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      Novel Avian Influenza H7N3 Strain Outbreak, British Columbia

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          Abstract

          Genome sequences of chicken (low pathogenic avian influenza [LPAI] and highly pathogenic avian influenza [HPAI]) and human isolates from a 2004 outbreak of H7N3 avian influenza in Canada showed a novel insertion in the HA0 cleavage site of the human and HPAI isolate. This insertion likely occurred by recombination between the hemagglutination and matrix genes in the LPAI virus.

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          Consed: a graphical tool for sequence finishing.

          D. Gordon, C Abajian, P. Green (1998)
          Sequencing of large clones or small genomes is generally done by the shotgun approach (Anderson et al. 1982). This has two phases: (1) a shotgun phase in which a number of reads are generated from random subclones and assembled into contigs, followed by (2) a directed, or finishing phase in which the assembly is inspected for correctness and for various kinds of data anomalies (such as contaminant reads, unremoved vector sequence, and chimeric or deleted reads), additional data are collected to close gaps and resolve low quality regions, and editing is performed to correct assembly or base-calling errors. Finishing is currently a bottleneck in large-scale sequencing efforts, and throughput gains will depend both on reducing the need for human intervention and making it as efficient as possible. We have developed a finishing tool, consed, which attempts to implement these principles. A distinguishing feature relative to other programs is the use of error probabilities from our programs phred and phrap as an objective criterion to guide the entire finishing process. More information is available at http:// www.genome.washington.edu/consed/consed. html.
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            Improved methods for building protein models in electron density maps and the location of errors in these models.

            T. Jones, J. Y. Zou, S Cowan … (1991)
            Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
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              Human Illness from Avian Influenza H7N3, British Columbia

              S. Aleina Tweed, Danuta M. Skowronski, Samara David … (2004)
              Avian influenza that infects poultry in close proximity to humans is a concern because of its pandemic potential. In 2004, an outbreak of highly pathogenic avian influenza H7N3 occurred in poultry in British Columbia, Canada. Surveillance identified two persons with confirmed avian influenza infection. Symptoms included conjunctivitis and mild influenzalike illness.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Emerg Infect Dis
                Journal ID (iso-abbrev): Emerging Infect. Dis
                Journal ID (publisher-id): EID
                Title: Emerging Infectious Diseases
                Publisher: Centers for Disease Control and Prevention
                ISSN (Print): 1080-6040
                ISSN (Electronic): 1080-6059
                Publication date (Print): December 2004
                Volume: 10
                Issue: 12
                Pages: 2192-2195
                Affiliations
                [* ]British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada;
                [† ]British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada;
                [‡ ]Ministry of Agriculture, Abbotsford, British Columbia, Canada;
                [§ ]Canadian Centre for Human and Animal Health, Winnipeg, Manitoba, Canada;
                []Simon Fraser University, Burnaby, British Columbia, Canada
                Author notes
                Address for correspondence: Caroline R. Astell, Genome Sciences Centre, Suite 100–570 West 7th Ave, Vancouver, B.C. V5Z 4S6, Canada; fax: 604-877-6085; castell@ 123456bcgsc.ca
                Article
                Publisher ID: 04-0743
                DOI: 10.3201/eid1012.040743
                PMC ID: 3323367
                PubMed ID: 15663859
                SO-VID: 236f22c2-05a0-496c-9a42-60d2f712f2a7
                History
                Categories
                Subject: Dispatch
                Subject: Dispatch

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: recombination,avian influenza,genomic sequence,homo sapiens,virulence
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: recombination, avian influenza, genomic sequence, homo sapiens, virulence

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