The structure and genome of influenza virus

Viruses which share a common ancestor can also be described as belonging to the same clade. The degree of genetic difference number of nucleotide differences between viruses is represented by the length of the horizontal lines branches in the phylogenetic tree. The further apart viruses are on the horizontal axis of a phylogenetic tree, the more genetically different the viruses are to one another. Phylogenetic trees of influenza viruses will usually display how similar sequences of the nucleotides for hemagglutinin HA genes of the vaccine virus and circulating viruses are to each other.

As part of this process, CDC compares the new virus sequence with the other virus sequences and looks for differences among them. CDC then uses a phylogenetic tree to visually represent how genetically similar the A H3N2 viruses are to each other. In Figure 1, virus b is more genetically similar to virus c than d. Viruses b and c share a common ancestor and the total length of the horizontal branches is short.

CDC performs genetic characterization of influenza viruses year-round. The analysis and selection are made twice each year to recommend vaccine viruses for both the Northern Hemisphere and Southern Hemisphere. In the months leading up to the WHO-facilitated vaccine consultation meetings , where the recommendations are made, CDC collects influenza viruses through surveillance and compares the HA and NA gene sequences of current vaccine viruses against those of circulating flu viruses.

This is one of the ways CDC assesses how closely related the circulating influenza viruses are to the viruses the seasonal flu vaccine was formulated to protect against.

Many other data, including antigenic characterization findings and human serology data , shape the vaccine selection decisions. One influenza sample contains many influenza virus particles that were grown in a test tube and that often have small genetic differences in comparison to one another among the whole population of sibling viruses.

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Kenyon, J. Aw, and Y. Wan for sharing protocols, J. Robertson for making the 1M7 reagent, J. This work was supported by a Wellcome Trust studentship no. ID to L.