Influenza Virus Resource Debuts

Each year in the USA, more than 200,000 patients are admitted to hospitals with influenza infections, and influenza-related deaths approach 36,000. Effective vaccines can reduce the numbers of hospitalizations and deaths, and the swift identification of new flu virus variants is an essential component in the development of such vaccines. The Influenza Genome Sequencing Project, funded by The National Institute of Allergy and Infectious Diseases (NIAID), aims to rapidly sequence flu viruses from samples collected throughout the world from humans and a variety of animals.

The viral nucleotide sequences resulting from this project, available in GenBank, along with the sequences of their encoded proteins, form the supporting database for NCBI's new Influenza Virus Resource (IVR). The IVR will enable scientists to quickly compare influenza virus strains so that emergent variants can be rapidly identified. As the library of viral sequences grows, this database will act as a reference to help further our understanding of the spread of animal viruses to humans, and the spread of influenza worldwide. Access the IVR home page at:

www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

The Flu sequence database link offers an interface to the viral sequences that allows searches by virus type, subtype, host organism, genome segment and country of origin. Restrictions on year of virus isolation and sequence length may also be applied and the results of the search can be sorted, sequentially, by up to three of the search fields. Individual nucleotide or protein sequences can also be retrieved by GenBank accession number.

Similarly, the Flu genome viewer tool can display viral nucleotide or protein sequences ordered by genome segments for each virus. All segments of the same virus are grouped together in the same background color, alternating in light blue and white, providing a convenient way to check the completeness of genome segments for viruses of interest. Database searches can be performed similarily as described above, and nucleotide or protein sequences can also be searched by adding a complete or partial virus name (e.g. Influenza A virus (A/New York/19/2003(H3N2)) or New York) in the box after “Name” and selecting “Find Nucleotides” or “Find Proteins”.

Sequences of interest can be selected within the search results from either tool by checking the boxes to the left of their GenBank accession numbers. Selected sequences can be downloaded or “Saved” to be combined with results from a subsequent search. Multiple alignments of selected nucleotide or protein se-quences generated by the MUSCLE1 alignment program can also be viewed. On the multiple sequence alignment display page, any two sequences can be selected for a pairwise comparison using BLAST 2 Sequences.

For more information on the resources above, access the Help document linked from each resource’s home page:

www.ncbi.nlm.nih.gov/genomes/FLU/SiteAbout.html

Additional resources are under development, including a multiple protein alignment tool that will allow users to statistically analyze and compare sets of protein sequences of the influenza virus. Protein datasets can be visually represented and analyzed using hierarchical clustering with user-selected similarity criteria and clustering algorithms.

Links to Reference Sequences (RefSeqs) of other influenza genomes, protein structures, other protein and nucleotide sequences, and the most recent influenza virus literature in PubMed, are also available from the IVR home page.

1Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 32(5), 1792-97.