REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
alkaline phosphatase-labeled goat anti-human (Fc-specific) antibody	Sigma-Aldrich	Cat#A0170; RRID: AB_257868
Biological Samples
Patient-derived plasma samples	van Loggerenberg et al., 2008, Abdool Karim et al., 2010	https://www.caprisa.org/
Critical Commercial Assays
Viral RNA mini kit	QIAGEN	Cat#52906
Bright-Glo luciferase assay system	Promega	Cat#E2650
Quikchange Lightning mutagenesis kit	Agilent	Cat#210519
Platinum Taq High Fidelity	Invitrogen	Cat#11304029
pcDNA3.1 directional topo cloning kit	Invitrogen	Cat#K4900-40
Experimental Models: Cell Lines
TZM-bl cell line	NIH-ARP Cat# 8129-442	RRID: CVCL_B478
HEK293T cell line	Laboratory of George Shaw (University of Alabama, Birmingham, AL).	RRID: CVCL_0063
Oligonucleotides
5’- GGGTTTATTACAGGGACAGCAGAG -3’	Integrated DNA Technologies (IDT)	N/A
5’-GCACTCAAGGCAAGCTTTATTGAGGCTTA -3’	Integrated DNA Technologies (IDT)	N/A
5’- CACC GGCTTAGGCATCTCCTATAGCAGGAAGAA-3’	Integrated DNA Technologies (IDT)	N/A
5’- TTGCCAATCAAGGAAGTAGCCTTGTGT -3’	Integrated DNA Technologies (IDT)	N/A
Recombinant DNA
pSG3Äenv	https://www.aidsreagent.org/	NIH ARP Cat#11501
Software and Algorithms
Custom HMM algorithm	Martin et al., 2015 and this paper	https://github.com/MurrellGroup/recombination-hmm