Table 1.

Labeling strategies for HIV-1 components.

Viral Component	Labeling Strategy	References
Capsid	CA-TC/FlAsH, ReAsH	[27]
	Cyclophilin A-DsRed—CypA-DsRed	[17]
	CA-eGFP	[28]
	GFP-CA	[18]
Matrix	MA-GFP	[27]
Vpr	Vpr-FP	[3,26]
	mCherry-2CL-YFP-Vpr (bifunctional marker for the content release and viral core tracking; 2 protease cleavage sites are inserted between mCherry and YFP-Vpr leading to their release upon maturation)	[32]
	Vpr-QDs	[44]
Integrase	IN-TC/FlAsH	[10]
	Vpr-IN-FP (protease cleavage site inserted between Vpr and IN)	[30,31]
	Gag-IN-eGFP (protease cleavage site inserted between Gag and IN leading to release of IN-GFP upon maturation)	[29]
Nucleocapsid	NC-GFP (GFP is inserted in place of Pol in Gag-Pol, which eliminates a viral protease cleavage site downstream of NC)	[45]
	NCp7-TC/FlAsH, ReAsH	[22,36]
vRNA	APOBEC3F-FP (A3F-FP) (cytidine deaminase that is incorporated into virions during production)	[37]
	MICDDRP (multiplex immunofluorescent-cell-based detection of DNA, RNA and proteins; bDNA FISH based vDNA and vRNA labeling combined with immunostaining)	[39]
	[Ru(phen)2(dppz)]2+	[27]
	BglG and MS2 technologies (insertion of specific RNA sequences into viral genome in combination with expression of BglG or MS2 proteins fused to FP in infected cells	[12,43]
	Incorporation of 5-ethynyl uridine (EU) into vRNA during viral production followed by click labeling	[16]
vDNA	ANCHOR technology: specific DNA sequence –ANCH3 is inserted into vDNA and recognized by OR protein (derived from bacterial parB protein) fused to GFP.	[7]
	ViewHIV (bDNA-FISH combined with immunostaining of capsid)	[38]
	MICDDRP	[39]
	Incorporation of EdU into vDNA during reverse transcription followed by click labeling	[40,41]
Transcription sites	Insertion of 18 Bgl binding stem loops into the viral genome in combination with expression of BglG-mCherry in infected cells	[12,18]
Integration sites	I-Sce1 reporter system (insertion of ISce1 target site into the viral genome results in induction of I-Sce1 specific double-strand break repair activity at the site of viral integration that leads to H2AX phosphorylation. The site of integration is then detected via immunoabeling of phosphorylated H2AX histone)	[46]
Integrated DNA	CRISPR Cas9-QD: U3 region of HIV-1 proviral DNA is targeted by guide RNA and labeled by QD-conjugated Cas9 mutants lacking the endonuclease activity	[47]
Membrane/Envelope	S15-mCherry (S15 corresponds to the 15 N-terminal amino acids of p60c-SRC protein that specifically targets the cell plasma membrane. Expression of this truncated form fused to mCherry (S15-mCherry) in producer cells leads to its incorporation into the membrane of newly formed viral particles)	[48]
	DiD lipid dye (Dioctadecyl-3,3,3 3 Tetramethylindodicarbocyanine)	[49]
	EcpH-ICAM1 (GFP related pH sensor fused to intercellular adhesion molecule 1, that is incorporated into HIV-1 virions during viral assembly)	[50]
	Incorporation of modified sugars (peracylated azidomannosamine (Ac4ManNAz)) in viral envelope glycoproteins followed by click labeling	[42]
Viral Content markers	Gag-iGFP, Gag-imCherry (FP flanked by a protease cleavage site inserted between CA and MA domains of Gag)	[33,34]