Reference total HIV-1 DNA Assay,Forward primer (5' to 3'),Reverse primer (5' to 3'),Probe primer (5' to 3'),"In silico evaluation (%)
(Probe mismatch = 3)","In silico evaluation (%)
(Probe mismatch = 2)","In silico evaluation (%)
(Probe mismatch = 1)","In silico evaluation (%)
(Probe mismatch = 0)","Annealing temperature 
ddPCR (°C)","Annealing temperature 
qPCR (°C)","Probe 
characteristics",References
Beloukas_2009,TCGACGCAGGACTCGGCTTGCTG,AACATATAGTATGGGCAAGCAGGG,TGGGTGCGAGAGCGTCAGTATTAAGCGG,88.41,81.57,42.09,17.15,NA,NA,NA,1
Besson_2012,TTTGGAAAGGACCAGCAAA,CCTGCCATCTGTTTTCCA,AAAGGTGAAGGGGCAGTAGTAATACA,99.58,99.05,95.11,70.41,58,NA,5' 6-FAM/ZEN/3'IBFQ,2
Bosman_2015,TGGGTAAAAGTAGTAGAAGAGAAGGCTTT,CCCCCCACTGTGTTTAGCAT,TCAGCATTATCAGAAGGAG,65.93,64.67,51.82,14.49,NA,NA,NA,3
Candotti_2004,TAAAGCTTGCCTTGAGTGCT,GTCTGAGGGATCTCTAGTTACCAG,AGTAGTGTGTGCCCGTCTGTTGTGTG,87.49,85.21,82.03,61.78,NA,NA,NA,4
Chomont_2009_1,TGTGTGCCCGTCTGTTGTGT,GAGTCCTGCGTCGAGAGAGC,CCCTCAGACCCTTTTAGTCAGTGTGGAA,18.88,11.7,7.66,3.91,NA,NA,NA,5
Chomont_2009_2,TGTGTGCCCGTCTGTTGTGT,GAGTCCTGCGTCGAGAGAGC,TCTCTAGCAGTGGCGCCCGAACAG,83.73,83.73,83.38,80.25,NA,NA,NA,5
Chun_2005,GGTCTCTCTGGTTAGACCAGAT,CTGCTAGAGATTTTCCACACTG,AGTAGTGTGTGCCCGTCTGTT,63.73,63.55,62.42,47.89,58,NA,5' 6-FAM/ZEN/3'IBFQ,6
Claiborne_2015,GTTATYCCAGCAGARACAGG,TGACTTTGRGGATTGTAGGG,RGCAGCCTGYTGGTGGGC,99.63,99.42,98.32,68.13,56,NA,5' 6-FAM/ZEN/3'IBFQ,7
Cochrane_2004,CTCAATAAAGCTTGCCTTGAG,TGTTCGGGCGCCACTGCTAGAGA,ACTCTGGTARCTAGAGATCCCTCAGA,94.69,94.25,91.95,85.91,NA,NA,NA,8
Côrtes_2015,CTGGCTAACTAGGGAACCCACTG,GTCTGAGGGATCTCTAGTTAC,AGCCTCAATAAAGCTTGCCTTGAGTGC,82.62,82.58,81.69,69.8,NA,NA,NA,9
Delobel_2006_1,TAGAGGTAAAAGACACCAAGGA,ATGTCCCCCCACTGTGTTTA,AGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCC,55.35,34.01,13.59,3.53,NA,NA,NA,10
Delobel_2006_2,TAGAGGTAAAAGACACCAAGGA,ATGTCCCCCCACTGTGTTTA,TGTTTTCAGCATTATCAGAAGGAGCCACCCCACA,70.47,65.47,47.64,11.85,NA,NA,NA,10
Désire_2001,TGGCATGGGTACCAGCACA,CTGGCTACTATTTCTTTTGCTA,TTTATCTACTTGTTCATTTCCTCCAATTCCTT,97.16,90.39,67.57,35.37,NA,NA,NA,11
Douek_2002,GGTGCGAGAGCGTCAGTATTAAG,AGCTCCCTGCTTGCCCATA,AAAATTCGGTTAAGGCCAGGGGGAAAGAA,88.27,76.8,48.96,19.97,NA,NA,NA,12
Drosten_2005,AAGCCTCAATAAAGCTTGCCTTGA,GTTCGGGCGCCACTGCTAG,TCTGGTAACTAGAGATCCCTCAGACC,94.68,93.8,91.29,79,NA,NA,NA,13
Durand_2012,CATGTTTTCAGCATTATCAGAAGGA,TGCTTGATGTCCCCCCACT,CCACCCCACAAGATTTAAACACCATGCT,84.84,63.53,39.21,13.29,NA,NA,NA,14
Ellis_2009_1,GACATCAAGCAGCCATGCAAATGTT,TGCTATGTCACTTCCCCTTGGTTCTCT,AAAGAGACCATCAATGAGGAAGCTGCAGAA,75.92,55.51,26.23,6.26,NA,NA,NA,15
Ellis_2009_2,GACATCAAGCAGCCATGCAAATGTT,TGCTATGTCACTTCCCCTTGGTTCTCT,ACCATCAATGAGGAGGCTGCAGAATGGGA,83.95,79.52,65.84,22.74,NA,NA,NA,15
Eriksson_2003,TGACTCAGATTGGTTGCACTTTAAA,YTTTGGGCCATCCATTCCT,TTTCCMATTAGTCCTATTGAAACTGTACCAGTAAAA,44.33,39.95,27.73,13.43,NA,NA,NA,16
Eriksson_2013,CTTTAAATTTTCCCATTAGCCCTA,GAAAAAATAAAAGCATTAGTAGAAAT,CCAGGAATGGATGGCC,32.91,32.86,32.08,20.94,NA,NA,NA,17
Fabre-Mersseman_2011_1_1,TAGAGGTAAAAGACACCAAGGA,ATGTCCCCCCACTGTGTTTA,AGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCC,55.35,34.01,13.59,3.53,NA,NA,NA,18
Fabre-Mersseman_2011_1_2,TAGAGGTAAAAGACACCAAGGA,ATGTCCCCCCACTGTGTTTA,TGTTTTCAGCATTATCAGAAGGAGCCACCCCACA,70.47,65.47,47.64,11.85,NA,NA,NA,18
Fabre-Mersseman_2011_2_1,AGACCCCAACCCACAAGAA,TGGACAGGCCTGTGTAATGA,GAGTGGGGTTAATTTTACACATGGCTTTAGGCTTTG,41.39,25.85,11.23,3.37,NA,NA,NA,18
Fabre-Mersseman_2011_2_2,AGACCCCAACCCACAAGAA,TGGACAGGCCTGTGTAATGA,TCCCATAAACTGATTATATCCTCATGCATCTGTTCTACC,35.71,21.98,9.19,3.3,NA,NA,NA,18
Soriano-Sarabia_2005_1,TAGTAGAAGAGAAGGCTTTCAGCCCA,TTGGTTCTCTCATCTGGCCTGGTG,GAGCCACCCCACAAGATTTAAACACCATGT,47.28,40.61,30.52,10.83,NA,NA,NA,19
Soriano-Sarabia_2005_2,TAGTAGAAGAGAAGGCTTTCAGCCCA,TTGGTTCTCTCATCTGGCCTGGTG,AACACAGTGGGGGGACATCAAGCAGCCAT,51.88,46.74,34.62,7.51,NA,NA,NA,19
Gandhi_2012_1,CAAGCAGCCATGCAAATGTT,TGCTATGTCACTTCCCCTTGGTTCTCT,AAAGAGACCATCAATGAGGAAGCTGCAGAA,83.51,61.97,29.75,6.59,NA,NA,NA,20
Gandhi_2012_2,CAAGCAGCCATGCAAATGTT,TGCTATGTCACTTCCCCTTGGTTCTCT,CTATCCCATTCTGC,94.88,94.73,89.23,56.22,NA,NA,NA,20
Gantt_2007,CAAGCAGCCATGCAAATGTT,TGCTATGTCACTTCCCCTTGGTTCTCT,AAAGATACCATCAATGAGGAGGCTGCAGAA,88.33,79.15,52.98,18,NA,NA,NA,21
Ghosh_2003,CAAGTAGTGTGTGCCCGTCTGT,CTGCTAGAGATTTTCCACACTGAC,TGTGACTCTGGTAACTAGAGATCCCTCAGACCC,55.1,53.75,47.26,18.43,NA,NA,NA,22
Yu_2008,TTAAGCCTCAATAAAGCTTGCC,GTTCGGGCGCCACTGCTAGA,CCAGAGTCACACAACAGACGGGCACA,86.4,86.01,84.99,67.37,58,60,5' 6-FAM/ZEN/3'IBFQ,23
Heeregrave_2009,GCCTCAATAAAGCTTGCCTTGA,GGGCGCCACTGCTAGAGAT,GTADCTAGAGATCCCTCAGAC,95.76,95.34,92.85,86.55,56,60,5' 6-FAM/ZEN/3'IBFQ,24
Hütter_2009_1,ATCAAGCAGCCATGCAAATGTT,TGAAGGGTACTAGTAGTTCCTGCTATGTC,ACCATCAATGAGGAAGCTGCAGAATGGGA,86.88,80.03,58.74,26.45,NA,NA,NA,25
Hütter_2009_2,ACCAGGCAGCTATGCAAATGTT,CTGAAGGGTACTAGTAGTTCCTGCTATATC,ACCATCAATGAGGAAGCTGCAGAATGGGA,61.08,56.16,39.98,18.38,NA,NA,NA,25
Julg_2010,GGCTAACTAGGGAACCCACTG,GCTAGAGATTTTCCACACTGACTAA,GGATCTCTAGTTACCAGAGTCA,38.66,38.45,38.26,35.05,NA,NA,NA,26
Koelsch_2011,CATGTTTTCAGCATTATCAGAAGGA,TGCTTGATGTCCCCCCACT,CCACCCCACAAGATTTAAACACCATGCTAA,80.95,61.84,37.7,11.94,58,NA,5' 6-FAM/ZEN/3'IBFQ,27
Kondo_2009,AGTRGGGGGACAYCARGCAGCHATGCARAT,TACTAGTAGTTCCTGCTATRTCACTTCC,ATCAATGARGARGCTGCAGAATGGGA,98.98,98.63,95.06,69.34,58,NA,5' 6-FAM/3'MGB Eclipse,28
Kostrikis_2002,GCCTCAATAAAGCTTGCCTTGAGTG,GTTCTTCTGATCCTGTCTGAAGGG,TCCCCCGCTTAATACTGACGCTCTC,40.39,30.66,16.56,7.79,NA,NA,NA,29
Lam_2012,AGTGGGGGGACATCAAGCAGCCATGCAAAT,TACTAGTAGTTCCTGCTATGTCACTTCC,ATCAATGAGGAAGCTGC,89.31,86.61,69.68,34.96,NA,NA,NA,30
Lewin_2008,TCTCTAGCAGTGGCGCCCGAACA,TCTCCTTCTAGCCTCCGCTAGTC,TACTCACCAGTCGCCGCCCC,86.96,62.61,15.78,8.7,NA,NA,NA,31
Luo_2005,TGCTTAAGCCTCAATAAAGCTTGCCTTGA,TCTGAGGGATCTCTAGTTACCAG,AAGTAGTGTGTGCCCGTCTGT,87.58,84.23,79.42,64.54,NA,NA,NA,32
MacNeil_2006,ATCTCTAGCAGTGGCGCCCGA,CCTTCTAGCCTCCGCTAGTCA,ACGCAGGACTCGGCTTGCTG,91.28,91.26,87.27,79.18,58,NA,5' 6-FAM/3'MGB Eclipse,33
Maenetje_2010,GGGGAAGTGAYATAGCAGGA,GGYCCTTGTYTTATGTCCAA,CTACTAGTAVCCTTCARGAACARATARCATGGATGA,95.06,88.3,69.79,32.5,NA,NA,NA,34
Malnati_2008,TCTCGACGCAGGACTCG,TACTGACGCTCTCGCACC,CTCTCTCCTTCTAGCCTC,92.56,92.48,91.21,84.76,58,NA,5' 6-FAM/3'MGB Eclipse,35
Mitsuyasu_2000,CTCTAAGAGCCGAGCAAGCTTC,GGTCCTCCTACTCCCTGACAT,AAGCATTGGGACCAGCGGCTACACT,13.07,9.2,4.73,0.11,NA,NA,NA,36
Mohey_2005,CTGCATTTACCATACCTAGT,AGATCCTACATACAAATCATC,ACCAGGGATTAGATATCAGTACAATGTGC,85.02,60.28,25.17,11.97,NA,NA,NA,37
Novitsky_2006,CAAGCAGCCATGCAAATGTT,GGTACTAGTAGTTCCTGCTAT,ATCAATGAGGAGGCTGCAGAATGGGA,97.44,93.6,75.57,25.37,58,NA,5' 6-FAM/ZEN/3'IBFQ,38
Ometto_2002,TTAAGTGTTTCAATTGTGGCAAAGA,AAAAAATTAGCCTGTCTCTCAGTACAATCT,CCCCTAGGAAAAAGGGCTGTTGGAAATG,59.12,55.73,43.26,16.81,58,NA,5' 6-FAM/ZEN/3'IBFQ,39
Pallikkuth_2015,CTGCATCCGGAGTACTTCAAGAACTG,TCCCAGGCTCAGATCTGGTCTA,AGTGGCGAGCCCTCAGATGCTGC,14.43,9.92,9.46,5.46,NA,NA,NA,40
Pasternak_2008,TCAGCCCAGAAGTAATACCCATGT,CACTGTGTTTAGCATGGTGTTT,ATTATCAGAAGGAGCCACCCCACAAGA,68.15,64.67,59.97,42.44,NA,NA,NA,41
Pasternak_2015,CAGATGCTGCATATAAGCAGCTG,CACAACAGACGGGCACACAC,GAGCTCTCTGGCTAACTAGGGAACCC,79.25,64.02,34.79,8.71,NA,NA,NA,42
Rousseau_2004,TACAGTGCAGGGGAAAGAATA,CTGCCCCTTCACCTTTCC,TTTCGGGTTTATTACAGGGACAGCAG,99.48,99.16,95.35,38.97,58,NA,5' 6-FAM/ZEN/3'IBFQ,43
Schvachsa_2007,GCCTCAATAAAGCTTGCC,GGCGCCACTGCTAGAGATTTT,AAGTRGTGTGTGCCC,95.59,95.59,89.19,84.86,56,60,5' 6-FAM/3'MGB Eclipse,44
Serrano-Villar_2016,GRAACCCACTGCTTAAGCCTCAA,TGTTCGGGCGCCACTGCTAGAGA,AGTAGTGTGTGCCCGTCTGTT,90.62,90.39,89.19,69.33,NA,NA,NA,45
Shete_2012,ACCCATGTTTACAGCATTATCAGAAG,GCTTGATGTCCCCCTACTGTATTT,AGCCACCCCACAAGATTTAAACACCATGT,63.94,59.41,44.29,16.39,NA,NA,NA,46
Soares_2006,GGGAGAATTAGATCGATGGGAAA,CTGCTTGCCCATACTATATGTTTTAATTTA,CCCTGGCCTTAACCGAATT,10.78,10.4,8.72,4.06,56,NA,5' 6-FAM/3'MGB Eclipse,47
Strain_2013,GCACTTTAAATTTTCCCATTAGTCCTA,CAAATTTCTACTAATGCTTTTATTTTTTC,AAGCCAGGAATGGATGGCC,31.73,31.56,30.36,20.2,58,NA,5' 6-FAM/3'MGB Eclipse,48
Torres-Cornejo_2014,TAGCGGAGGCTAGAAGGAGA,CCCTGGCCTTAACCGAATT,TACCGACGCTCTCGCACCCA,94.33,91.14,44.55,2.55,NA,NA,NA,49
Van_der_Sluis_2013,GCCTCAATAAAGCTTGCCTTGA,GGGCGCCACTGCTAGAGAT,GTADCTAGAGATCCCTCAGA,95.76,95.34,94.43,89.27,56,60,5' 6-FAM/3'MGB Eclipse,50
Vandergeeten_2014,CTGGGTCTCTCTDGTTAGAC,CTGAGGGATCTCTAGTTACC,CACTCAAGGCAAGCTTTATTGAGGC,91.61,91.56,91.26,84,58,NA,5' 6-FAM/ZEN/3'IBFQ,51
Viard_2004,GCCTCAATAAAGCTTGCCTTGA,GGCGCCACTGCTAGAGATTTT,AAGTAGTGTGTGCCCGTCTGTTRTKTGACT,87.12,85.3,79.35,62.95,58,60,5' 6-FAM/ZEN/3'IBFQ,52
Wada_2004,CAAGCAGCCATGCAAATGTT,GCATGCACTGGATGCAATCT,TCCATTCTGCAGCTTCCTCATTGATG,50.29,36.4,13.14,0,NA,NA,NA,53
Wilkonson_2016,AGTGGGGGGACACCAGGCAGCAATGCAAAT,TAGTAGTTCCTGCTATGTCACTTCC,ATCAATGAGGAAGCTGC,64.65,63.31,55.41,31.23,NA,NA,NA,54
Williams_2014,GRAACCCACTGCTTAASSCTCAA,TGTTCGGGCGCCACTGCTAGAGA,AGTRGTGTGTGCCCGTCTGTTG,90.21,90.01,85.41,68.46,NA,NA,NA,55
Yukl_2010,AGCAGCYATGCAAATGTTA,TCACTTCCCCTTGGTTCTCT,CCATCAATGAGGA*,97.52,96.92,91.02,62.64,58,NA,5' 6-FAM/ZEN/3'IBFQ,56
Yun_2002,GCCTCAATAAAGCTTGCCTTGA,GGGCGCCACTGCTAGAGA,CCAGAGTCACACAACAGACGGGCACA,87.18,86.4,85.35,67.77,58,60,5' 6-FAM/ZEN/3'IBFQ,57
Zhu_2011,TGTGTGCCCGTCTGTTGTGT,GAGTCCTGCGTCGAGAGAGC,CAGTGGCGCCCGAACAGGGA,84.06,83.77,83.43,81.03,NA,NA,NA,58
* locked bases are underlined,,,,,,,,,,,