ISU FLUture
Swine Disease Reporting System
Swine Disease Detection Dashboards
Aggregate swine diagnostic data describing dynamics of pathogen detection by PCR-based assay over time, specimen, age group, and geographical area.
How to Cite
If you use data provided by ISU FLUture in your work, please credit in the following format:
Zeller, M. A., Anderson, T. K., Walia, R. R., Vincent, A. L., & Gauger, P. C. (2018). ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of Influenza A virus in swine. BMC bioinformatics, 19(1), 397.
(data retrieved 21 Nov, 2024).
Contact
By Phone
515-294-1950 (Mon-Fri, 8 am - 5 pm CST)
By Email
Megan Neveau ude.etatsai@uaevenm
Phillip Gauger DVM, PhD ude.etatsai@reguagcp
By Mail
Veterinary Diagnostic Laboratory
College of Veterinary Medicine
Iowa State University
1850 Christensen Dr
Ames, IA 50011-1134
Changelog
Variables
The ISU FLUture database curates information related to the individual swine cases. An explanation of each of the variables that ISU FLUture allows searching for can be found below.
Age
The age of the pig at the time the flu positive sample was collected.
- Neonate: 0-5 days
- Suckling: 5-21 days
- Nursery: 3 – 10/11 weeks
- Grow/Finish: 10/11 – 26 weeks
- Adult: > 26 weeks
Bacterial culture results from submitted samples of influenza positive cases. Majority of samples are lung tissue.
Data Source
The stream that handled sequencing of the sample. Samples with cycle threshold (CT) values ≤ 25 for lung and nasal swab and ≤ 20 for oral fluid are routed through the USDA traceable or anonymous stream. Samples with CT values ≤ 38 are processed by the ISU VDL stream. Samples with CT values above 38 are considered negative.
Day
The day of the year that the flu positive sample was collected.
HA Clade
The phylogenetic clade of a corresponding hemagglutinin sequence. Currently, the ISU FLUture database tracks only H1 and H3 subtype hemagglutinin, thus clades will be derived from one of these subtypes.
HA Sequence
The genetic sequence of the hemagglutinin gene of a specific influenza virus by case. Sequencing restricted to samples with cycle threshold (CT) values ≤ 38.
Month
The month of the year that the flu positive sample was collected.
NA Clade
The phylogenetic clade of a corresponding neuraminidase. Currently, the ISU FLUture database tracks only N1 and N2 subtype neuraminidase, thus clades will be derived from one of these subtypes. Only samples with cycle threshold (CT) values ≤ 25 are sequenced, and applicable for this type of data.
PCR Specimen
The specimen from which the subtyping RT-PCR was derived.
Sequence Specimen
The specimen used to attempt sequencing.
