Recombinomics | Elegant Evolution

Home Founder What's New In The News Contact Us

Paradigm Shift

Viral Evolution

Intervention Monitoring

Vaccine Screening

Vaccine Development

Expression Profiling

Drug Discovery

Custom Therapies



Qinghai H5N1 Confirmed On South Korean Farms
Recombinomics Commentary
December 15, 2006

South Korea confirmed a highly pathogenic bird flu outbreak on Nov. 25 at a poultry farm in Iksan, about 230 kilometers south of Seoul, the country's first case in three years. Two additional cases of highly virulent avian influenza were discovered Nov. 27 and earlier this week, respectively, in nearby poultry farms.

Genetic analysis of the N5H1 virus sample specimens from the first two cases showed traits similar to ones found in China's midwestern province of Qinghai.

 The above comments confirm that the recent H5N1 infections in South Korea are from the Qinghai strain of H5N1 and are due to migratory birds.  This result was expected based on genetic analysis of H5N1 from South Korea / Japan in 2003 / 2004.  The earlier isolates were closely related to each other and pieces of genetic information were found in the Qinghai strain, first reported in May 2005 at Qinghai lake.  The Qinghai strain was a recombinant composed of genetic information from high and low path H5 from eastern Asia, as well as additional genetic information found in bird and swine isolates in Europe.  The presence of then genetic information from Korea helped define a northern H5N1 migration route.

The Qinghai strain spread to Russia, Mongolia, and Kazakhstan in the summer of 2005, and then to Europe, the Middle East, and Africa in late 2005 / early 2006.  In this time frame, Russia, Mongolia, Kazakhstan, India, Afghanistan, and multiple countries in the Middle East, Europe, and Africa reported H5N1 infections for the first time, and all infections were the Qinghai strain.

In the same time frame, H5N1 was detected ion live markets throughout southern China.  The recent PNAS paper had 404 HA isolates, and most were the Fujian strain.  There was only one Qinghai isolate (in Shantou).  The paper concluded that the Fujian strain was a new wave of H5N1 infections that would displace the Qinghai strain.  However, the report failed to consider the migratory bird distribution route, which followed well defined pathways which did not include live markets in eastern China, the source of most of the H5N1 in the study..  There were no Fujian isolates in the over than  700 H5N1 positives in Europe in 2006.  The samples were exclusively the Qinghai strain.  A recent H5N1 isolate form a patient in Egypt had a number of additional changes when compare to Egyptian isolates from early 2006, but all isolates were clearly the Qinghai strain.  Similarly, spring and summer isolates of H5N1 in Afghanistan and southern Siberia were also the Qinghai strain, indicating the Fujian strain was limited to eastern and southeastern Asia, and was not a new wave that would displace the Qinghai strain.

The transmission routes are now reinforced by the discover of the Qinghai strain in South Korea.  H5N1 has been found in whooper swans in Mongolia, and tracking data shows movement of whooper swans from Mongolia to the precise location on the western South Korean coast, where the recent H5N1 infections were reported.  These swans have since migrated to the eastern coast of Korea, and infections in Japan in the upcoming weeks would not be a surprise.  This time line and location match the 2003 outbreak in December 2003 in South Korea and predict early 2007 outbreaks in Japan.

The movement of H5N1 by wild birds is firmly established.  The wild birds facilitate the transport and transmission of H5N1, which leads to genetic evolution via recombination.  This process is not new, but the increasing genetic diversity of H5N1 has led to an acceleration in the rate of H5N1 change.  This rapid change has led to 4 distinct vaccine targets because of limit cross reactivity between Clade 1 in southeast Asia, Clade 2 Sub-clade I in Indonesia, Clade 2 Sub-clade II (Qinghai strain in multiple countries west of China, and now spreading into South Korea), Clade 2 Sub-clade III (Fujian strain in China and spreading into southeast Asia).
Media sources

Phylogenetic Trees

Home | Founder | What's New | In The News | Contact Us

© 2006 Recombinomics.  All rights reserved.