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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Research Project #431795

Research Project: USDA Swine Influenza Virus Surveillance System: Computational Evolutionary Biology of Whole Genome Sequences - Continuation

Location: Virus and Prion Research

Project Number: 5030-32000-120-13-I
Project Type: Interagency Reimbursable Agreement

Start Date: Sep 23, 2016
End Date: Sep 30, 2020

Objective:
The USDA Influenza A Virus Swine (IAV-S) Surveillance System was initiated in 2009 and over 3500 isolates have entered into the system. A systematic approach for analyzing and reporting summarized results of the sequencing efforts on a single gene or whole virus genome level has been established and continues at the National Animal Disease Center (NADC), ARS. A continuation of these analyses will provide useful output from the surveillance system for determination of significant virus evolution and identification of viruses of interest.

Approach:
ARS will perform computational evolutionary biology analyses where the fully assembled sequences are analyzed in the context of contemporary and historical swine influenza virus (SIV) for determination of phylogenetic relationships, lineages, and reassortment. From the HA and NA gene analyses, a randomized selection of HA and NA subtype- and clade-stratified isolates will be identified for whole genome sequencing by the cooperator. Unusual or unique findings (such as subtype changes or novel gene constellations) during sequence analysis will be communicated to Cooperator as warranted as soon as possible and before communication to external stakeholders. ARS will coordinate GenBank deposits with Cooperator prior to depositing sequence to insure no dual entry of sequence from National Animal Health Laboratory Network (NAHLN), the Cooperator or other entities.