Biodetection of low pathogenic avian influenza virus (LPAIV) infected mallards data set

Metadata:

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

Below you will find a list and description of the files available in this data publication.

DATA FILES (5)
Blue text is used to help denote columns that contain formulas. Also note there is summary information in the final rows/columns of these files.

1) \Data\2_LPAI_viral_shed_and_ferret_response_PLOS.xlsx: Microsoft Excel Open XML spreadsheet file containing the results from the accuracy of the ferrets' response during training and testing to familiar fecal samples containing live LPAIV. Also included is viral shed timeline.

This file contains 4 worksheets, which are described below.

Worksheet 1 - 'Variable Descriptions' contains a list and description of the variables provided in this data file.
Variables include:
Worksheet Name = name of worksheet
Variable Name = name of variable
Variable Description = description of variable

Worksheet 2 - 'Viral Shedding Summary' contains means of the calibrated qPCR results of fecal samples from ducks inoculated with LPAIV across sample collection days.
Variables include:
1-14 = day after infection the sample was collected
Average = mean of viral shedding for all dosages on a specific collection day after infection
* See Golden et al. (2021) for more specifics on these data.

Worksheet 3 - 'Accuracy based on CD' (CD = collection data) contains accuracy of ferrets during training and testing.
Variables include:
A.I.D. = animal identification number
Date = date of training or testing
Blind = double-blind status (trial run with handler and ferret blind to location of CS+)
Trials = trial number (1-12)
Reward = rewarded trial or non-rewarded trial (generalization)
Position = location of the fecal sample collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
CS-_1 = first fecal sample from noninfected duck location
CS-_2 = second fecal sample from noninfected duck location
CS-_3 = third fecal sample from noninfected duck location
CS-_4 = fourth fecal sample from noninfected duck location
CS+ = Identification of the infected duck that provided sample
Donor = animal identification number for the duck supplying fecal sample in the CS+ box of the sample
CD = day pre or post infection that the sample was collected
Hit = a correct choice by scratch alert on the box containing the CS+
Miss = a incorrect choice by scratch alert on the box containing any CS-
Choice = the fecal sample in the box chosen incorrectly
Alert = position of box ferret scratched at whether correctly or incorrectly
Result = denotes hit or miss
Identity = animal identification number for the duck supplying fecal sample
Day = denotes day the fecal sample was collected

Worksheet 4 - 'Shed and % 0-14' contains a figure (and data) showing virus shedding (red line) imposed over ferret accuracy (grey bars).
Variables include:
Day = day of collection
Shed = viral shed
% Correct = accuracy of ferrets
SEM = standard error of the mean
* Also included is a graphic displaying the results.


2) \Data\3_Ferret_AI_10^4_testing_stats.xlsx: Microsoft Excel Open XML spreadsheet file containing the results from the accuracy of the ferrets' response during testing to novel fecal samples containing live LPAIV with a novel viral dose.

This file contains 2 worksheets, which are described below.

Worksheet 1 - 'Variable Descriptions' contains a list and description of the variables provided in this data file.
Variables include:
Worksheet Name = name of worksheet
Variable Name = name of variable
Variable Description = description of variable

Worksheet 2 - 'LPAI 10^4 Test adj 4 days'
Variables include:
A.I.D. = animal identification number
Date = date of training or testing
Blind = double-blind status (trial run with handler and ferret blind to location of CS+)
Trials = trial number (1-12)
Reward = rewarded trial or non-rewarded trial (generalization)
Position = location of the fecal sample collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
CS-_1 = first fecal sample from noninfected duck location
CS-_2 = second fecal sample from noninfected duck location
CS-_3 = third fecal sample from noninfected duck location
CS-_4 = fourth fecal sample from noninfected duck location
CS+ = Identification of the infected duck that provided sample
Donor = animal identification number for the duck supplying fecal sample in the CS+ box of the sample
CD = day pre or post infection that the sample was collected
Hit = a correct choice by scratch alert on the box containing the CS+
Miss = a incorrect choice by scratch alert on the box containing any CS-
Choice = the fecal sample in the box chosen incorrectly
Alert = position of box ferret scratched at whether correctly or incorrectly
Result = denotes hit or miss
Identity = animal identification number for the duck supplying fecal sample
Day = denotes day the fecal sample was collected


3) \Data\4_Ferret_AI_collection_day_test_stats.xlsx: Microsoft Excel Open XML spreadsheet file containing the results from the accuracy of the ferrets' response during testing to novel and familiar fecal samples in a panel that had four of the five samples collected all on the same collection day and one sample that was collected on a different day.

This file contains 3 worksheets, which are described below.

Worksheet 1 - 'Variable Descriptions' contains a list and description of the variables provided in this data file.
Variables include:
Worksheet Name = name of worksheet
Variable Name = name of variable
Variable Description = description of variable

Worksheet 2 - 'Collection Day Test': To determine if the time since infection was utilized in making a correct choice in lieu of infection odor identity, we challenged the ferrets by offering a panel where one CS- sample was from a different collection day in comparison to the remainder of the panel.
Variables include:
A.I.D. = animal identification number
Date = date of training or testing
Blind = double-blind status (trial run with handler and ferret blind to location of CS+)
Trials = trial number (1-12)
Reward = rewarded trial or non-rewarded trial (generalization)
Position = location of the fecal sample collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
CS-_1 = first fecal sample from noninfected duck location
CS-_2 = second fecal sample from noninfected duck location
CS-_3 = third fecal sample from noninfected duck location
CS-_4 = fourth fecal sample from noninfected duck location
CS+ = Identification of the infected duck that provided sample
Donor = animal identification number for the duck supplying fecal sample in the CS+ box of the sample
CD = day pre or post infection that the sample was collected
Hit = a correct choice by scratch alert on the box containing the CS+
Miss = a incorrect choice by scratch alert on the box containing any CS-
Choice = the fecal sample in the box chosen incorrectly
Alert = position of box ferret scratched at whether correctly or incorrectly
Result = denotes hit or miss
Identity = animal identification number for the duck supplying fecal sample
Day = denotes day the fecal sample was collected

Worksheet 3 - 'Two CS+ Panel': To determine if the time since infection was utilized in making a correct choice in lieu of infection odor identity, we challenged the ferrets by offering a panel where there were two potentially correct choices, but only one of the two choices represented an odd collection date.
Variables include:
A.I.D. = animal identification number
Date = date of training or testing
Blind = double-blind status (trial run with handler and ferret blind to location of CS+)
Trials = trial number (1-12)
Reward = rewarded trial or non-rewarded trial (generalization)
Position 1 = location of the fecal sample collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
Position 2 = location of the 2nd fecal sample (if applicable) collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
CS-_1 = first fecal sample from noninfected duck location
CS-_2 = second fecal sample from noninfected duck location
CS-_3 = third fecal sample from noninfected duck location
CS+ 2 = Identification of the infected duck that provided sample
CS+ 1 = Identification of the infected duck that provided sample
Donor = animal identification number for the duck supplying fecal sample in the CS+ box of the sample
CD = day pre or post infection that the sample was collected
Hit = a correct choice by scratch alert on the box containing the CS+
Miss = a incorrect choice by scratch alert on the box containing any CS-
Choice = the fecal sample in the box chosen incorrectly
Alert = position of box ferret scratched at whether correctly or incorrectly
Result = denotes hit or miss
Identity = animal identification number for the duck supplying fecal sample
Day = denotes day the fecal sample was collected


4) \Data\5a_Ferret_AI_CSU_sample_test_stats.xlsx: Microsoft Excel Open XML spreadsheet file containing the results from the accuracy of the ferrets' response during testing to novel fecal samples collected from a different cohort of ducks raised in a different environment and fed a different diet.

This file contains 2 worksheets, which are described below.

Worksheet 1 - 'Variable Descriptions' contains a list and description of the variables provided in this data file.
Variables include:
Worksheet Name = name of worksheet
Variable Name = name of variable
Variable Description = description of variable

Worksheet 2 - 'LPAI Cohort 2 sample test'
Variables include:
A.I.D. = animal identification number
Date = date of training or testing
Blind = double-blind status (trial run with handler and ferret blind to location of CS+)
Trials = trial number (1-12)
Reward = rewarded trial or non-rewarded trial (generalization)
Position = location of the fecal sample collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
CS-_1 = first fecal sample from noninfected duck location
CS-_2 = second fecal sample from noninfected duck location
CS-_3 = third fecal sample from noninfected duck location
CS-_4 = fourth fecal sample from noninfected duck location
CS+ = Identification of the infected duck that provided sample
Donor = animal identification number for the duck supplying fecal sample in the CS+ box of the sample
CD = day pre or post infection that the sample was collected
Hit = a correct choice by scratch alert on the box containing the CS+
Miss = a incorrect choice by scratch alert on the box containing any CS-
Choice = the fecal sample in the box chosen incorrectly
Alert = position of box ferret scratched at whether correctly or incorrectly
Result = denotes hit or miss
Identity = animal identification number for the duck supplying fecal sample
Day = denotes day the fecal sample was collected


5) \Data\5b_Ferret_LPAI_specificity_test_stats.xlsx: Microsoft Excel Open XML spreadsheet file containing the results from the accuracy of the ferrets' response during testing to novel fecal samples including samples from ducks infected with alternate pathogens suggest to determine if the odor cue used by ferrets to detect avian influenza is specific to AIV infection and is not a general immune response resulting from infection.

This file contains 3 worksheets, which are described below.

Worksheet 1 - 'Variable Descriptions' contains a list and description of the variables provided in this data file.
Variables include:
Worksheet Name = name of worksheet
Variable Name = name of variable
Variable Description = description of variable

Worksheet 2 - 'Specificity Test': To determine if ferrets identified the location of the single sample derived from an infected donor based on a pathogen specific infection odor, ferrets trained to detect an odor representative of LPAIV infection were tested with a panel that included fecal samples negative for LPAIV infection but collected from ducks infected with Newcastle's Disease Virus and/or infectious laryngotracheitis in addition to non-infected controls.
Variables include:
A.I.D. = animal identification number
Date = date of training or testing
Blind = double-blind status (trial run with handler and ferret blind to location of CS+)
Trials = trial number (1-12)
Reward = rewarded trial or non-rewarded trial (generalization)
Position = location of the fecal sample collected from ducks confirmed by PCR to contain avian influenza virus (confirmed positive)
CS-_1 = first fecal sample from noninfected, Newcastles disease virus infected-, or infectious laryngotracheitis infected duck location
CS-_2 = second fecal sample from noninfected duck location
CS-_3 = third fecal sample from noninfected duck location
CS-_4 = fourth fecal sample from noninfected duck location
CS+ = Identification of the infected duck that provided sample
Donor = animal identification number for the duck supplying fecal sample in the CS+ box of the sample
CD = day pre or post infection that the sample was collected
Hit = a correct choice by scratch alert on the box containing the CS+
Miss = a incorrect choice by scratch alert on the box containing any CS-
Choice = the fecal sample in the box chosen incorrectly
Alert = position of box ferret scratched at whether correctly or incorrectly
Result = denotes hit or miss
Identity = animal identification number for the duck supplying fecal sample
Day = denotes day the fecal sample was collected

Worksheet 3 - 'Positive sample key' contains a color-coded key that explains how testing (generalization) trials were structured.
Five panels (the five boxes in each trial), which include:
1 fecal sample from non-infected cohort 1 duck
1 fecal sample from non-infected cohort 2 duck
1 fecal sample from infectious laryngotracheitis virus infected cohort 2 duck
1 fecal sample from Newcastles disease virus infected cohort 2 duck
1 fecal sample from avian influenza virus infected cohort 2 duck

Entity_and_Attribute_Detail_Citation:

Golden, Glen J.; Grady, Meredith J.; McLean, Hailey E.; Shriner, Susan A.; Hartwig, Airn; Bowen, Richard A.; Kimball, Bruce A. 2021. Biodetection of a specific odor signature in mallard feces associated with infection by low pathogenic avian influenza A virus. PLOS One 16(5): e0251841. https://doi.org/10.1371/journal.pone.0251841

Metadata_Reference_Information:

Metadata_Date: 20210527

Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Glen J. Golden

Contact_Organization: Colorado State University ; USDA, APHIS, Wildlife Service, National Wildlife Research Center

Contact_Position: Research Scientist

Contact_Address:

Address_Type: mailing and physical

Address: Colorado State University

Address: 1683 Campus Delivery

City: Fort Collins

State_or_Province: CO

Postal_Code: 80523-1683

Country: USA

Contact_Voice_Telephone: 970-266-6082

Contact_Electronic_Mail_Address: glen.golden@colostate.edu

Metadata_Standard_Name: FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001.1-1999