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United States Department of Agriculture

Agricultural Research Service

Research Project: USDA Swine Influenza Virus Surveillance System: Computational Evolutionary Biology of Whole Genome Sequences
2012 Annual Report


1a.Objectives (from AD-416):
To conduct computational evolutionary sequence analysis in the context of contemporary and historical SIV for determination of phylogenetic relationships, lineages, and reassortment events.


1b.Approach (from AD-416):
The USDA SIV Surveillance System was initiated in 2009 and roughly 150 SIV isolates have entered into the system. Currently, 3 gene segments (HA, NA, and M) are being sequenced routinely by participating NAHLN laboratories and the sequences submitted to the GenBank database. There has not been a systematic approach for analyzing and reporting summarized results of the sequencing efforts on a single gene or whole virus genome level. This is a gap in providing a useful output from the surveillance system for determination of significant virus evolution and identification of viruses of interest. Additionally, NVSL will conduct whole virus sequencing on approximately 400 viruses currently in the SIV repository using the Illumina-based approach developed at St. Jude Children’s Research Hospital and adapted at NADC. NADC will be instrumental in transferring this technique to NVSL for use at the ISU Sequencing and Synthesis core facility. Preliminary data generated from the Illumina sequencing run will be initially assessed and assembled at NADC with subsequent transfer of the bioinformatics methods developed by the NADC to APHIS-VS personnel. ARS will then perform a computational evolutionary biology analysis where the fully assembled sequences are analyzed in the context of contemporary and historical SIV for determination of phylogenetic relationships, lineages, and reassortment. To conduct large scale sequences analyses and subsequent quarterly analyses, a dedicated temporary scientist must be hired who has skills in sequence analysis as well as an understanding of influenza biology and ecology in the swine host. The results will be shared with APHIS-VS NVSL and NSU staff for reporting purposes as well as appropriate GenBank sequence deposition and peer-reviewed publication. The temporary scientist will interact and liaise with NVSL staff to transfer knowledge and skills as appropriate and with NADC scientific staff for associated in vitro and in vivo study of select SIV isolates.


3.Progress Report:

This project was established to share protocols and facilitate the sequencing of approximately 500 viruses from the USDA swine influenza virus (SIV) surveillance system using the Illumina pipeline. The sequence run was successfully completed and the raw sequence data transferred to NADC. The sequences are currently being assembled and assessed for quality by the NADC bioinformaticist. The final genome annotation, submission to GenBank, and phylogenetic analyses will be completed by the post doc funded by this agreement.


Last Modified: 7/30/2014
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