?This directory contains data associated with the manuscript:
PONE-D-17-20276R1
Pathogenesis of Oral FIV Infection
by Craig Miller, Karen Boegler, Scott Carver, Martha MacMillan
Helle Bielefeldt-Ohmann, Susan VandeWoude

Abstract: 
Feline immunodeficiency virus (FIV) is the feline analogue of human immunodeficiency virus (HIV) and features many hallmarks of HIV infection and pathogenesis, including the development of concurrent oral lesions.  While HIV is typically transmitted via parenteral transmucosal contact, recent studies prove that oral transmission can occur, and that saliva from infected individuals contains significant amounts of HIV RNA and DNA.  While it is accepted that FIV is primarily transmitted by biting, few studies have evaluated FIV oral infection kinetics and transmission mechanisms over the last 20 years.  Modern quantitative analyses applied to natural FIV oral infection could significantly further our understanding of lentiviral oral disease and transmission. We therefore characterized FIV salivary viral kinetics and antibody secretions to more fully document oral viral pathogenesis.  Our results demonstrate that: (i) saliva of FIV-infected cats contains infectious virus particles, FIV viral RNA at levels equivalent to circulation, and lower but significant amounts of FIV proviral DNA; (ii) the ratio of FIV RNA to DNA is significantly higher in saliva than in circulation; (iii) FIV viral load in oral lymphoid tissues (tonsil, lymph nodes) is significantly higher than mucosal tissues (buccal mucosa, salivary gland, tongue); (iv) salivary IgG antibodies increase significantly over time in FIV-infected cats, while salivary IgA levels remain static; and, (v) saliva from nave Specific Pathogen Free cats inhibits FIV growth in vitro. Collectively, these results suggest that oral lymphoid tissues serve as a site for enhanced FIV replication, resulting in accumulation of FIV particles and FIV-infected cells in saliva. Failure to induce a virus-specific oral mucosal antibody response, and/or viral capability to overcome inhibitory components in saliva may perpetuate chronic oral cavity infection.  Based upon these findings, we propose a model of oral FIV pathogenesis and suggest alternative diagnostic modalities and translational approaches to study oral HIV infection.

Data inventory: This directory contains 5 folders:
1. antibody_data/ contains IgA and IgG measurements from FIV-infected and sham-inoculated cats. ExcelArchival Tool was used to export comma separated value files from each spreadsheet tab. The Visual representation folder contains an HTML representation of the original spreadsheet, including graphs. The formulas folder contains a list of formulas in the data table where applicable. See the OutputReport.txt for mored details. Files contained in each folder are listed below.

Formulas/
Output_Report.txt									
Saliva_IgA_Luitpiold_d22_061813_Albumin_(13).csv		
Saliva_IgA_Luitpiold_d22_061813_IgA_(63).csv			
Saliva_IgA_Luitpiold_d22_rProtein_062113_Albumin_(13).csv	
Saliva_IgA_Luitpiold_d22_rProtein_062113_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d22_061813_Albumin_(13).csv
Saliva_IgA_Luitpiold_d22_rProtein_062113_Capsid_(C36)_(35).csv	Saliva_IgG_Luitpiold_d22_061813_IgG_(77).csv
Saliva_IgA_Luitpiold_d22_rProtein_062113_Fc_(29).csv		Saliva_IgG_Luitpiold_d22_062113_Albumin_(13).csv
Saliva_IgA_Luitpiold_d22_rProtein_062113_FeLV_(28).csv		Saliva_IgG_Luitpiold_d22_062113_IgG_(77).csv
Saliva_IgA_Luitpiold_d36_062613_Albumin_(13).csv		Saliva_IgG_Luitpiold_d22_rProtein_062113_Albumin_(13).csv
Saliva_IgA_Luitpiold_d36_062613_IgA_(63).csv			Saliva_IgG_Luitpiold_d22_rProtein_062113_C36_SU-Fc_(65).csv
Saliva_IgA_Luitpiold_d36_rProtein_062413_Albumin_(13).csv	Saliva_IgG_Luitpiold_d22_rProtein_062113_Capsid_(C36)_(35).csv
Saliva_IgA_Luitpiold_d36_rProtein_062413_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d22_rProtein_062113_Fc_(29).csv
Saliva_IgA_Luitpiold_d36_rProtein_062413_Capsid_(C36)_(35).csv	Saliva_IgG_Luitpiold_d22_rProtein_062113_FeLV_(28).csv
Saliva_IgA_Luitpiold_d36_rProtein_062413_Fc_(29).csv		Saliva_IgG_Luitpiold_d36_062613_Albumin_(13).csv
Saliva_IgA_Luitpiold_d36_rProtein_062413_FeLV_(28).csv		Saliva_IgG_Luitpiold_d36_062613_IgG_(77).csv
Saliva_IgA_Luitpiold_d36_rProtein_062513_Albumin_(13).csv	Saliva_IgG_Luitpiold_d36_rProtein_062413_Albumin_(13).csv
Saliva_IgA_Luitpiold_d36_rProtein_062513_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d36_rProtein_062413_C36_SU-Fc_(65).csv
Saliva_IgA_Luitpiold_d36_rProtein_062513_Capsid_(C36)_(35).csv	Saliva_IgG_Luitpiold_d36_rProtein_062413_Capsid_(C36)_(35).csv
Saliva_IgA_Luitpiold_d36_rProtein_062513_Fc_(29).csv		Saliva_IgG_Luitpiold_d36_rProtein_062413_Fc_(29).csv
Saliva_IgA_Luitpiold_d36_rProtein_062513_FeLV_(28).csv		Saliva_IgG_Luitpiold_d36_rProtein_062413_FeLV_(28).csv
Saliva_IgA_Luitpiold_d57_070113_Albumin_(13).csv		Saliva_IgG_Luitpiold_d57_070113_Albumin_(13).csv
Saliva_IgA_Luitpiold_d57_070113_IgA_(63).csv			Saliva_IgG_Luitpiold_d57_070113_IgG_(77).csv
Saliva_IgA_Luitpiold_d57_rProtein_062613_Albumin_(13).csv	Saliva_IgG_Luitpiold_d57_070313_Albumin_(13).csv
Saliva_IgA_Luitpiold_d57_rProtein_062613_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d57_070313_IgG_(77).csv
Saliva_IgA_Luitpiold_d57_rProtein_062613_Capsid_(C36)_(35).csv	Saliva_IgG_Luitpiold_d57_080113_Albumin_(13).csv
Saliva_IgA_Luitpiold_d57_rProtein_062613_Fc_(29).csv		Saliva_IgG_Luitpiold_d57_080113_IgG_(77).csv
Saliva_IgA_Luitpiold_d57_rProtein_062613_FeLV_(28).csv		Saliva_IgG_Luitpiold_d57_rProtein_062613_Albumin_(13).csv
Saliva_IgA_Luitpiold_d57_rProtein_062813_Albumin_(13).csv	Saliva_IgG_Luitpiold_d57_rProtein_062613_C36_SU-Fc_(65).csv
Saliva_IgA_Luitpiold_d57_rProtein_062813_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d57_rProtein_062613_Capsid_(C36)_(35).csv
Saliva_IgA_Luitpiold_d57_rProtein_062813_Capsid_(C36)_(35).csv	Saliva_IgG_Luitpiold_d57_rProtein_062613_Fc_(29).csv
Saliva_IgA_Luitpiold_d57_rProtein_062813_Fc_(29).csv		Saliva_IgG_Luitpiold_d57_rProtein_062613_FeLV_(28).csv
Saliva_IgA_Luitpiold_d57_rProtein_062813_FeLV_(28).csv		Saliva_IgG_Luitpiold_d57_rProtein_062813_Albumin_(13).csv
Saliva_IgA_Luitpiold_d71_070813_Albumin_(13).csv		Saliva_IgG_Luitpiold_d57_rProtein_062813_C36_SU-Fc_(65).csv
Saliva_IgA_Luitpiold_d71_070813_IgA_(63).csv			Saliva_IgG_Luitpiold_d57_rProtein_062813_Capsid_(C36)_(35).csv
Saliva_IgA_Luitpiold_d71_080213_Albumin_(13).csv		Saliva_IgG_Luitpiold_d57_rProtein_062813_Fc_(29).csv
Saliva_IgA_Luitpiold_d71_080213_IgA_(63).csv			Saliva_IgG_Luitpiold_d57_rProtein_062813_FeLV_(28).csv
Saliva_IgA_Luitpiold_d71_rProtein_070213_Albumin_(13).csv	Saliva_IgG_Luitpiold_d71_070813_Albumin_(13).csv
Saliva_IgA_Luitpiold_d71_rProtein_070213_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d71_070813_IgG_(77).csv
Saliva_IgA_Luitpiold_d71_rProtein_070213_Capsid_(C36)_(35).csv	Saliva_IgG_Luitpiold_d71_rProtein_070213_Albumin_(13).csv
Saliva_IgA_Luitpiold_d71_rProtein_070213_Fc_(29).csv		Saliva_IgG_Luitpiold_d71_rProtein_070213_C36_SU-Fc_(65).csv
Saliva_IgA_Luitpiold_d71_rProtein_080813_Albumin_(13).csv	Saliva_IgG_Luitpiold_d71_rProtein_070213_Capsid_(C36)_(35).csv
Saliva_IgA_Luitpiold_d71_rProtein_080813_C36_SU-Fc_(65).csv	Saliva_IgG_Luitpiold_d71_rProtein_070213_Fc_(29).csv
Saliva_IgA_Luitpiold_d71_rProtein_080813_Capsid_(C36)_(35).csv	
Saliva_IgA_Luitpiold_d71_rProtein_080813_Fc_(29).csv		
Saliva_IgA_Luitpiold_d71_rProtein_080813_FeLV_(28).csv		Saliva_IgG_Luitpold_d57_and_d71_071113_Albumin_(13).csv
Saliva_IgG_Luitpold_d57_and_d71_071113_IgG_(77).csv	
Visual Representation (HTML Snapshot)/		

2. FIV_oral_histology scores contains histology data from from FIV-infected and sham-inoculated cats. ExcelArchival Tool was used to export comma separated value files from each spreadsheet tab. The Visual representation folder contains an HTML representation of the original spreadsheet, including graphs. See the OutputReport.txt for mored details. Files contained in each folder are listed below.

FIV_Oral_Histology_Scores_Histo_All_Tissues.csv
Output_Report.txt
FIV_Oral_Histology_Scores_Histo_Lymphoid_vs_Mucosal.csv
Visual Representation (HTML Snapshot)/

3. PPR_C36_saliva_inhibition_data: contains data data from from FIV-infected and sham-inoculated cats. ExcelArchival Tool was used to export comma separated value files from each spreadsheet tab. The Visual representation folder contains an HTML representation of the original spreadsheet, including graphs. The formulas folder contains a list of formulas in the data table where applicable.See the OutputReport.txt for mored details. Files contained in each folder are listed below.

Output Report.txt					
PPR_C36_Saliva_Inhibition_Data_02.11.2016_Sheet1.csv
Formulas/
Visual Representation (HTML Snapshot)/

4. qPCR_data/ contains raw qPCR reports from FIV-infected and sham-inoculated cats in pdf format. The standard curve tables from each PDF have been extracted into standard_curves.csv.

Luitpold_PBMC_DNA_FIVC_10-21-11.pdf
Luitpold_PBMC_DNA_FIVC_10-26-11.pdf
Luitpold_PBMC_DNA_GAPDH_10-19-11.pdf
Luitpold_PBMC_DNA_GAPDH_10-24-11.pdf
Luitpold_Salivary_DNA_FIV_C_5-20-11.pdf
Luitpold_Salivary_DNA_FIV_C_5-25-11.pdf
Luitpold_Salivary_DNA_FIV_C_5-31-11.pdf
Luitpold_Salivary_DNA_FIV_C_6-10-11.pdf
Luitpold_Salivary_DNA_FIV_C_6-3-11.pdf
Luitpold_Salivary_DNA_FIV_C_6-7-11.pdf
Luitpold_Salivary_DNA_GAPDH_5-19-11.pdf
Luitpold_Salivary_DNA_GAPDH_5-25-11.pdf
Luitpold_Salivary_DNA_GAPDH_5-26-11.pdf
Luitpold_Salivary_DNA_GAPDH_6-2-11.pdf
Luitpold_Salivary_DNA_GAPDH_6-3-11.pdf
Luitpold_Salivary_DNA_GAPDH_6-7-11.pdf
Luitpold_Salivary_DNA_GAPDH_6-9-11.pdf
Luitpold_Salivary_cDNA_Buccal_Mucosa_4-12-12.pdf
Luitpold_Salivary_cDNA_RPLN_4-6-12.pdf
Luitpold_Salivary_cDNA_RPLN_gapdh_4-11-12.pdf
Luitpold_Salivary_cDNA_Tongue_4-17-12.pdf
Luitpold_Salivary_cDNA_Tonsil_4-11-12.pdf
OralTissueRNA_SalGland090710report.pdf
d28_PBMC_FIV_A_6-20-11.pdf
d35_PBMC_DNA_6-23-11.pdf


5. viral_DNA_RNA_data/ contains FIV  DNA and RNA levels in cat saliva ExcelArchival Tool was used to export comma separated value files from each spreadsheet tab. The Visual representation folder contains an HTML representation of the original spreadsheet, including graphs. The formulas folder contains a list of formulas in the data table where applicable. See the OutputReport.txt for mored details. Files contained in each folder are listed below.

Luitpold_Saliva_Data_in_R_Format_Data_for_R.csv
Luitpold_Saliva_Data_in_R_Format_Proviral_DNA.csv
Luitpold_Saliva_Data_in_R_Format_Viral_RNA.csv
Visual Representation (HTML Snapshot)/
Output_Report.txt

