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Japan Swan H5N1 Linked to Wild Birds in Hong Kong
Recombinomics Commentary 11:07
May 20, 2008

The release of sequences from all eight gene segments of whooper swan isolates from Japan allows for phylogenetic analysis.  Phylogenetic analysis is used to assign the sequences to related sub-clades, and an analysis indicates the HA sequences from the Hokkaido isolates are clade 2.3.2.  They lie on a branch that is rooted with sequences from Vietnam collected in 2005.  However, the 2008 sequences have evolved markedly from these 2005 sequences and map to a location similar to the clade 2.3.2 vaccine target, A/common magpie/Hong Kong/5052/2007.  This 2007 isolate is from a dead wild bird in Hong Kong.  H5N1 infected wild birds appear annually near the beginning of the year in Hong Kong.  Although the sequence has been withheld, it is mapped in the WHO report on vaccine targets.  The phylogenetic tree helps fill in the gap between the 2005 isolates in Vietnam (most of which also have M230I) and the 2008 isolates in Japan.  This gap would likely be filled by the other wild bird isolates from Hong Kong in 2007 / 2008 which are being hoarded in the WHO private database, which is password protected and only available to a small group of WHO consultants.

The NA sequence of the recent isolates from Japan map with clade 2.3.4 isolates, and are most closely related to a human isolate from Guangdong province, A/human/China/GD02/2006.  This isolate is not included in the WHO phylogenetic tree, but is on the branch with other wild bird isolates from Hong Kong in 2006, including A/chicken/Hong Kong/282/2006, which is on the WHO tree in the pandemic vaccine report.  Other isolates on that branch (but not listed in the WHO report) include A/magpie robin/Hong Kong/75/2006 and A/magpie robin/Hong Kong/366/2006.  Thus, although the NA sequences map with another Fujian sub-clade (2.3.4), both sequences are traced to magpie isolates in Hong Kong in 2006 or 2007.

The tracing of the whooper swan sequences in Japan back to the magpie sequences in Hong Kong helps define the migration path of H5N1 sequences in eastern Asia.  In the past this mapping has been hampered by the emphasis on poultry and trade and the discounting of wild birds.  However, earlier sequences from isolates collected at wet markets in South Korea in 2003 had clear examples of recombination which involved sequences from South Korea and Hong Kong.  Although several examples of recombination were withheld, those released had clear examples in multiple genes.

Thus, like clade 2.2 sequences which are transported and transmitted by wild birds migrating in Europe, the Middle East, and Africa, as well as resident wild birds which maintain local versions of H5N1, migratory and resident birds in eastern Asia also control the movement and evolution of H5N1.

This phylogenetic analysis provides additional evidence for movement via the East Asian flyway, which connects H5N1 in Indonesia, southeast Asia, and eastern China, with Japan, South Korea, eastern Russia, and Alaska.  The migration on this flyway also helps explain the North American PB2 sequences in the whooper swan isolate from Japan.

Thus, the mapping of the movement of viruses and individual polymorphisms is facilitated by a robust database, and is inhibited by the hoarding of sequences, including those selected as pre-pandemic vaccine targets.

The time for releases of the sequences hoarded by WHO and their consultants has long since passed.

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