As we come into the fall season, Swine flu is back in the news again. Although it may have disappeared from the public in the last several months, those who have been dealing with the sequencing and functional relationships of the swine flu genome and genes have not.

NCBI GenBank has been designated as the international repository for Swine Flu (H1N1) sequence and related clinical information. In a tight cooperation between the CDC nationally and the WHO internationally, NCBI has been uploading genome and gene sequence and related information for each separately identified clinical isolate in “real-time” . To enable ready retrieval of the sequence data by those not familiar with the nuances of searching and retrieving biosequence data, NCBI has created a new set of access and retrieval tools.  The tight cooperation between the CDC and WHO to make H1N1 sequence data immediately available has been complemented by the rapid publication of  H1N1 influenza research articles by  journals such as The New England Journal of Medicine and Science.  The result has been an unprecedented publication of data, information, and tools related to manipulating the H1N1 genome and its sequences.  NCBI currently archives >19,400 H1N1 DNA sequences, almost 25,000 protein sequences of  the H1N1 genome.  Protein and domain structures are being added regularly. Truly translating between first the bed to the bench and then back again, the result has been the rapid advancement of vaccine and diagnostics R&D.  Below is a short list of highlighted swine flu bioinformatics resources, including diagnostic sequence and gene primer set  information. As we come into the flu season, the UB Health Sciences Library will update this posting as needed.

NCBI Resources

1: The WHO-designated 2009 Pandemic H1N1 diagnostic gene set.

The WHO has identified eight segments of the earliest H1N1 California isolate as diagnostic for the new H1N1 strain. They have been given NCBI GenBank accession numbers FJ966079-FJ966086.

• To download the entire set of 8 records, go to NCBI Nucleotide and copy/paste the following into the query box to run the search: FJ966079:FJ966086[Accession]
• To match the name of a diagnostic gene to its corresponding accession number, download the WHO Viral gene sequences to assist update diagnostics for influenza A (H1N1)_GenBank Accession PDF document. (Clicking on this link will launch the PDF download immediately). You can then run a search for a specific set of diagnostic gene sequences by ORing the necessary accession numbers together in the NCBI Nucleotide search box in the following format: FJ966079 OR FJ966084.

2: The NCBI H1N1 2009 Pandemic GenBank Resource web page is a component of NCBI’s much larger Influenza Viral Resource.  From the H1N1 Pandemic GenBank resource you can:

• Access the GenBank record for any of the 2009 Pandemic isolates uploaded to NCBI. For each isolate, you can open the record of any of the 8 diagnostic genes if they are available. Make sure you click on the at the bottom of the web page to fully open ALL available records, not just the most recent ones.
• BLAST your sequence against all influenza sequences, or check only the Influenza A box at the bottom of the web page to BLAST only against H1N1 sequences.
• An Advanced Query Builder has just been released that includes such features as restricting searches to a specific host, diagnostic gene set or geographical region. See the tutorial for instructions.

3. The NCBI Index of H1N1 and its various isolates

NCBI collates all information on organisms into its central Taxonomy Browser,  including for the H1N1 influenza virus. Click on the link of the desired isolate to open its specific webpage at the Index, or click on the H1N1 subtype link to view all the records of H1N1 at NCBI. In the upper right-hand corner of each webpage will be a table with links to each isolate’s nucleotide and protein records. If you choose the H1N1 subtype index, table includes links specifically to DNA, protein, structure, domain, PubMed Central publications and more. The information available here is contextual. What links exist are determined by what records are available for each isolate and will change over time.

PCR and Priming Protocols and Related Information

• CDC protocol of realtime RTPCR for influenza A (H1N1)
• WHO swine genome sequencing primer sets and protocols
• Instruction on obtaining CDC’s realtime PCR (RT_PCR) diagnostic kits for detecting Swine Flu
• Gene sequences of the reassortant candidate vaccine viruses for the novel influenza A (H1N1)
• Influenza A Virus Primer Sets from the J. Craig Venter Institute
  • This resource contains the primer sets for various Influenza A strains and their clinical isolates. Scroll to locate either the human or swine H1N1 primer sets.  They will download as an Excel file to your hard drive.

Additional H1N1 Resources:

H1N1 Structural Protein Structure Model Database at the Riken National Institute of Japan contains a summary of the predicted 3D structures of novel influenza (swine-origin influenza A/H1N1) proteins. These proteins are necessary for virus proliferation, and make ideal targets for the development of anti-influenza drugs. It also contains a summary of the amino acid differences between the swine flu proteins and those in the Protein Databank which are generated by RPS-BLAST. The origin of the sequence data for modeling is from NCBI which is updated daily by Riken if needed. You can view and compare all these data from each novel H1N1 gene of any clinical isolate simultaneously on the same web page.

NIAID Influenza Research Database (IRD) is an integrated resource for the analysis and visualization of influenza viral proteins, genes and strains. The resource contains several types of viral search and analysis tools including mutation analysis, phenotype, protein structure and surveillance data searches. IRD has built-in H1N1 to its search and visualization resources. Just make sure to specify the H1N1 viral subtype if the option is available. A tutorial is also available. (Clicking on this link will launch the PDF download immediately).

Tags: EBI, NCBI, PCR primers, Swine flu, WHO

This entry was posted on Tuesday, September 15th, 2009 at 3:43 pm and is filed under News. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.