Table 1:

List of probes to target vRNA and vDNA of HIV-1 and SIV.

Single Plex RNA/DNAscope Probe Sets
Name	ACD Catalog #	Number of ZZ	Description
SIVmac239 (Anti-Sense)	312811	83	Anti-sense probe targeting within 1251-9420bp of D01065.1 (gag, pol, vif, vpx, vpr, tat, env, and nef)
SIVmac239 (Sense)	314071	83	Sense probe targeting reverse strand within 1251-9420bp of D01065.1 (gag, pol, vif, vpx, vpr, tat, env, and nef)
V-HIV1-Clade A (Anti-Sense)	416101	80	Anti-sense probe targeting within 879-7629bp of HIV-1 Clade A Consensus (gag, pol, vif, vpr, tat, rev, vpu, env, and nef)
V-HIV1-Clade A (Sense)	426341	80	Sense probe targeting reverse strand within 879-7629bp of HIV-1 Clade A Consensus (gag, pol, vif, vpr, tat, rev, vpu, env, and nef)
V-HIV1-Clade B (Anti-Sense)	416111	78	Anti-sense probe targeting within 854-8291bp of AF324493.2, HIV-1 Clade B NL4-3 (gag, pol, vif, vpr, tat, rev, vpu, env, and nef)
V-HIV1-Clade B (Sense)	425531	78	Sense probe targeting reverse strand within 854-8291bp of AF324493.2, HIV-1 Clade B NL4-3 (gag, pol, vif, vpr, tat, rev, vpu, env, and nef)
V-HIV1-Clade D (Anti-Sense)	416121	76	Anti-sense probe targeting within 894-7697bp of HIV-1 Clade D Consensus (gag, pol, vif, vpr, tat, rev, vpu, env, nef)
V-HIV1-Clade D (Sense)	426351	76	Sense probe targeting reverse strand within 894-7697bp of HIV-1 Clade D Consensus (gag, pol, vif, vpr, tat, rev, vpu, env, nef)
Multi-Plex RNA/DNAscope Probe Sets
Name	ACD Catalog #	Number of ZZ	Description
V-SIVmac239-gag-pol-Sense-C1	416141-C1	40	Sense probe targeting reverse strand within 1251-4093bp of D01065.1 (gag and pol)
V-SIVmac239-vif-env-nef-tar-C2 (Anti-sense)	416131-C2	47	Anti-sense probe targeting within 5381-10257bp of D01065.1(vif, vpx, vpr, tat, env, nef, and the TAR element)
V-HIV1-Clade_B-gag-pol-sense-C1	444051-C1	40	Sense probe targeting reverse strand within 854-3940bp of AF324493.2, HIV-1 Clade B NL4-3 (gag and pol)
V-HIV1-Clade_B-vif-vpr-tat-rev-vpu-env-nef-tar-C2 (Anti-sense)	444061-C2	40	Anti-sense probe targeting within 5042-9673bp of AF324493.2,, HIV-1 Clade B NL4-3 (vif, vpr, tat, env, nef, and the TAR element)
V-HIV1-Clade_C-gag-pol-sense-C1	444021-C1	48	Sense probe targeting reverse strand within 888-5032bp of HIV-1 Clade C concensus sequence (gag and pol)
V-HIV1-Clade_C-vif-vpr-rev-vpu-env-nef-tar-C2 (Anti-sense)	444041-C2	49	Anti-sense probe targeting within 5078-9698bp of HIV-1 Clade C concensus sequence (vif, vpr, tat, env, nef, and the TAR element)
V-HIV1-Clade_AE-gag-pol-sense-C1	444011-C1	55	Sense probe targeting reverse strand within 890-4812bp of AF259954.1, HIV-1 Clade AE (gag and pol)
V-HIV1-Clade_AE-vif-vpr-tat-rev-vpu-env-nef-tar-C2 (Anti-sense)	444031-C2	57	Anti-sense probe targeting within 5052-9694bp of AF259954.1, HIV-1 Clade AE (vif, vpr, tat, env, nef, and the TAR element)