H5N1 Polymorphism, Q296H, Arises in Singapore, World’s Busiest Port

A review of HA:296 is in order based on today’s releases.

The polymorphism, Q296H, was found in the 11 year old female death in SaoPaulo43812, is widely conserved in the Northeastern US, is conserved in Italy and is found in Northwestern Europe.

This change has moved into Singapore, a major gateway to the world. Singapore shares the title of Busiest Port in the World with Shanghai in different categories. 296H emerged in Singapore in one of the four sequences sampled on 2009-06-14 and deposited yesterday, A/Singapore/TLL54. No other segments for this sample are on file for review.


  • 2E
  • 35I
  • 66E
  • 296H 
The Glutamate (E) near the beginning matches 1918 and most H5N1. This HA homology additionally occurs with SaoPaulo2233, Italy127 and NY4197, each of which also share 296H with this SingaporeTLL54 specimen under review.

The 296H change is rare on PF11 sequences in Asia with only 2 matches in China (Shanghai143T, Shandong1) and 1 in Japan (Tokushima1).  On the PF11 background, only 31 sequences across the globe now carry 296H.

New York obviously provides a substantial international vector from the airports and seaports.  Shanghai and Singapore vector air and sea extensively.  The Italian port of Ancona provides a significant trans-Adriatic ferry service.

An intra-segment exclusivity exists presently in PF11 between 296H and 206T though donors are proximal in China, Japan, SaoPaulo, Finland and Canada with extensive coverage in New York and Italy.

We suggest tracking for interplay between 296H and the recent RBD changes noted in QC1 and QC2.

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