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Sequence From Taiwan H6N1 Case Has G228S
Recombinomics Commentary 15:15
June 27, 2013

The patient, who lives in central Taiwan and works at a breakfast shop, developed mild pneumonia in early May and was hospitalized on May 5, Yang said.

"The patient was discharged from the hospital on May 11 after recovering from her illness," Yang said.

According to Yang, the patient had never been abroad and had no history of contact with poultry.

The CDC later found that 36 people had come into contact with the patient, and four of them had flu-like symptoms.

"But after examining them, we found that none were infected with the H6N1 virus," Yang said.

The above comments describe the first reported H6N1 case (20F).  Although the patient was discharged on May 11, the case was reported on May 20, so investigation of the symptomatic contacts was unlikely to yield a positive H6N1 or influenza A result, since contacts would have recovered prior to sample collection.

The Taiwan CDC recently released a full sequence, A/Taiwan/2/2013 (at GISAID from a May 7 collection), which was most closely related to chicken H6N1 sequences from Taiwan.  The Taiwan CDC is to be commended for the prompt release of full sequences from this case. The sequences had some evidence of reassortment within this serotype, but in several instances the most closely related sequences were collected 8-11 years ago. 

However, the Animal Health Research Institute released a full set of bird flu sequences (at GISAID) from a healthy chicken, A/chicken/Taiwan/A2837/2013, collected May 15 and they are also commended for the rapid release of these important sequences.  These sequences were much more closely related to the human sequences, but some segments were still evolutionarily distant, signaling an absence of a robust database representing the human sequences.

Both sequences, as well as the most closely related sequences from earlier collections, had key H6 changes that would enhance binding to mammalian receptors in the upper respiratory tract, including the absence of a glycosylation site at position 158, and the presence of receptor binding domain changes E189V and G228S.

The presence of G228S is of concern because it was present in H2N2 in the 1957 pandemic as well as H3N2 in the 1968 pandemic and it was introduce in H5 sequences used in transmission studies.  Q226L was also in the H2N2 and H3N2 pandemic sequences, as well as H7N9 sequences in human cases in the Shanghai area, and a traveler to Taiwan (represented by A/Taiwan/1/2013). 

Thus, the presence of Q226L in Taiwan/1/2013 and G228S in Taiwan/2/2013 is of concern.

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