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New Bird Flu Sequences Needed to Correct Mis-Matched Primers

Recombinomics Commentary

June 28, 2005

l>>  Efforts to monitor avian influenza in Asia continue to be hampered by a lack of viral sequence data from China, a World Health Organization (WHO) expert told The Scientist today (June 28). Without appropriate data, she said, it is impossible to compare Chinese virus with the strain circulating in Vietnam or to confirm the sensitivity of the PCR primers being used in China and elsewhere.

It's very important to get the sequence data for the development of diagnostic reagents and to compare it with the Vietnamese strain and [to fulfill] China's request for us to check the sensitivity of the China-made primers. Even more importantly, we need to see if the PCR primers developed by WHO, China, and other countries are sensitive enough to detect it in humans," she said.  <<

The above comments relate to technical difficulties caused by a rapidly evolving H5N1,  There have now been several reports out of Vietnam indicating false negatives were being generated by mis-matched primers.  The false negatives have led to a decrease in the number of new 2005 isolates.  There are no 2005 H5N1 sequences publicly available at GenBank.

These sequences can be used to design new primers to eliminate the false negatives generated by the primers based on the older sequences. 

As noted above, China is unsure of the sensitivity of their primers.  Thus the two patients who had bird flu symptoms after contact with the H5N1 infected birds at Qinghai Lake way be false negatives.  Similarly, earlier screening of meningitis cases in China may also be false negatives.  The bar headed geese that were H5N1 positive originated in India and there was an meningitis outbreak there that coincided in time and location with the migration of birds to Qinghai Lake.

H5N1 is known to be neurotropic.  Its ability to grow in mouse brain is a standard lab test for pathogenicity.  The number of H5N1 isolates able to grow without adaptation in mice and ability to grow in mouse brains has been on the rise.

Much greater screening of birds and people are required.  Creation of a database of H5N1 sequences in migratory birds at Qinghai Lake will also help create primers that will detect the diversity which almost certainly exists there.

Qinghai lake is at the intersection of two flyways that cover virtually all of Asia.  The intermingling of various species leads to dual infections and exchange of genetic information via reassortment and recombination.  The sequences at Qinghai lake will predict new sequences in the fall, which may fuel the pandemic growing in China, Vietnam and silently spreading throughout Asia and beyond.

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