Novel DNA Biosensing Platform for Detecting HIV Integrase for Highly Sensitive and Quantitative HIV Detection, Diagnosis, and Therapeutic Monitoring

Overview

Journal ACS Omega

Publisher American Chemical Society

Specialty Chemistry

Date 2024 Jun 17

PMID 38882085

Authors

Fuming Chen

Jing Wang

Jie Ma

Li Song

Haojie Yan

Feng Wang

Zhengrong Yang

Furong Li

Affiliations

Soon will be listed here.

Abstract

Straightforward, sensitive, and specific human immunodeficiency virus (HIV) assays are urgently needed. The creation of a point-of-care (POC) device for decentralized diagnostics has the potential to significantly reduce the time to treatment, especially for infectious diseases. Notably, however, many POC solutions proposed to date fall short of meeting the ASSURED guidelines, which are crucial for effective deployment in the field. Herein, we developed a DNA biosensor platform for the specific and quantitative detection of HIV. The platform contains a rolling circle amplification (RCA)-based DNA biosensor and a portable fluorescence detector, in which HIV-encoded integrase (IN) enzyme activity is used as a biomarker to achieve HIV-specific detection. The cleavage and integration reaction of IN on the sensor surface and RCA are combined in this detection platform to perform detection signal cascade amplification, ultimately achieving a detection limit of 0.125 CFU/μL of HIV particles. Moreover, the DNA sensor system exhibited high sensitivity and accuracy for detecting HIV in clinical samples, suggesting that it has potential for application in clinical settings to detect retroviruses other than HIV. In addition, quantitative detection based on this biosensing platform was significantly correlated with the CD4+ lymphocytes count, which can provide guidance for antiretroviral therapy and which affects long-term death risk assessment in HIV patients. Therefore, this DNA biosensing platform based on IN activity is expected to be useful for rapid HIV testing, diagnosis, and treatment monitoring, enabling the development of new POC diagnostic tests and will thus be highly valuable for developing HIV prevention strategies and effective treatments.

References

Brendish N, Poole S, Naidu V, Mansbridge C, Norton N, Wheeler H . Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study. Lancet Respir Med. 2020; 8(12):1192-1200. PMC: 7544498. DOI: 10.1016/S2213-2600(20)30454-9. View

van Kerckhoven I, Fransen K, Peeters M, De Beenhouwer H, Piot P, van der Groen G . Quantification of human immunodeficiency virus in plasma by RNA PCR, viral culture, and p24 antigen detection. J Clin Microbiol. 1994; 32(7):1669-73. PMC: 263757. DOI: 10.1128/jcm.32.7.1669-1673.1994. View

Lillis L, Lehman D, Siverson J, Weis J, Cantera J, Parker M . Cross-subtype detection of HIV-1 using reverse transcription and recombinase polymerase amplification. J Virol Methods. 2016; 230:28-35. PMC: 4767662. DOI: 10.1016/j.jviromet.2016.01.010. View

Ajbani S, Velhal S, Kadam R, Patel V, Bandivdekar A . Immunogenicity of Semliki Forest virus based self-amplifying RNA expressing Indian HIV-1C genes in mice. Int J Biol Macromol. 2015; 81:794-802. DOI: 10.1016/j.ijbiomac.2015.09.010. View

Sohrab S, Aly El-Kafrawy S, Azhar E . Effect of insilico predicted and designed potential siRNAs on inhibition of SARS-CoV-2 in HEK-293 cells. J King Saud Univ Sci. 2022; 34(4):101965. PMC: 8925144. DOI: 10.1016/j.jksus.2022.101965. View

Li J, Wang J, Zhang W, Tu Z, Cai X, Wang Y . Protein sensors combining both on-and-off model for antibody homogeneous assay. Biosens Bioelectron. 2022; 209:114226. PMC: 8968183. DOI: 10.1016/j.bios.2022.114226. View

Zhen D, Zhang S, Yang A, Ma Q, Deng Z, Fang J . A supersensitive electrochemical sensor based on RCA amplification-assisted "silver chain"-linked gold interdigital electrodes and CRISPR/Cas9 for the detection of Staphylococcus aureus in food. Food Chem. 2023; 440:138197. DOI: 10.1016/j.foodchem.2023.138197. View

Du M, Li N, Mao G, Liu Y, Wang X, Tian S . Self-assembled fluorescent Ce(Ⅲ) coordination polymer as ratiometric probe for HIV antigen detection. Anal Chim Acta. 2019; 1084:116-122. DOI: 10.1016/j.aca.2019.08.010. View

Cardenas A, Baughan E, Hodinka R . Evaluation of the Bio-Rad Multispot HIV-1/HIV-2 Rapid Test as an alternative to Western blot for confirmation of HIV infection. J Clin Virol. 2013; 58 Suppl 1:e97-e103. DOI: 10.1016/j.jcv.2013.08.021. View

10.

Xu S, Wang X, Wu C, Zhu X, Deng X, Wu Y . MscI restriction enzyme cooperating recombinase-aided isothermal amplification for the ultrasensitive and rapid detection of low-abundance EGFR mutations on microfluidic chip. Biosens Bioelectron. 2023; 247:115925. DOI: 10.1016/j.bios.2023.115925. View

11.

McClure P, Curran R, Boneham S, Ball J . A polymerase chain reaction method for the amplification of full-length envelope genes of HIV-1 from DNA samples containing single molecules of HIV-1 provirus. J Virol Methods. 2000; 88(1):73-80. DOI: 10.1016/s0166-0934(00)00179-8. View

12.

Marsden M, Zhang T, Du Y, Dimapasoc M, Soliman M, Wu X . Tracking HIV Rebound following Latency Reversal Using Barcoded HIV. Cell Rep Med. 2020; 1(9):100162. PMC: 7762775. DOI: 10.1016/j.xcrm.2020.100162. View

13.

Cajazeiras J, Melo L, Albuquerque E, Radis-Baptista G, Cavada B, Freitas V . Analysis of protein expression and a new prokaryotic expression system for goat (Capra hircus) spermadhesin Bdh-2 cDNA. Genet Mol Res. 2009; 8(3):1147-57. DOI: 10.4238/vol8-3gmr639. View

14.

Gashti A, Chahal P, Gaillet B, Garnier A . Purification of recombinant vesicular stomatitis virus-based HIV vaccine candidate. Vaccine. 2023; 41(13):2198-2207. DOI: 10.1016/j.vaccine.2023.02.058. View

15.

Ma Y, Shen X, Zeng Q, Wang H, Wang L . A multi-walled carbon nanotubes based molecularly imprinted polymers electrochemical sensor for the sensitive determination of HIV-p24. Talanta. 2017; 164:121-127. DOI: 10.1016/j.talanta.2016.11.043. View

16.

McFall S, Wagner R, Jangam S, Yamada D, Hardie D, Kelso D . A simple and rapid DNA extraction method from whole blood for highly sensitive detection and quantitation of HIV-1 proviral DNA by real-time PCR. J Virol Methods. 2015; 214:37-42. DOI: 10.1016/j.jviromet.2015.01.005. View

17.

Tosiano M, Mar H, Hoeth D, Eron J, Gandhi R, McMahon D . Comparative sensitivity of automated (Abbott M2000) and manual plasma HIV-1 RNA PCR assays for the detection of persistent viremia after long-term antiretroviral therapy. J Virus Erad. 2022; 8(4):100095. PMC: 9720429. DOI: 10.1016/j.jve.2022.100095. View

18.

Dabis F, Bekker L . We still need to beat HIV. Science. 2017; . DOI: 10.1126/science.aao4197. View

19.

Hao L, Yang W, Xu Y, Cui T, Zhu G, Zeng W . Engineering light-initiated afterglow lateral flow immunoassay for infectious disease diagnostics. Biosens Bioelectron. 2022; 212:114411. PMC: 9119864. DOI: 10.1016/j.bios.2022.114411. View

20.

Jiang Y, Qiu Z, Le T, Zou S, Cao X . Developing a dual-RCA microfluidic platform for sensitive E. coli O157:H7 whole-cell detections. Anal Chim Acta. 2020; 1127:79-88. DOI: 10.1016/j.aca.2020.06.046. View