H5N1 Sequences in India and Bangladesh
Recombinomics Commentary 07:51
February 5, 2008
Bangladesh has refused to share the genetic details of its H5N1 bird flu virus with India. In a blow to India's efforts to find the origin of the highly pathogenic avian influenza strain that is presently wreaking havoc in West Bengal, Bangladesh has informed the external affairs ministry that they are "yet to genetically sequence the H5N1 virus strain circulating there".
"We know for a fact that Bangladesh completed genetic sequencing of its virus as early as in mid-2007. The OIE Reference Laboratory for Avian Influenza in Weybridge, UK, has completed the sequencing. The lab officials can't divulge the details till Bangladesh agrees to share the information."
Although release of recent sequences from India and Bangladesh will be useful, it is likely that both sets of sequences will be similar. Moreover, it is also likely that the H5N1 currently in circulation in both countries will be more complex than earlier isolates.
Sequences from Pakistan have just been released. The sequences were from 2006 and 2007 isolates and were most closely related to 2006 sequences from Afghanistan. All of the above were clade 2.2.3 and it is likely that H5N1 currently in Pakistan, India, and Bangladesh are also clade 2.2.3.
These sequences are transported and transmitted by wild birds, and sequences from samples that are geographically close are likely to also be genetically closely related.
In the Pakistan sequences, the 2006 sequences were virtually identical to 2006 sequences from Afghanistan isolates from the same geographic region. As was seen in Egypt, sequences from the following season were similar to earlier isolates, but more complex. Therefore it is likely that the H5N1 sequences from the current season are more complex than sequences from early 2007.
The same relationship was seen in a recently released sequence from France, A/mute swan/France/06299/2006. It was collected in 2006 and closely related to 2006 sequences from southern Germany or Switzerland. In Egypt, the 2006 sequences were closely related to sequences from Djibouti, Israel and Gaza. Similarly, 2006 sequences from northern Germany are closely related to sequences from Denmark, Sweden, and Scotland. In the European examples above, the sequences were from wild birds, and not linked to trade.
The hoarding of sequences is not new. Weybridge still has not released 2005 H5n1 sequences from Europe. They say there are restrictions from the country of origin, while the country of origin claims there are restrictions by Weybridge. Sequences from earlier outbreaks involving free range turkeys from last year also haven’t been released. These sequences are useful for determining the movement of H5n1 polymorphisms by wild birds. The contribution of trade to these movements is minimal because most sequences are from wild birds.
Thus, sequence data from recent outbreaks in India and Bangladesh will be useful, but the sequences from the two countries will be very similar.
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