Commentary
H5N1
Sequences Migrate Into India
Recombinomics Commentary
12:11
December 4, 2008
More detailed genomic analysis will show where this recent Assam HPAI strain is most likely from. - Mod.MHJ]
The above comments on the Assam outbreak and sequences are curious. Sequence analysis strongly points toward a migratory bird origin, as noted by officials in India. The comments from India are based on sequence analysis of early outbreaks in India and neighboring Bangladesh.
Sequences from outbreaks in the 2005/2006 season have been made public and all sequences west of China, including sequences from India are clade 2.2, the Qinghai strain isolated at the Qinghai Lake Nature Reserve in the spring of 2005. One sub-clade, 2.2.3 was found in south Asia (India and Afghanistan), and regions adjacent to the Caspian Sea (in Russia and Iran) as well as one isolate from Italy.
More recently 2006/2007 sequences have been published from Pakistan, which were also clade 2.2.3, and the cleavage site of sequences from the 2007 outbreak in Bangladesh were also clade 2.2. Similarly, the sequences from the outbreaks in West Bengal and Bangladesh a year ago were also described as the Qinghai strain. Thus, all sequence analysis to date supports a wild bird origin for these outbreaks.
An extensive sequence analysis could be used to prove or disprove movement from one farm to the next. Sequence evidence for such trade-related movement is limited. The best example was found in 2007 outbreaks in Hungary and England which were virtually identical (99.96%), but this outbreak was the exception. Analysis of other sequences demonstrates near identity between multiple isolates from the same outbreak, but comparisons with other outbreaks, even when collections are close in time and space, are distinct, demonstrating independent introductions.
These independent introductions were demonstrated once again by sequences recently released fro 2007/2008 outbreaks in Europe. These sequences involve clade 2.2.3 isolates that grew out of another large scale die off of migratory birds. The outbreak was in the summer of 2006 at Uvs Lake in Mongolia and lead to sequences that were related to the earlier 2006 sequences, but distinct. These Uvs Lake sequences were subsequently detected in South Korea and Japan at the end of 2007, followed by Kuwait at the beginning of 2007.
The sequences then unexpected appeared in the Czech Republic, Germany, and France in the summer of 2007. Although all sequences were the Uvs Lake strain, each outbreak represented an independent introduction. Those outbreaks were followed by additional outbreaks in the fall of 2007 and beginning of 2008 in the Middle East and Europe and several of these sequences were recently released. The Uvs Lake sequences in Europe fall onto two branches. One branch has sequences from Krasnodar and three of the isolates from Germany. The other branch has sequences from Romania, the Czech Republic, Germany, and the two outbreaks in England (free range turkeys at the end of 2007 and swans at the beginning of 2008). Sequences from the same outbreak are identical (a chicken and swan isolate from Krasnodar or a chicken, turkey and cat sequence from Romania). However, sequences from separate outbreaks, such as the four in Germany in the summer of 2007, are readily distinguishable from each other.
Thus, sequences from Assam are likely to be related to recent sequences from Bangladesh, but the sequences are also likely to be distinct enough to once again demonstrate independent introductions.
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