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S188T On 22/41 Recent H1N1 Sequences In England
Recombinomics Commentary 23:55
January 6, 2011

The Health Protection Agency has recently published a paper in Eurosuveillance entitled “Virological analysis of fatal influenza cases in the United Kingdom during the early wave of influenza in winter 2010/11.”  The paper includes a HA phylogenetic tree which includes 41 sequences from the recent outbreak, including the four sequences that were released at GISAID.  One of the released sequences, A/England/4880374/2010, contained S188T, which was seen in early 2010 in a swine from Thailand and was subsequently found in human isolates from Thailand, India, Australia, New Zealand, Ghana, Japan, and Iran, raising concerns that the location adjacent to the receptor binding domain at position 190 would lead to immunological escape, similar to changes seen in seasonal H1N1 associated with the fixing of H274Y.

Vaccine escape had been reported in Australia and the rapid spread of H1N1 in England suggested that the sequences there were also allowing such sequences to spread widely and rapidly.

The phylogenetic confirmed this concern since S188T (labeled S185T in the tree here) was in 22 of the 41 sequences.  The tree also had several examples of recombination.  D100N (labeled D97N) was not in the released sequence with S188T, but it was in A/England/4780352/2010.  However, D100N was appended onto many of the S188T sequences in the phylogenetic tree.  Moreover, two sequences with S188T and D100N also had D225G (labeled 222G) which were from two severe cases, A/England/4880378/2010 and A/England/4940476/2010, and the two sequences were identical, signaling transmission.

Information on the relationship between the two severe cases with D225G, as well as release of the 37 sets of H1N1 sequences used in the tree in the paper would be useful.

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