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Pandemic Unpreparedness - No 2005 H5N1 GenBank Sequences

Recombinomics Commentary
May 17, 2005
>>  Many influenza experts have issued grave warnings of an imminent pandemic. The hope inherent in all planning for a pandemic is that if we are able to detect a pandemic early in its course, we may be able to undertake necessary preparations in both prevention and medical care. This will not be possible without comprehensive and reliable surveillance.  <<

The above closing to the Clinician's Biosecurity Network commentary entitled "Avian Influenza: Inadequate Surveillance Undermines Pandemic Preparedness" emphasizes the realization that the poor surveillance of H5N1 and other influenza can have serious consequences.

The recent Nature report on lack of H5N1 sharing pointed out the fact that the number of 2005 H5N1sequences at WHO is remarkably low.  Although WHO attributed this to a poor yield in isolating virus, that explanation is just the tip of the scandalously poor surveillance by WHO and affected countries.

Reports on false negatives in both southern and northern Vietnam have generated a serious undercount in human cases. The cited examples suggest that almost 80% of the H5N1 cases in the south have been missed,  Since the north has reported milder cases, it seems likely that the number of missed cases in the north may be markedly higher.

The north has yet to report results from H5N1 outbreaks in Quang Binh, Haiphong, and Quang Ninh.  Media reports indicated 1000 samples had been collected and some or all were being sent to the CDC in mid April, yet no results have been announced.

In marked contrast to 2004, there are no 2005 H5N1 sequences at Genbank.  At this time last year there were 65 isolates and 139 gene sequences from 2004 H5N1 isolates.  The number of publicly available sequences by the end of May totaled 111 from 60 isolates.  As of today there are zero 2005 sequences available at GenBank.  The number of 2004 sequences currently available has grown to 610 from 156 isolates throughout eastern Asia, yet there are no 2005 H5N1 sequences publicly available.

The rich database of 2004 isolates allows for rapid analysis of new 2005 H5N1 sequneces, yet WHO is looking for reassortment with human genes, which has never been reported for H5N1 in spite of 4 distinct human outbreaks in 1997, 2003, 2004, 2005.  WHO still believes the evolving H5N1 genetic changes are from random mutations instead of elegant evolution via recombination.

2005 H5N1 infections in Vietnam, Cambodia, Thailand, and Indonesia have all been acknowledged.

If sharing isn't a problem, then why no sequences at GenBank?

Pandemic unpreparedness is becoming increasingly obvious.

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