As the World Health Organization (WHO) works to contain avian influenza on the ground, researchers work to find the best ammunition for the front-line fight. Two recent papers in the Jan. 26, 2006, issues of Sciencexpress and Nature shed light on influenza virus replication.

In Sciencexpress, scientists from St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, both located in Memphis, present the results of a large-scale sequencing study that pinpoints one particular motif as important for determining the mortality of a given flu strain, depending on whether it originates in people or birds.

The influenza virus consists of eight separate segments, which can recombine independently of one another in an infected animal or human host. That means that while there are influenza viruses with humans as main host and others with birds as primary host, in practice, a virus can exist that combines human and bird segments. In fact, one origin of annual flu epidemics are pigs, which can become infected with both kinds of virus and serve as a sort of mixing bowl.

The St. Jude’s team sequenced about 2,200 genes, including 170 complete genomes from different flu strains, and compared them to each other and to another 2,100 genes from the database GenBank. They found that viral surface proteins changed much more frequently than core proteins, presumably due to selective pressure, as the surface proteins are what interacts with the host.

The scientists specifically compared the sequences of the carboxy-terminus of the NS1 protein and found it contains a previously unknown binding site for PDZ motifs. PDZ motifs (the PDZ stands for the first three proteins in which they were found) are sequences that allow proteins to bind, and they serve to organize a number of cellular signalling pathways.

When the St. Jude’s team related the virulence of different flu strains to the sequence of the PDZ binding site in a given strain, they found that the high-mortality H5N1 virus has a sequence suggesting it originated in birds, while the PDZ binding site in the flu pandemics of 1957 and 1968, which were much milder than H5N1, have a human-like sequence. The 1918 pandemic flu strain had a unique PDZ binding site motif.

When they synthesized PDZ binding peptides with either avian or human motifs, the scientists found that the peptides with avian motifs bound strongly to 30 different PDZ sequences, while the human-derived peptides bound either weakly or not at all. They concluded that "disruption of [PDZ-dependent] pathways at the cellular level may well contribute to the higher mortality rates reported for the recent outbreaks compared to those seen in previous pandemics; though it is clear multiple genes and gene products are involved."

In the Nature study, scientists from the University of Wisconsin-Madison; the University of California at Davis; the University of Tokyo; the Karolinska Institutet in Stockholm, Sweden; Japan’s Science and Technology Agency; and Hokkaido University elucidated how the eight RNA segments are assembled into virus particles.

The scientists did not look at H5N1 influenza virus, but given that they found the same organizational principles in a number of viral strains, it is likely that H5N1 assembles in the same manner. And such garden-variety strains are important for public health in their own right; in fact, currently they are more important than H5N1. H5N1 infections have killed fewer than 100 people globally so far, whereas an average flu season death toll in the Unites States alone ranges from 30,000 to 50,000.

The researchers used electron microscopy to look at budding virus particles, or virions, either longitudinally or in cross-section. They found that in cross-section, the virions looked essentially like a minimalist drawing of a flower: One dot, or RNA segment, in the middle, surrounded by seven more.

The next question was whether the segments were ordered randomly, or whether they always line up in the same order. The authors used electron tomography, a technique that gives a near-molecular resolution of electron density of the virus, to further characterize the relationship of the eight segments to each other. Their results suggested that the segments assemble in a specific order, rather than randomly. How the segments lined up so specifically remains unclear, but the results suggested that disrupting the lineup might be a useful antiviral strategy.

The executive board of the WHO met at the end of January for its twice-yearly session. Director-General Lee Jong-Wok began his opening speech to the board by summarizing the significance of the recent appearance of human and bird infections with avian influenza in Turkey.

"The unique feature in the Turkey situation was the unexpected appearance of human cases of avian influenza. There was almost no prior warning of infection in poultry in the eastern part of the country," leading to the conclusion that "a pandemic could arise with little or no warning from the animal side," he said in his opening speech.

But Lee’s assessment was not all bleak; he went on to say that "this recent experience has also illustrated just how fast both governments and the international community can move in a crisis. In Turkey, within one day, patient samples were collected, shipped and received in the United Kingdom. The results were available within 24 hours. One hundred thousand treatment courses of oseltamivir were delivered one day after the first cases were confirmed."

Since Jan. 30, the WHO has confirmed a fatal human case of H5N1 infection in Iraq and outbreaks of avian influenza in poultry in Iraq and Nigeria. Iraq is the first country where a human case was reported before surveillance had indicated the presence of the virus in birds.

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