Implementation and new insights in molecular diagnostics for HIV infection

References

• Pinkerton SD. How many sexually-acquired HIV infections in the USA are due to acute-phase HIV transmission? AIDS. 2007;21(12):1625–1629.
   PubMed Web of Science ®Google Scholar
• Prabhu VS, Hutchinson AB, Farnham PG, et al. Sexually acquired HIV infections in the United States due to acute-phase HIV transmission: an update. AIDS. 2009;23(13):1792–1794.
   PubMed Web of Science ®Google Scholar
• Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol. 2007;81(19):10209–10219.
   PubMed Web of Science ®Google Scholar
• Hollingsworth TD, Anderson RM, Fraser C. HIV-1 transmission, by stage of infection. J Infect Dis. 2008;198:687–693.
   PubMed Web of Science ®Google Scholar
• Elisa FL. HIV screening via fourth-generation immunoassay or nucleic acid amplification test in the United States: a cost-effectiveness analysis. PLoS One. 2011;6(11):e27625.
   PubMed Web of Science ®Google Scholar
• Garland FC, Garland CF, Gorham ED, et al. Western blot banding patterns of HIV rapid progressors in the U.S. Navy Seropositive Cohort: implications for vaccine development. AEP. 1996;6(4):341–347.
   Web of Science ®Google Scholar
• Wang S, Xu F, Demirci U. Advances in developing HIV-1 viral load assays for resource-limited settings. Biotechnol Adv. 2010;28(6):770–781.
   PubMed Web of Science ®Google Scholar
• Eshleman SH, Khaki L, Laeyendecker O, et al. Detection of individuals with acute HIV-1 infection using the ARCHITECT HIV Ag/Ab combo assay. J Acquir Immune Defic Syndr. 2009;52(1):121–124.
   PubMed Web of Science ®Google Scholar
• Wwsolowski LG, Delaney KP, Hart C, et al. Performance of an alternative laboratory-based algorithm for diagnosis of HIV infection utilizing a third generation immunoassay, a rapid HIV-1/HIV-2 differentiation test and a DNA or RNA-based nucleic acid amplification test in persons with established HIV-1 infection and blood donors. J Clinic Virology. 2011;52(Suppl1):S45–49.
   PubMedGoogle Scholar
• Patel P, Mackellar D, Simmons P, et al. Detecting acute human immunodeficiency virus infection using 3 different screening immunoassays and nucleic acid amplification testing for human immunodeficiency virus RNA, 2006–2008. Arch Intern Med. 2010;170(1):66–74.
   PubMed Web of Science ®Google Scholar
• Tiwari RP, Jain A, Khan Z, et al. Designing of novel antigenic peptide cocktail for the detection of antibodies to HIV-1/2 by ELISA. J Immunol Methods. 2013;387(1–2):157–166.
   PubMed Web of Science ®Google Scholar
• Branson BM, Stekler JD. Detection of acute HIV infection: we can’t close the window. J Infect Dis. 2012;205:521–524.
   PubMed Web of Science ®Google Scholar
• Esseghaier C, Ng A, Zourob M. A novel rapid assay for HIV-1 protease detection using magnetic bead mediation. Biosens Bioelectron. 2013;41:335–341.
   PubMed Web of Science ®Google Scholar
• Owen SM, Yang C, Spira T, et al. Alternative algorithms for human immunodeficiency virus infection diagnosis using tests that are licensed in the United States. J Clin Microbiol. 2008;46(5):1588–1595.
   PubMed Web of Science ®Google Scholar
• Shen F, Sun B, Kreutz JE, et al. Multiplexed quantification of nucleic acids with large dynamic range using multivolume digital RT-PCR on a rotational slip chip tested with HIV and hepatitis C viral load. J Am Chem Soc. 2011;133(44):17705–17712.
   PubMed Web of Science ®Google Scholar
• Quinn TC, Brookmeyer R, Kline R, et al. Feasibility of pooling sera for HIV-1 viral RNA to diagnose acute primary HIV-1 infection and estimate HIV incidence. AIDS. 2000;14(17):2751–2757.
   PubMed Web of Science ®Google Scholar
• Gueudin M, Plantier JC, Lemée V, et al. Evaluation of the Roche Cobas TaqMan and Abbott real time extraction-quantification systems for HIV-1 subtypes. J Acquir Immune Defic Syndr. 2007;44(5):500–505.
   PubMed Web of Science ®Google Scholar
• Oliveira D, Yap SF, Wongwanich S, et al. Establishing a quality assurance plain for nucleic acid-based diagnostic laboratories from planning to implementation. Accreditation Qual Assur. 2010;15(2):89–97.
   Web of Science ®Google Scholar
• Pilcher CD, McPherson JT, Leone PA, et al. Real-time, universal screening for acute HIV infection in a routine HIV counseling and testing population. JAMA. 2002;288(2):216–221.
   PubMed Web of Science ®Google Scholar
• Gueudin M, Leoz M, Lemée V, et al. A new real-time quantitative PCR for diagnosis and monitoring of HIV-1 group O infection. J Clin Microbiol. 2012;50(3):831–836.
   PubMed Web of Science ®Google Scholar
• Qiao YC, Xu Q, Wei JC, et al. Detection of HIV-infected patients without antiviral therapies. AIDS Res Hum Retroviruses. 2017;33(9):898–899.
   PubMed Web of Science ®Google Scholar
• Morley AA. Digital PCR: a brief history. Biomol Detect Quantification. 2014;1(1):1–2.
   PubMedGoogle Scholar
• Wong YK, Tsang HF, Xuw VW, et al. Applications of digital PCR in precision medicine. Expert Rev Precision Med Drug Dev. 2017;2(3):177–186.
   Web of Science ®Google Scholar
• Strain MC, Lada SM, Luong T, et al. Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One. 2013;8(4):e55943.
   PubMed Web of Science ®Google Scholar
• Sedlak RH, Jerome, Jerome KR. Viral diagnostics in the era of digital polymerase chain reaction. Diagn Microbiol Infect Disease. 2012;75:1–4.
   PubMed Web of Science ®Google Scholar
• Mallal S, Nolan D, Witt C, et al. Association between presence of HLA-B*5701, HLA-DR7, HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. Lancet. 2002;359(9308):727–732.
   PubMed Web of Science ®Google Scholar
• Mallal S, Phillips E, Carosi G, et al. HLA-B*5701 screening for hypersensitivity to abacavir. N Engl J Med. 2008;358:6.
   PubMed Web of Science ®Google Scholar
• Gootenberg JS, Adudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356:438–442.
   PubMed Web of Science ®Google Scholar
• Wilburn KM, Mwandumba HC, Jambo KC, et al. Heterogeneous loss of HIV transcription and proviral DNA from 8E5/LAV lymphoblastic leukemia cells revealed by RNA FISH:FLOW analyses. Retrovirology. 2016;13:55.
   PubMed Web of Science ®Google Scholar
• Vyboh K, Ajamian L, Mouland AJ. Detection of viral RNA by fluorescence in situ hybridization (FISH). J Vis Exp. 2012;63:4002.
   Google Scholar
• Ferrer M, Clerte C, Chamontin C, et al. Imaging HIV-1 RNA dimerization in cells by multicolor super-resolution and fluctuation microscopies. Nucleic Acids Res. 2016;44(16):7922–7934.
   PubMed Web of Science ®Google Scholar
• Porichis F, Hart MG, Griesbeck M, et al. High throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry. Nat Commun. 2014;5:5641.
   PubMed Web of Science ®Google Scholar
• McNeil SE. Nanotechnology for the biologist. J Leukoc Biol. 2005;78(3):585–594.
   PubMed Web of Science ®Google Scholar
• Rosi NL, Mirkin CA. Nanostructures in biodiagnostics. Chem Rev. 2005;105(4):1547–1562.
   PubMed Web of Science ®Google Scholar
• Tang S, Hewlett I. Nanoparticle-based immunoassays for sensitive and early detection of human immunodeficiency type 1 capsid (p24) antigen. J Infect Dis. 2010;201(Suppl 1):S59–S64.
   PubMedGoogle Scholar
• Kheiri F, Sabzi RE, Jannatdoust E, et al. A novel amperometric immunosenor based on acetone-extracted propolis for the detection of the HIV-1 p24 antigen. Biosens Bioelectron. 2011;26(11):4457–4463.
   PubMed Web of Science ®Google Scholar
• Mahmoud KA, Hrapovic S, Luong JH. Picomolar detection of protease using peptide/single walled carbon nanotube/gold nanoparticle-modified electrode. ACS Nano. 2008;2(5):1051–1057.
   PubMed Web of Science ®Google Scholar
• Kosaka PM, Pini V, Calleja M, et al. Ultrasensitive detection of HIV-1 p24 antigen by a hybrid nanomechanical-optoplasmonic platform with potential for detecting HIV-1 at first week after infection. PLoS One. 2017;12(2):e0171899.
   PubMed Web of Science ®Google Scholar
• Sano T, Smith CL, Cantor CR. Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science. 1992;258(5079):120–122.
   PubMed Web of Science ®Google Scholar
• Barletta JM, Edelman DC, Constantine NT. Lowering the detection limits of HIV-1 viral load using real-time immuno-PCR for HIV-1 p24 antigen. Am J Clin Pathol. 2004;122:20–27.
   PubMed Web of Science ®Google Scholar
• Zhang H, Zhao Q, Li XF, et al. Ultrasensitive assays for proteins. Analyst. 2007;132:724–737.
   PubMed Web of Science ®Google Scholar
• Tsai CT, Robinson PV, Cortez FDJ, et al. Antibody detection by agglutination-PCR (ADAP) enables early diagnosis of HIV infection by oral fluid analysis. PNAS. 2018;115:1250–1255.
   PubMed Web of Science ®Google Scholar
• Wang K, Fan D, Liu Y, et al. Cascaded multiple amplification strategy for ultrasensitive detection of HIV/HCV virus DNA. Biosens Bioelectron. 2017;87:116–121.
   PubMed Web of Science ®Google Scholar
• Rohrman BA, Leautaud V, Molyneux E, et al. A lateral flow assay for quantitative detection of amplified HIV-RNA. PLoS One. 2012;7(9):e45611.
   PubMed Web of Science ®Google Scholar
• Wang JH, Cheng L, Wang CH, et al. An integrated chip capable of performing sample pretreatment and nucleic acid amplification for HIV-1 detection. Biosens Bioelectron. 2013;41:484–491.
   PubMed Web of Science ®Google Scholar
• Gerasimov JY, Lai RY. An electrochemical peptide-based biosensing platform for HIV detection. ChemCommum. 2010;46(3):395–397.
   PubMed Web of Science ®Google Scholar
• Jangam SR, Agarwal AK, Sur K, et al. A point-of-care PCR test for HIV-1 detection in resource-limited settings. Biosens Bioelectron. 2013;42:69–75.
   PubMed Web of Science ®Google Scholar
• Zhang D, Peng Y, Qi H, et al. Label-free electrochemical DNA biosensor array for simultaneous detection of the HIV-1 and HIV-2 oligonucleotides incorporating different hairpin-DNA probes and redox indicator. Biosens Bioelectron. 2010;25(5):1088–1094.
   PubMed Web of Science ®Google Scholar
• Sara ML, Maria CP, Cristina G, et al. Sensitive quantification of the HIV- reservoir in gut-associated lymphoid tissue. PLoS One. 2017;12(4):e0175899.
   PubMed Web of Science ®Google Scholar
• Schlatzer D, Haqqani AA, Li X, et al. A targeted mass spectrometry assay for detection of HIV gag protein following induction of latent viral reservoirs. Anal Chem. 2017;89(10):5325–5332.
   PubMed Web of Science ®Google Scholar
• Eriksson S, Graf EH, Dahl V, et al. Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog. 2013;9:e1003174.
   PubMed Web of Science ®Google Scholar
• Finzi D, Hermankova M, Pierson T, et al. Identification of a reservoir for HIV-a in patients on highly active antiretro-viral therapy. Science. 1997;278:1295–1300.
   PubMed Web of Science ®Google Scholar
• Plantin J, Massanella M, Chomont N. Inducible HIV RNA transcription assays to measure HIV persistence: pros and cons of a compromise. Retrovirology. 2018;15:9.
   PubMed Web of Science ®Google Scholar
• Schito ML, D’Souza MP, Owen SM, et al. Challenges for rapid molecular HIV diagnostics. J Infect Dis. 2011;201(Suppl 1):S1–S6.
   Google Scholar