Project Number: 6612-32000-051-01
Project Type: Specific Cooperative Agreement

Start Date: Sep 07, 2006
End Date: Sep 30, 2008

Objective:
SeqWright and Southeast Poultry Research Laboratory (SEPRL) wish to collaborate on a project to sequence 1000 complete genomes of Avian Influenza. SeqWright will research and develop reagents (primers) for rapid sequencing of avian influenza and will create methods for rapid annotation of the genome. SEPRL will utilize the annotated genomic information corresponding to 1000 avian influenza isolates to study epidemiology and evolution.

Approach:
SEPRL will isolate viral RNA from our collection of 1000 avian influenza viruses and the viral RNA will be sent to Seqwright. Seqwright will assign a scientist to analyze previously known avian influenza genomic sequences and to design (using primer design software) sufficient sets of primers for amplification and sequencing of all genes from all different serotypes existing in our collection. Primers will be used to generate cDNAs, and for bi-directional DNA sequencing (performed by automated ABI Prism¿ 3730xl DNA sequencers). Seqwright will score \mutations/heterozygotes/ heteroindels and will assign an expert curator to review and re-sequence (if necessary) all called mutations to confirm their accuracy. Results containing the raw data, full-length consensus text sequence, and genotype calls will be provided to SEPRL. SEPRL will review the data and analyze evolutionary and phylogenetic relationship among isolates.