GERMAN SCIENTISTS at the Institute of Diagnostic Virology have developed an improved method for processing avian bird flu samples with the Genome Sequencer FLX instrument.
The highly pathogenic avian influenza A virus (HPAIV) of subtype H5N1 has caused global concern as a potential pandemic threat, killing millions of poultry and fatally crossing over to humans in a number of documented cases.
 "One of the primary risks of an avian influenza pandemic is if the viral sequence were to mutate in ways which cause an increase in pathogenicity, or in other words an increase in the virus' ability to infect humans. Therefore, in order to understand the full biological impact of the virus and to prevent the spread of disease in the case of an outbreak, whole genome sequence information is necessary," a 454 Life Sciences spokesperson told The News. "454 sequencing delivers the speed, depth of genome coverage, and accuracy necessary for potential use in the case of a viral pandemic and to save human lives. The system's long sequencing reads (400-600 bp now, 1,000 bp soon) and quick instrument run time (10 hours) make it unique in comparison to other high-throughput sequencing systems which offer dramatically shorter reads and can take more than a week and up to 12 days to run."
Indeed, the researchers managed to sequence complete, high-quality avian influenza genomes within three days after sample receipt.
"(Scientists) believe that this method could be applied to other Avian influenza subtypes. Other research has demonstrated the ability of the system to detect low-frequency drug-resistant mutations in HIV and to accurately characterize HIV tropism. There are many potential medical sequencing applications for the 454 sequencing system," added the spokesperson.
Dirk Höper of the Institute of Diagnostic Virology explained that the new method allows for sequencing of complete HPAIV H5N1 genomes from routine samples, without virus propagation in eggs, cell culture or cloning.
"This method is simply not comparable with conventional sequencing and by far surpasses the single reads of 'diagnostic'-relevant sites of the hemagglutinin gene of avian influenza as generated in former studies," said Höper. "Our approach permits sequencing of up to eight complete viral genomes within only three days at an unprecedented depth and consequently, reliability of the sequence. The procedure has the potential to seamlessly integrate into the normal diagnostic routine."
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