Development of a multiassay algorithm (MAA) to identify recent HIV infection in newly diagnosed individuals in Indonesia

. 2023 Sep 21;26(10):107986. doi: 10.1016/j.isci.2023.107986

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins

Diethylamine	Merck Millipore	Cat# 803010
Invitrogen™ PBS Tablets	Thermo Fisher Scientific	Cat# 003002
Applied Biosystems™ Anode Buffer Container (ABC)	Thermo Fisher Scientific	Cat# 4393927
Applied Biosystems™ Cathode Buffer Container (CBC)	Thermo Fisher Scientific	Cat# 4408256
Applied Biosystems™ POP-7™ Polymer for 3500	Thermo Fisher Scientific	Cat# 4393708
Invitrogen™ BlueJuice™ Gel Loading Buffer (10X)	Thermo Fisher Scientific	Cat# 10816105
Invitrogen™ 100 bp DNA Ladder	Thermo Fisher Scientific	Cat# 15628019
Invitrogen™ SYBR™ Safe DNA Gel Stain	Thermo Fisher Scientific	Cat# S33102
Invitrogen™ Nuclease-Free Water	Thermo Fisher Scientific	Cat# AM9937
Agarose, LE, Analytical Grade	Promega	Cat# V3121
TBE Buffer, 10X, Molecular Biology Grade	Promega	Cat# V4251
Sigma-Aldrich Ethyl alcohol, Pure	Merck	Cat# E7023-500ML

Critical commercial assays

GenScreen™ Ultra HIV Ag-Ab	Bio-Rad	Cat# 72388
QIAamp Viral RNA Mini Kit	Qiagen	Cat# 52906
Invitrogen™ SuperScript™ III First-Strand Synthesis System	Thermo Fisher Scientific	Cat# 18080051
Invitrogen™ Platinum™ SuperFi™ DNA Polymerase	Thermo Fisher Scientific	Cat# 12351010
Applied Biosystems™ ExoSAP-IT™ Express PCR Product Cleanup Reagent	Thermo Fisher Scientific	Cat# 75001.4X.1.ML
Invitrogen™ SuperScript™ III Reverse Transcriptase	Thermo Fisher Scientific	Cat# 18080093
Invitrogen™ Ribonuclease H	Thermo Fisher Scientific	Cat# 18021014
Invitrogen™ dNTP Mix (10 mM ea)	Thermo Fisher Scientific	Cat# 18427013
Applied Biosystems™ BigDye v3.1 Cycle Sequencing Kit	Thermo Fisher Scientific	Cat# 4337455
Applied Biosystems™ BigDye XTerminator™ Purification Kit	Thermo Fisher Scientific	Cat# 4376486

Deposited data

Raw and analyzed data	This paper	https://data.mendeley.com/datasets/ktg27krty7/1
HIV-1 pol DNA sequence	This paper	Genbank: OR139650 – OR139679

Oligonucleotides

Primer: PanHIV-1_1F Forward: AGCCYGGGAGCTCTCTG	Gall et al.⁷⁴	N/A
Primer: PanHIV-1_4R Reverse: CTTWTATGCAGCWTCTGAGGG	Gall et al.⁷⁴	N/A
Primer: PanHIV-1_2F Forward: GGGAAGTGAYATAGCWGGAAC	Gall et al.⁷⁴	N/A
Primer: PanHIV-1_2R Reverse: CTGCCATCTGTTTTCCATARTC	Gall et al.⁷⁴	N/A
Primer: KVL84 Reverse: TCCTGTATGCARACCCCAATATG	Van Laethem et al.⁷⁵	N/A
Primer: Rty Reverse: GTGTCTCATTGTTTATACTAGG	Yabar et al.⁷⁶	N/A
Primer: MAW26 Forward: TTGGAAATGTGGAAAGGAAGGAC	Yabar et al.⁷⁶	N/A
Primer: 1243 Reverse: ACTAAGGGAGGGGTATTGACAAACTC	Yabar et al.⁷⁶	N/A
Primer: Rta Forward: GTTGACTCAGATTGGTTGCAC	Yabar et al.⁷⁶	N/A
Primer: Rtb Forward: CCTAGTATAAACAATGAGACAC	Yabar et al.⁷⁶	N/A
Primer: MAW70 Reverse: TAATCCCTGCGTAAATCTGACTTGCCCA	Yabar et al.⁷⁶	N/A

Software and algorithms

Applied Biosystems 3500/3500xL Genetic Analyzer System	Thermo Fisher Scientific	Cat# 4405673; RRID:SCR_021901
Sequencher v5.4.6	Genecodes,	RRID:SCR_001528
GraphPad Prism v9.3.0	GraphPad	RRID:SCR_002798
jpHMM (jumping profile Hidden Markov Model)	Schultz et al., 2009⁷⁷	http://jphmm.gobics.de/
RIP (Recombinant Identification Program)	Siepel et al., 1995⁷⁸	https://www.hiv.lanl.gov/content/sequence/RIP/RIP.html
HIVdb Program: Sequence Analysis	Rhee et al., 2003⁷⁹	https://hivdb.stanford.edu/hivdb/by-sequences/