AAAV	Avian Adeno-Associated Virus
AIVs	Avian Influenza Viruses
A ALV	Avian Leukosis Virus
ALV-J	Avian Leukosis Virus Subgroup J
ASF	African Swine Fever
BCL-2	B-Cell Lymphoma 2
BMECs	bovine mammary epithelial cells
BVD	Bovine Viral Diarrhea
BVD	Bovine viral diarrhea
BVDV	BVD virus
CCNE1	Cyclin E
CLCF1	Cardiotrophin Like Cytokine Factor 1
CMT	California mastitis test
DE	differentially expressed
DIAP1	Drosophila Inhibitor Of Apoptosis Protein 1
DLG5	Discs Large MAGUK Scaffold Protein 5
DOAJ	Directory Of Open Access Journals
ELK1	ETS-Like Gene 1
ENTV	Enzootic Nasal Tumor Virus
FMD	foot and mouth disease
FMDV	FMD virus
GaHV-2	Gallid Herpesvirus 2
hpi	hours post-infection
Hsp70	Heat Shock Protein Family A
IBDV	Infectious Bursal Disease Virus
IC	ileum control
IFN-α	type I interferon
IFN-β	beta interferon
IL7R	Interleukin 7 Receptor
IR	ileum resistant
IRAK1	interleukin-1 receptor-associated kinase 1
IRAK2	Interleukin-1 Receptor-Associated Kinase 2
IRF1	Interferon Regulatory Factor 1
IS	ileum susceptible
JAK1	Janus kinase 1
JD	Johne’s disease
KLF4	Krüppel-like factor 4
LD	Linear Dichroism
LS	low Salmonella shedding
MAP	M. avium subsp. paratuberculosis
MAPK	Mitogen-Activated Protein Kinase
MDA5	Melanoma Differentiation-Associated Gene 5
MDPI	Multidisciplinary Digital Publishing Institute
MDV	Marek’s Disease Virus
MHC	Major Histocompatibility Complex
miRNA-Seq	miRNA sequencing
ncRNAs	Non-Coding Rnas
NFAT5	Nuclear Factor Of Activated T-Cells 5
NFATC4	Nuclear Factor Of Activated T Cells 4
NFIA	nuclear factor IA
NF-kappaB	nuclear factor-kappa B
NGS	Next-Generation Sequencing
NPEPPS	Aminopeptidase Puromycin Sensitive
ORF4	open reading frame 4
P.I.	Post-Infection
PCR	Polymerase Chain Reaction
PCV2	Porcine circovirus type 2
PDCD4	Programmed Cell Death 4 Gene
PID	Post-Infection Day
PPR	Peste Des Petits Ruminants
PPRV	PPR Virus
PRRS	Porcine Reproductive and Respiratory Syndrome
PRRSV	Porcine reproductive and respiratory syndrome virus
PS	persistent Salmonella shedding
REV	Reticuloendotheliosis Virus
RXRB	retinoid X receptor β
SOCS5	Suppressor Of Cytokine Signaling 5
SRP14	signal recognition particle 14
TGS	Third-Generation Sequencing
TLA	Three-Letter Acronym
VP1	Virus Protein
YAP1	Targeting and Repressing Yes-Associated Protein 1