate, A/Moscow/IIV-33/2010, is from October, while the recently release Japan isolate (by NIID at GISAID), A/NIIGATA/1581/2010, is from December.

Thus, there are seventeen December isolates from the UK, Iran, and Japan and fifteen have S188T and the other two have S186P.
These data indicate these two sub-clades will dominate in 2011, and S188T may be fixed. 

A recent isolate, A/India/5103/2010 had both markers and was designated a “low reactor” by the CDC, signaling immunological escape, which is a prerequisite for an emerging and dominating sub-clade.

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