Viruses and associated abb’ns
α β γ δ	Coronavirus (CoV) types
ACoV	avian CoV
BCoV	bovine respiratory CoV
CoV	coronavirus
CCoV	canine CoV
CoV HKU1	a species of CoV that infects humans
HCoV-OC43	another species of CoV that infects humans
Covid-19	the disease caused by CoV-2
FCoV	feline CoV
FIPV	feline infectious peritonitis virus
HAV, HBV, HCV	hepatitis A, B or C coronavirus
HCoV	human CoV
H1N1	an influenza A viral subtype; swine flu
H5N1	an influenza A viral subtype; asian avian flu
IBV or AIBV	avian infectious bronchitis coronavirus (avian CoV)
MERS	middle east respiratory syndrome
MHV	murine (mouse) hepatitis coronavirus
NDV	Newcastle disease virus
PEDV or PDCoV	porcine epidemic diarrhea coronavirus
PHEV	porcine hemagglutinating encephalomyelitis virus
RSV	respiratory syncytial virus
RV	Rhino virus
SARS, SARS-CoV or SARS-CoV-1	severe acute respiratory syndrome coronavirus-1
SARS-CoV-2 or CoV-2	severe acute respiratory syndrome coronavirus-2
SFV	semliki forest virus
TGEV	transmissible gastroenteritis coronavirus
VSV	vesicular stomatitis virus
VIRAL PROTEINS and RNAs
E	envelope protein
H	helicase
HE	hemagglutinin esterase
M	membrane matrix protein
N	nucleocapsid protein
nsp or NSP	(viral) non-structural protein (e.g., nsp3a 3b, 4a, 5, 6, 7a, etc.)
P	protease
PLP	PLpro, papain-like protease
Pp	polyprotein (i.e., pp1a (Orf1a) is spliced to give nsp1–11 pp1ab (Orf1b) is spliced to give nsp12 - 16.
RdRp	RNA-dependent RNA polymerase
S	spike protein (the S1 domain binds ACE2, receptor for several CoVs the S2 domain induces membrane fusion)
gRNA	guide RNA
gsRNA	single guide RNA
ssRNA	single stranded RNA
dsRNA	double stranded RNA
TRS	transcription regulating sequence
HOST ENZYMES AND OTHER PROTEINS
ACE2	angiotensin-converting enzyme-2, receptor for several CoVs
ATG5	an autophagy (ATG) protein - promotes fusion of phagocytic vesicles with lysosomes
Bcl-2	an apoptosis regulator it contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins.
Beclin1	a regulator of autophagy, ATG.
CCAAT	enhancer-binding proteins transcription factors
CCL1, 2, 3, 4	CxCL2, proinflammatory chemokines
CDRH1, 2, 3	the first, second, third complementarity-determining variable region of antibody heavy chains
Cdk	PKR-like endoplasmic reticulum (ER) kinase
C/EBP	CCAAT-enhancer binding protein
CHOP	C/EBP homologous protein (transcription factor)
Cyclin	protein involved in the cell cycle (e.g., cyclin D3, cyclin E)
DC-SIGN	dendritic cell-specific intercellular adhesion molecule grabbing nonintegrin also, CD209
DUB	deubiquitinating enzyme
DPP4	dipeptidyl peptidase 4 (adenosine deaminase complexing protein 2)
DUSP	dual specificity phosphatase
eIF2	eukaryotic initiation factor 2
GRP	glucose regulated protein (e.g., GPR78, GRP94)
HSP	heat shock protein
IFN	interferon
IL	interleukin (i.e., IL-1β)
IPS-1	INFβ promoter stimulator
IRE1	inositol-requiring enzyme (protein kinase a sensor)
IRF3	interferon regulatory factor 3
ISG	INF stimulated gene
JNK	cJUN amino terminal kinase
LC3	cytosolic ubiquitin-like protein (regulates macroautophagy (autophagy, ATG))
MAPK	MAP kinase, Mitogen-activated protein kinase
MBL	mannose binding lectin
MHCI and II	major histocompatibility complex, classes I and II
NF-κB or NFκB	a protein complex that controls transcription of DNA, cytokine production and cell survival.
NLRP3	NLR family pyrin domain-containing protein-3
PALS1	protein associated with Lin seven 1, a Maguk PDZ guanylate kinase
PARP	poly ADP-ribose polymerase
PDI	protein disulfide isomerase
PERK	protein kinase RNA (PKR)-like ER kinase
p53 or TP53	protein that regulates the cell cycle and hence functions as a tumor suppressor.
PIKfyve	phosphoinositol 3-kinase (makes PI-3,5-bisphosphate - a regulator of endosome sorting)
PKR	protein kinase R
Proteases
CTP	cathepsin protease
DPP4	dipeptidyl peptidase-4
Furin	a host protease
HAT	human airway trypsin-like protease
MASP1	MASP2, mannose-binding lectin (MBL)-associated serine proteases 1,2
PLP or PLpro	papain-like protease
TMPRSS-2 or -4	transmembrane serine protease-2 or -4
PRR	pattern recognition receptor
Rb or pRb	retinoblastoma protein
STING	a key regulator of antiviral interferon (IFN)
Syntenin-1	contains tandemly repeated PDZ domains that bind the cytoplasmic C-terminal domains of a variety of transmembrane proteins.
TBK1	Tank-binding kinase-1
TLR	Toll-like receptor
TNF	tumor necrosis factor
TPC	two pore calcium (cation) channel
TPC1 and 2 are in endosomes
TRAF3	TNF receptor-associated protein 3
XBP	X-box binding protein - a transcription factor involved in endoplasmic reticulum (ER) stress
(UPR)	regulates the unfolded protein response
INTRACELLULAR MEMBRANE STRUCTURES AND PROCESSES
CM	convoluted intracellular membrane
CTL	cytotoxic T lymphocyte involved in the T-cell immune response
DMS	double membrane spherule
DMV	double membrane vesicle
EM	electron microscopy
ER	endoplasmic reticulum
ERB	ER body
ERGIC	ER-golgi intermediate compartment (a mobile complex that delivers cargo from the ER to the golgi)
GV	giant vesicle; giant vesiculation
IRF3	interferon (INF) regulatory factor 3
ISR	interferon-stimulated response;
ISRE	ISR element
JNK	the C-Jun N-terminal kinase signaling pathway
LCVC	lysosomal virion-containing cisternae (golgi-derived)
MLB	multilamellar (maze-like) body
NMR	nuclear magnetic resonance
Omegasome	a cell membrane-enclosed compartment enriched for phosphatidylinositol-3-P
PPI	protein-protein interaction
PTM	post translational modification
RO	(viral) replication organelle
RTC	replication-transcription complex
RVN	reticulovesicular network
TRS	transcription regulating sequence (at the beginning of a gene)
UPR	unfolded protein response
VLP	vesicle-like particle
VP,	vesicle packet or vesicle particle
zipped membranes	ER membranes that fold to form spherules
TERMS
aa	amino acyl residue
AP-MS	affinity purification-mass spectrometry
ARDS	acute respiratory distress syndrome
BrU	bromouridine (U uridine)
CDRH	complementarity-determining region of heavy chain antibody (variable region)
Click chemistry	simple chemistry involving the joining of two molecules
CPZ	chlorpromazine (a clathrin inhibitor)
Cryo EM	cryogenic electron microscopy
CTD	C-terminal domain
dpi	days post infection
DPUP	domain preceding Ubi2 and PL2pro
ESR	electron spin resonance
Fab	antigen-binding fragment of an antibody
FP	fusion peptide
GI (tract)	gastrointestinal (tract)
HD	hydrophobic domain (in a protein)
usually forms TMSs
HMA	hexamethylene amiloride
hpi	hours post infection
HR1 HR2	heptad repeat 1, 2…
IC	ion channel across a membrane
ISRE	interferon-stimulated response element
Mac	macrodomain
MβCD	methyl-β-cyclodextrins
Mitophagy	autophagy of mitochondria
NTD	N-terminal domain
ORF	open reading frame (a protein encoding gene)
PAMP	pathogen-associated molecular pattern
PBM	PDZ binding motif
PDZ	a protein domain in proteins that recognizes motifs in other proteins and is therefore a protein-protein interaction (PPI) domain
perinuclear	the cytoplasm immediately surrounding the nucleus
PPI	protein-protein interaction
PTM	post translational modification
RBD	receptor binding domain
RNP	ribonuclear protein
ROS	reactive oxygen species
RTC	replication-transcription complex
SUD	SARS unique domain
TM	transmembrane
TMD	transmembrane domain
TMS	transmembrane (α-helical) segment
TRS	transcription-regulating sequence
Ubl1	ubiquitin-like (domain) 1
VLP	virus-like particle