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H5N1 Garut Cluster Sequences Similar to Western Java
Recombinomics Commentary

September 5, 2006

Sequences from three recent isolates from Indonesia, A/Indonesia/CDC739/2006(H5N1), A/Indonesia/CDC742/2006(H5N1), A/Indonesia/CDC759/2006(H5N1) were made public today.  The HA of all three have the common cleavage site of RESRRKKR.  Two of the HA, sequences are similar to A/Indonesia/CDC/669/2006(H5N1).

One of these sequences appears to be from the second confirmed fatality (35F) of the Garut cluster.  Its similarity to recent isolates from the Jakarta / West Java area indicates that the H5N1 in human cases continue to evolve and spread into new areas.

Although there were only three confirmed cases in the Garut cluster, several relatives of the positives died earlier with bird flu symptoms.  However, samples were not collected from these contacts, highlighting surveillance failures.  This poor surveillance also eliminates clusters, because index cases are not tested.  Similarly, the negatives in contacts with symptoms may be false because of the use of a Tamiflu blanket.

Thus, the similarity in the H5N1 in Garut with other human cases on Java suggested that human cases and clusters are far more widespread than indicated by the confirmed cases.

These recent sequences were easily distinguished from the only avian isolate to date with the RESRRKKR cleavage site.  Sequence data from birds linked to recent outbreaks in Indonesia would be useful.

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