a
A549	human lung cells
ACE2	angiotensin-converting enzyme 2
AKT-mTOR signaling	protein kinase B-mammalian target of rapamycin complex
APCs	antigen presenting cells
Arl8b	Arf-like GTPases
ARP2/3	actin-related protein 2/3 complex
ARH-77	B lymphoblast cell line
ASC	adaptor apoptosis-associated speck-like protein with a caspase-1 recruitment domain
ATG	autophagy-related genes
ATP6AP1	S1 subunit of the enzyme V-type proton ATPase.
b
BCL-xL	B-cell lymphoma-extra large
BECN1(Beclin-1)	mammalian ortholog of the yeast autophagy-related gene 6
BORC-ARL8b	complex multisubunit complex- regulates lysosome positioning
c
Calu-3	human bronchial epithelial cells
CARD	caspase recruitment domain
CatB/L	cathepsin B and L
CAV	Coxsackie viruses
c-Myc	proto-oncogene
CNS	central nervous system
CXCR-4	C-X-C chemokine receptor type 4
d
3D organoids	miniature 3-dimensional structures that can mimic the structure and function of different tissues
DAMPs	damage-associated molecular patterns
DENV	Dengue virus
DMV	double-membrane vesicles
Dolutegravir	antiretroviral medication
e
EBV	Epstein Bar virus
eIF2a	translation elongation factor
Emtricitabine	nucleoside reverse-transcriptase inhibitor
ER	endoplasmic reticulum
f
FAM134	reticulon protein- ER-phagy receptor
g
GABARAP	GABA type receptor-associated protein
GSDMD	gasdermin D
GTPase	hydrolase enzyme binding nucleotide guanosine triphosphate
h
HCV	hepatitis C virus
HEK 293T	human embryonic kidney cells
HIF-1	hypoxia-induced transcription factor-1
Hsc70	heat shock cognate 71 kDa protein
HSV	herpes simplex virus type I
HOPS	homotypic fusion and protein sorting
i
ICP34.5	infected cell protein 34.5
IFN	interferon
iPSCs	human induced pluripotent stem cells
j
JAK1/2	Janus kinase- (tyrosine kinases)
k
KSHV	Kaposi’s sarcoma-associated herpes virus
l
LAMP1	lysosomal associated membrane glycoprotein 1
LAMP2A	lysosomal associated membrane protein 2
LC3	microtubule associated protein 1 light chain 3B
LIR	LC3-interacting region
Lopinavir	antiretroviral protease inhibitor
m
MAVS	mitochondrial antiviral-signaling protein
MCL-1	induced myeloid leukemia cell differentiation protein
MHC	major histocompatibility complex
MHV	murine hepatitis virus
mTORC1/S6K/4EBP1	mammalian target of rapamycin complex 1/p70 ribosomal S6 kinases/4E-binding protein 1
n
NBR1	neighbor of BRCA1 gene
NCI-BL 2171	small cell lung carcinoma
NDP52	calcium binding and coiled-coil domain 2
NF-kB	nuclear factor-κB (transcription factor)
NIC	niclosamide
NK	natural killer cells
NLRP3	NLR family pyrin domain containing 3 inflammasome
NS4B	membrane-associated protein involved in viral replication or assembly
NSPs	non-structural proteins
o
OPTN	Organ Procurement and Transplantation Network
ORFs	Open Reading Frames
ORF3a	encodes a viral accessory protein
ORF8	encodes viral accessory protein, Betacoronavirus NS8 protein
p
p62	SQSTM1(sequestosome 1)- ubiquitin-binding scaffold protein
PAMPs	pathogen-associated molecular patterns
PCD	programmed cell death
PEX3	peroxisomal Biogenesis Factor
PI3K	phosphoinositide 3-kinase, also known as VPS34.
PI3P	phosphatidylinositol 3-phosphate
PINK1	PTEN induced kinase 1
PKR	protein kinase R
PMP	peroxisome membrane protein
PP1a	protein phosphatase 1
PRKN	Parkin RBR E3 ubiquitin protein ligase
PTEN	fosfatidilinositol-3,4,5-trisfosfato 3-fosfatasa
PV	Poliovirus
PYCARD	apoptosis-associated speck-like protein containing a CARD (or ASC)
PYD	pyrin domain
r
Rab-7a	Ras-related protein late-endosomal / lysosomal GTPase
RCD	regulated cell death
RHIM	homotypic interaction motif
Ribavirin	antiretroviral medication inhibits- RNA/DNA viruses
RIP	proteins containing a receptor-interacting protein
Ritonavir	antiretroviral medication, protease inhibitors
RNP	ribonucleoprotein complexes
ROS	reactive oxygen species
RTC	replication and transcription complex
Ruxolitinib	Janus kinase inhibitor
s
SMVs	single-membrane vesicles
SNAP	soluble N-ethylmaleimidesSensitive factor attachment proteins
SNAP29	synaptosome associated protein 29, SNARE protein, in autophagy
SNARE	SNAP receptor
SNX27	sorting nexin family member 27
STX17	Syntaxin 17, autophagosomal SNARE protein
t
TAK1	transforming growth factor beta-activated kinase 1
Tax1BP1	Tax1-binding protein 1
TGN	trans-Golgi network
TNFR1	tumor necrosis factor receptor 1
TMEM41B	transmembrane protein 41B
TMPRSS2	transmembrane serine 2 protease
Tenofovir DF	tenofovir disoproxil fumarate, HIV medication
v
VAMP8	vesicle-associated membrane protein 8
Vero E6	epithelial cell from African green monkey
Viroporin	small hydrophobic multifunctional viral proteins
VMP1	vacuolar membrane protein 1
VPS	vacuolar protein sorting proteins (as VPS26, VPS29 and VPS35)
Vps34	class III phosphoinositide 3-kinase (PI3K)
VZV	Varicella zoster virus
w
WHO	World Health Organization
z
ZBP1	Z-DNA binding protein