H5N1 Fujian Qinghai Recombinant in Romania
Recombinomics Commentary
November 4, 2006
Romania has released a partial sequence of a duck isolate from 2005, A/duck/Romania/2005(H5N1). Like the vast majority of HA sequences from H5N1 in Europe in 2005 and 2006, it has the common cleavage site of GERRRKKR. However, the first 60 BP do not match any other Qinghai isolate, but does match 2005 and 2006 Fujian bird isolates from a number of provinces in China as well as Fujian isolates outside of mainland China. These sequence are also found in the human isolates from China, again show recombination between Qinghai and Fujian sequences.
The number of sequences released from H5N1 isolates in Europe has been limited, by phylogenetic trees of the isolates sent to Weybridge indicate they are all the Qinghai strain. However, a number of isolates from Romania for a separate branch and it seems likely that the newly released sequence falls on this branch (see tree). Although many of the samples were collected in 2005 and early 2006, Weybridge continues to hoard the sequences. Thus far, from 80 sequences on the tree, only one has been released.
Recently WHO has complained about China hoarding sequences. However, WHO maintains a private database at Los Alamos which are password protected. In August the government of Indonesia requested that the sequences from Indonesian patients be released, and the sequences were available at Los Alamos as soon as the password protection was removed.
The sequences released by Weybridge (one turkey and five patients) were released by simply removing the password protection. Clearly, the sequences currently be hoarded could just as easily be released. The Fujian / Qinghai recombinant released from Romania was the second sequence from Romania. Recently sequences from Slovenia and Slovakia were released. Previously, sequences from Italy, France, Germany, Denmark, Czech Republic and Croatia were released, so it seems that the European sequence hoarded by Weybridge are being password protected at the WHO database solely for publication reasons.
Similarly, the China sequences released by Hong Kong / St Jude in association with this weeks PNAS paper included 404 HA sequences. However, only 152 PB2 sequences were released and no sequences were released for the other 6 gene segments even though the MP sequences had to have been generated to describe which sequences were and were not sensitive to Amantadine.
Thus, although China should release full sequence for bird and human H5N1 from 2005 and 2006, the complaint by WHO lacks validation because it is hoarding more sequences than China.
The time for release of the hoarded sequences, and completion of the partial sequences already released is long past due. WHO and China should released the hoarded sequences immediately, which in many instances involves a simple removal of the password protection on the WHO private H5N1 database.
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Phylogenetic Trees