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United States Department of Agriculture

Agricultural Research Service

Research Project: USDA Swine Influenza Virus Surveillance System: in Vivo Pathogenesis and Transmission and Associated in Vitro Studies
2012 Annual Report


1a.Objectives (from AD-416):
In vitro and in vivo study of swine influenza viruses identified in the USDA Swine Influenza Virus (SIV) Surveillance System.


1b.Approach (from AD-416):
The USDA Swine Influenza Virus (SIV) Surveillance System was initiated in 2009 and roughly 600 SIV isolates have entered into the system. Currently, 3 gene segments (HA, NA, and M) are being sequenced routinely by participating National Animal Health Laboratory Network (NAHLN) laboratories and the sequences submitted to the GenBank database. Approximately 150 isolates have the 3 gene sequences deposited (December 2011). 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, the NVSL-APHIS will conduct whole virus sequencing on approximately 600 viruses currently in the SIV repository using the Illumina-based approach developed at St. Jude Children’s Research Hospital and adapted at the NADC-ARS. The NADC will be instrumental in transferring this technique to NVSL for use at the Iowa State University Sequencing and Synthesis core facility. Preliminary data generated from the Illumina sequencing run will be initially assessed and assembled at the NADC with subsequent transfer of the bioinformatics methods developed by the NADC to APHIS personnel. The NADC will then perform a computational evolutionary biology analysis in the context of contemporary and historical SIV for determination of phylogenetic relationships, lineages, and reassortment. From the sequence analysis, novel viruses will be selected for associated in vitro and in vivo study of SIV isolates. Additionally, influenza A virus isolates may be identified through public health investigations of zoonotic transmission events or from the animal health sector for unusual phenotypes or evasion of vaccine immunity. The studies funded in this interagency agreement include in vivo and in vitro pathogenesis and transmission, antigenic characterization, or vaccine protection experiments.


3.Progress Report:

This project was established to share protocols and facilitate the sequencing of approximately 500 viruses using the Illumina pipeline. The sequence run was completed and the raw sequence data transferred to NADC. The sequences are currently being assembled and assessed for quality by the NADC bioinformaticist. Select viruses identified from the sequence analyses will be evaluated further in in vitro and in vivo experiments. A number of naturally occurring H1N1pdm09 and endemic swine influenza viruses (SIV) reassortant viruses were identified in the U.S. swine population, were fully sequenced, and compared to human and swine sequences available in public databases. Novel or antigenically drifted viruses continue to be identified and used to immunize pigs for antigenic characterization. Based sequence and antigenic analysis, a vaccine study was conducted to evaluate the level of protection from a fully licensed commercial vaccine against the newly emerged H3N2 reassortant SIV.

A collaboration with the Influenza Research Database (IRD) was established and an SIV working group identified. The group will evaluate if the IRD can be used for the SIV sequences generated from the USDA SIV surveillance system as well as work with IRD to update the website with new tools specific for SIV.


Last Modified: 10/24/2014
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