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H5N1 Qinghai Fujian Recombination in China
Recombinomics Commentary

November 1, 2006

The recent paper in the Proceedings of the National Academy of Sciences describes the widespread detection of the Fujian strain of H5N1 in China.  The spread in China  was clear from earlier sequences from fatal human infections in late 2005 and early 2006 as well as isolates from Laos and Malaysia followed by sequences made public from wild birds in Hong Kong.  The paper indicated that birds positive for the Fujian strain had low antibody titers and the new strain may have evolved away from the vaccine being used for the birds.  Moreover, the detection rate of the Fujian strain continued to rise, indicating the strain was becoming dominant.
Sequences from 404 isolates were made available which include full or partial HA sequences as from all 404 isolates, as well as 152 PB2 sequence.  Included in these sequences was one Qinghai strain from Shantou, A/Gunea fowl/Shantou/1341/2006.  However, analysis of the other sequences indicate widespread acquisition of regions of identity with the Qinghai strain (see identities here), indicating the H5N1 was evolving via recombination, and the Qinghai strain was one of the contributing parents, in the vast majority of the Fujian isolates.
Origins could be traced using probes of various regions of the new isolates and this analysis indicated many contained regions that traced back to wild bird isolates in Hong Kong in 2003, or isolates from northern China in 2003. These data indicate wild birds are responsible for the transport and transmission of the evolving H5N1.  Qinghai matches were also found in Indonesia isolates.  These matches had been noted previously, and include the Qinghai cleavage site in on Indonesia isolate.
The latest sequences allow for tracing of the evolution of H5N1.  This could be done with regions of HA and PB2.  The PB2 tracing was somewhat limited, because the more extensive changes were in the 5’ end of the gene and in many instances this region was missing from the deposited sequences.
The widespread recombination and exchange of portions of genes highlight the need for a robust database, including both high and low path H5N1 from wild birds.  Although the current sequence database has grown dramatically in recent weeks because of complete sequences from Indonesia, Qinghai sequences from the Capua lab via the NIAID influenza sequencing project, and China sequences from the Beijing Genome Institute, many holes in the database remain.  The recent sequences from China significantly increased the number of H5 sequences in the database.  However, many were partial sequences and there should be eight complete sequences per isolate, or 3232 sequences.  Thus far, 556 of the 3232 have been made public.  Similarly, most of the H5N1 sequences of the larger genes (PB2, PB1, PA, NP) are only partial sequences.  Those isolates, which data back to 2000 should be completed, which can be done at no charge by the NIAID sequencing program.

In addition, the vast majority of the Qinghai sequences from Europe have not been released.  Although Weybridge presented phylogenetic trees on approximately 80 isolates, only 6 have been made public even though some samples were collected over a year ago. 

Similarly, only 4 of the 8 genes from H5 isolates in Canada have been released from the samples collected in August 2005.  No sequences from this year isolated by the United State or Canada have been released. 

In addition, 2005 and 2006 bird isolates collected in China have also been withheld including a large series from Qinghai Lake in the summer of 2005 as well as the many outbreaks in Chain reported in 2005 and 2006.  A description of these isolates indicates many are also the Fujian strain, but additional strains, which likely include the Qinghai strain have also been described.
The latest data show that H5N1 continues to rapidly evolve and a full dataset is required to address both the evolution of H5N1 as well as match failures in Indonesia.  An increased surveillance and release of hoarded sequences is long overdue.

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