Indonesian H5N1 Sequences in North America
Recombinomics Commentary
August 31, 2007
The recently released paper, “Characterization of Low Pathogenicity H5N1 Avian Influenza Viruses from North America”, provides detail on the H5N1 isolates from the United States and Canada. Although these isolates are low path H5N1 with polymorphisms commonly found in North America, they fill a gap in knowledge about recent H5 sequences, first described in 2005 in Canada.
A survey of live wild birds across southern Canada identified an unexpectedly high frequency of H5 sequences. In British Columbia, 24% of the samples were PCR H5 positive. H5N1 was found in Manitoba. Although H5N1 was not reported in the United States in 2005, an expanded surveillance program identified H5N1 in multiple states in 2006.
The paper includes six H5N1 isolates. All are low path. The HA sequences of two isolates, A/Mallard/MB/458/05(H5N1) and A/Mallard/ON/499/05(H5N1) were released at GenBank yesterday. Polymorphism tracing of newly acquired polymorphisms identified multiple polymorphisms that are in high path H5N1 in Asia and clade 2.2. Clade 2.2 is the Qinghai strain, which is the strain found in all recent high path H5N1 west of China.
Of interest was a pair of polymorphisms, C85T and T97C, which were present in most high path H5N1 isolates. An expanded region of identity was found almost exclusively in Indonesian isolates (see list).
The region of identity between H5N1 in Canada and HPAI H5N1 in Indonesia is cause for concern. Movement of H5N1 polymorphisms have focused on clade 2.2 because all H5N1 west of China is clade 2.2 and has been found in dozens of wild bird species. However, recent sequences from waterfowl in Indonesia suggest they are also a key vector in H5N1 movement of clade 2.1 (found exclusively in Indonesia).
The distribution of these polymorphism in North America is unclear, because most of the sequences described in the above paper have not yet been made public. The phylogenetic tree however, indicates that the three United States H5N1 isolates in 2006 (A/BlackDuck/NC/674-694/06
A/Duck/PA/454069-9/06, A/MuteSwan/MI/451072-2/06 are closely related to the two Canadian isolates, as is an H5N2 2007 isolate from Florida, A/NorthenPintail/FL/598/07(H5N2).
Polymorphisms tracing is a powerful technique used to monitor H5N1 evolution (described here, here, and here). However, the technique is most useful when the database is robust. The public sequences released yesterday were from samples collected over two years ago. They were deposited at Genbank in January, 2007. Full sequences are currently at GenBank, but only HA and NA sequences have been made public (and for sample A/Mallard/ON/499/05, sequences from only one of the two clones have been released).
The holding of sequences pending publication, extends well beyond the H5N1 sequences in the recent paper. Similarly, 2005 H5N1 sequences from Europe are also being withheld, as are 100’s or 1000’s of sequences from 2006 and 2007.
The movement of H5N1 polymorphisms remains a cause for concern, as is the continued hoarding of the sequences.
Media Sources
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Recombinomics Paper at Nature Precedings