Commentary
Novel
H5N1 At Qinghai Lake Nature Reserve
Recombinomics Commentary
14:50
November 27, 2008
Although H5N1 was also reported in Qinghai Province a year later, the outbreak at Uvs Lake in the summer of 2006 led to the widespread distribution of the Uvs Lake strain, a clade 2.2.3 derivative of the Qinghai strain. The Uvs Lake strain migrated to South Korea and Japan at the end of 2006 followed by the Middle East and Europe in 2007 and west Africa in 2008.
Moreover, the outbreaks in Japan, South Korea, and Russia in the spring of this year were linked to wild birds, including migratory whooper swans, which were infected with the Fujian strain (clade 2.3) of H5N1, leading to concerns of spread of the Fujian strain into the same countries affected by the Qinghai strain.
However, the H5N1 at Qinghai Lake this year ,A/environment/Qinghai/1/2008(H5N1), was not the Qinghai (clade 2.2) or Fujian (clade 2.3) strains. Instead, the H5N1 was closely related to H5N1 found in poultry and swine in northern China in 2003. Moreover, the isolate had a PB1 gene which was an exact match of low path PB1 in mallards from northern China isolated in 2006 (A/mallard/SanJiang/113/2006(H6N2)). Exact matches were also found for PB2 with A/chicken/Hubei/wn/2003(H5N1) and A/swine/Shandong/2/2003(H5N1), as well as PA with the swine sequence and NP with the chicken sequence.
Since the level of this novel H5N1 (clade 0) at Qinghai Lake and elsewhere is unknown, the potential for this strain to distribute remains unclear. The sequences which exactly match that H5N1 isolates from 2003 have not been reported in the past five years and the identity in these large internal genes suggests there has been little interaction with other H5N1 isolates. However, the HA cleavage site of RERRRKKR has appeared on an Egyptian clade 2.2 genetic background in 2008 isolates in the Nile Delta suggesting additional H5N1 may have been circulating beyond China, but has gone undetected.
Germany recently isolate H5N1 that is virtually identical to 2006 isolates in Germany, which have circulated undetected between early 2006 and late 2008, highlighting limitations in current surveillance approaches. Recently, new H5N1 outbreaks were reported in Vietnam and Thailand in southeast Asia, as well as Bangladesh and India in south Asia, which reflect H5N1 migration into the area.
Release of sequences from these outbreaks so they can be compared to the novel H5N1 isolates from the Qinghai Lake Nature Reserve would be useful.
Recombinomics Presentations
Recombinomics
Publications
Recombinomics
Paper
at Nature Precedings