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Karo Cluster H5N1 Matches Duck in East Java
Recombinomics Commentary

September 15, 2006

Yesterday 19 HA sequences from H5N1 collected in 2005 from birds in Indonesia were made public.  Prior analysis of the sequences from the Karo cluster identoified many polymorphisms shared by Qinghai isolates.  Moreover, a number of Indonesian bird isolates were closely related to the Karo cluster, but there were a number of positions ion the Karo cluster that did not match any Indonesian isolate.

However, one of the newly released isolates matches the Karo cluster in all but three positions.  All three positions are silent, so the 568 amino acids coded by the HA gene segment are exact matches between the duck isolate, A/Duck/Madiun/BBVW1358/2005(H5N1).  This matches is clearly the closest out of 77 H5N1 isolates from Indonesia including six isolates from 2006 and a number of isolates from Karo.  However, this match is with a 2005 isolate from Madium, which is located in East Java.

These matches are similar to the relationship between human H5N1 isolates from Java and two chicken isolates on Sumatra. The failure to find a close match on Java also raises questions about the reservoir for the human infections in Indonesia.

These data indicate the H5N1 in Indonesia is heterogeneous and the H5N1 in poultry is not representative of the H5N1 in patients.  These differences highlight the need for more extensive surveillance in hosts other than domestic poultry.  The wild bird sequences in the human isolates suggest H5N1 is evolving in hosts other than domestic poultry and a more aggressive surveillance program is indicated.

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