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A Rapid and Sensitive Detection of HIV-1 with a One-Pot Two-Stage Reverse Transcription Recombinase Aided Real-Time PCR Assay. Trop Med Infect Dis 2023; 8:tropicalmed8020105. [PMID: 36828521 PMCID: PMC9960739 DOI: 10.3390/tropicalmed8020105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) attacks the immune system, making people susceptible to various diseases, thus increasing their risk of death. Comprehensive detection of major HIV-1 strains circulating in China is vital for effective HIV-1 infection prevention and treatment. HIV-1 nucleic acid detection is considered effective for HIV-1 diagnosis since traditional immunological testing may fail to detect HIV-1 infection during the window period. This work demonstrates a one-pot two-stage amplification assay (RT-RAP), a combination of reverse transcription recombinase (RT- RAA), and quantitative real-time polymerase chain reaction (qRT-PCR). The turn-around time of the assay is only 50 min and can be performed with commonly available laboratory equipment, the qPCR devices. The RT-RAP assay could detect approximately 5 and 14 copies/reaction of HIV-1 DNA and RNA using recombinant plasmids and standard reference strains, respectively. Additionally, we found that the clinical performance of RT-RAP (detected 169 samples out of 170 specimens) was consistent with that of qRT-PCR. The sensitivity and specificity of RT-RAP were 100.00% (99/99) and 98.59% (70/71), respectively, while its positive and negative predictive values were 99.00% (99/100) and 100.00% (70/70), respectively. The total coincidence rate of the RT-RAP was 99.41% (169/170), with a kappa value of 0.988 (p < 0.05). We demonstrated that RT-RAP could rapidly detect the common HIV-1 subtypes commonly circulating in China with comparable sensitivity and specificity to qRT-PCR.
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Ehret R, Harb K, Breuer S, Obermeier M. Performance assessment of the new Xpert® HIV-1 Viral Load XC assay for quantification of HIV-1 viral loads. J Clin Virol 2022; 149:105127. [DOI: 10.1016/j.jcv.2022.105127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/07/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022]
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Zhao J, Ao C, Wan Z, Dzakah EE, Liang Y, Lin H, Wang H, Tang S. A point-of-care rapid HIV-1 test using an isothermal recombinase-aided amplification and CRISPR Cas12a-mediated detection. Virus Res 2021; 303:198505. [PMID: 34271038 DOI: 10.1016/j.virusres.2021.198505] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/26/2022]
Abstract
Human immunodeficiency virus type one (HIV-1) infection is one of the major public health problems worldwide. Effective control of HIV-1 epidemic relies on early diagnosis of HIV-1 infection by using simple, rapid point-of-care test (POCT). An integrated assay was developed and evaluated in this study to combine a real-time isothermal reverse-transcription recombinase-aided amplification (rRT-RAA) and CRISPR Cas12a-mediated detection for HIV-1. The testing results could be directly observed with naked eye using a blue light imager, making it a suitable on-site testing assay. Our preliminary data indicated that the assay was capable of detecting 20 copies of purified HIV-1 DNA or RNA per reaction or as low as 123 copies/ml of HIV-1 viral load in clinical samples. When screening 155 clinical samples with or without HIV-1 infection, the sensitivity and specificity of the rRT-RAA assay were 98.95% (94/95) and 100% (60/60), respectively. The coefficient value was 0.986 when compared with the Chinese FDA approved HIV-1 RT-qPCR assay. Furthermore, the newly developed HIV-1 rRT-RAA assay could detect the major HIV-1 genotypes CRF01_AE, CRF07_BC, CRF08_BC, CRF08_BC and subtype B in China. Our preliminary results indicated that the rRT-RAA assay or its combination with CRISPR Cas12a-mediated detection could serve as a rapid, convenient, and robust assay for HIV-1 detection.
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Affiliation(s)
- Jianhui Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Cailing Ao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhengwei Wan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Emmanuel Enoch Dzakah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Yuanhao Liang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Hongqing Lin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; Wenzhou Institute, University of Chinese Academy of Sciences, China.
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Kress J, Vermeulen M, Chudy M, Reissinger A, Hanschmann KM, Saville A, Nübling CM. Reliability of CE-marked NATs for HIV-1 subtype C detection and quantitation. J Clin Virol 2020; 132:104649. [PMID: 33027700 DOI: 10.1016/j.jcv.2020.104649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
We compared seven CE-marked HIV-1 RNA nucleic acid amplification technology (NAT) based assays for their detection efficiency and quantitation concordance in regard to HIV-1 subtype C. We used 398 plasma samples from South African repeat blood donors identified as HIV positive at occasion of routine screening NAT performed mainly during the years 2010-2013, with most plasma samples reflecting recent HIV-1 infections. All HIV-1 subtype C specimens were detected, independent of mono- or dual-target assay design. In the same time period new variants of HIV-1 subtype B had been identified which were missed by some mono-target assays, a finding which was not corroborated for subtype C in our study. A high level of concordance of HIV-1 subtype C quantitation was determined for the HIV-1 NATs, showing successful standardization in this diagnostic field.
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Affiliation(s)
- J Kress
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - M Vermeulen
- South African National Blood Service, Constantia Kloof, Johannesburg, South Africa
| | - M Chudy
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - A Reissinger
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - K-M Hanschmann
- Section of Biostatistics, Paul-Ehrlich-Institut, Langen, Germany
| | - A Saville
- South African National Blood Service, Constantia Kloof, Johannesburg, South Africa
| | - C M Nübling
- Division of Major Policy Issues, Coordination, Paul-Ehrlich-Institut, Langen, Germany.
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Liu C, Chang L, Wang L. HBV DNA Test Among Blood Donations May Require Two Amplification Targets. Indian J Hematol Blood Transfus 2019; 35:544-550. [PMID: 31388271 DOI: 10.1007/s12288-018-01064-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/13/2018] [Indexed: 12/25/2022] Open
Abstract
To analyze the risk and reason of false-negative HBV DNA results of NAT reagents among blood donations of China and discuss the necessity of two amplification targets for HBV DNA tests among donations. In this study, samples that showed discordant results on two commercially available assay platforms were further detected by established in-house methods based on conserved regions of the HBV genome. The HBV concentration of these samples was determined using two commercially available reagents. The samples with high titers of HBV were detected by an in-house method. The samples showing high Ct differences between two regions in the in-house method were further sequenced and aligned with primers and probes. The results showed that the established method has a good detection performance. The mismatch between reverse primers and sample sequences led to decreased detection capacity of S and C regions by the in-house method, but it could be compensated by another region. Among the false-negative samples detected by commercial reagents, most were because of low titers; however, there were 7 samples with HBV DNA concentrations much higher than the LOD of the commercial reagents, which may be due to mismatch of the primer or probe. This study highlights the potential risk of HBV false-negative detection by commercial NAT reagents. The dual-target assay may be helpful for HBV screening and reduce the risk of false-negative detection.
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Affiliation(s)
- Chao Liu
- 1National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730 People's Republic of China
- 2Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
- 3Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Le Chang
- 1National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730 People's Republic of China
- 2Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Lunan Wang
- 1National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730 People's Republic of China
- 2Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
- 3Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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Avidor B, Matus N, Girshengorn S, Achsanov S, Gielman S, Zeldis I, Schweitzer I, Adler A, Turner D. Comparison between Roche and Xpert in HIV-1 RNA quantitation: A high concordance between the two techniques except for a CRF02_AG subtype variant with high viral load titters detected by Roche but undetected by Xpert. J Clin Virol 2017; 93:15-19. [PMID: 28564629 DOI: 10.1016/j.jcv.2017.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/14/2017] [Accepted: 05/14/2017] [Indexed: 12/01/2022]
Abstract
BACKGROUND HIV-1 viral load (VL) testing is important to predict viral progression and to monitor the response to antiretroviral therapy. New HIV-1 VL tests are continuously introduced to the market. Their performance is usually compared to Abbott and/or Roche HIV-1 VL assays, as reference. The Xpert HIV-1 VL test was recently introduced, but its performance compared to Roche has not been sufficiently studied. OBJECTIVES To compare the Xpert assay with Roche and to assess its use in the HIV clinical laboratory. STUDY DESIGN A total of 383 plasma samples of HIV-1 infected patients previously tested by Roche, were retrospectively tested by Xpert to determine concordance between the two assays. Samples included a diversity of HIV-1 subtypes and a wide range of VLs. RESULTS There was a high concordance between the two assays, except for a CRF02_AG subtype variant with high VL titters, that was detected by Roche but undetected by Xpert. The 5' long terminal repeat gene region of this virus, targeted by the Xpert assay, was amplified and sequenced. A 25 nucleotide insert was identified, but was unmatched to any known sequences of HIV-1. This particular insert, however could not explain the false-negativity by the Xpert assay. CONCLUSIONS This study underlines the challenge to routine VL testing due to the high genetic diversity of HIV-1. Clinicians should, therefore be advised that a negative VL in cases where the clinical picture does not match the laboratory report, might in fact be, a false-negative result of the VL assay.
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Affiliation(s)
- Boaz Avidor
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Natalia Matus
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shirley Girshengorn
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Svetlana Achsanov
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Simona Gielman
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Irene Zeldis
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Inbal Schweitzer
- Laboratory for Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Amos Adler
- Laboratory for Microbiology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dan Turner
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Liu C, Chang L, Jia T, Guo F, Zhang L, Ji H, Zhao J, Wang L. Real-time PCR assays for hepatitis B virus DNA quantification may require two different targets. Virol J 2017; 14:94. [PMID: 28494793 PMCID: PMC5427580 DOI: 10.1186/s12985-017-0759-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/27/2017] [Indexed: 12/13/2022] Open
Abstract
Background Quantification Hepatitis B virus (HBV) DNA plays a critical role in the management of chronic HBV infections. However, HBV is a DNA virus with high levels of genetic variation, and drug-resistant mutations have emerged with the use of antiviral drugs. If a mutation caused a sequence mismatched in the primer or probe of a commercial DNA quantification kit, this would lead to an underestimation of the viral load of the sample. The aim of this study was to determine whether commercial kits, which use only one pair of primers and a single probe, accurately quantify the HBV DNA levels and to develop an improved duplex real-time PCR assay. Methods We developed a new duplex real-time PCR assay that used two pairs of primers and two probes based on the conserved S and C regions of the HBV genome. We performed HBV DNA quantitative detection of HBV samples and compared the results of our duplex real-time PCR assays with the COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. The target region of the discordant sample was amplified, sequenced, and validated using plasmid. Results The results of the duplex real-time PCR were in good accordance with the commercial COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. We showed that two samples from Chinese HBV infections underestimated viral loads when quantified by the Roche kit because of a mismatch between the viral sequence and the reverse primer of the Roche kit. The HBV DNA levels of six samples were undervalued by duplex real-time PCR assays of the C region because of mutations in the primer of C region. Conclusions We developed a new duplex real-time PCR assay, and the results of this assay were similar to the results of commercial kits. The HBV DNA level could be undervalued when using the COBAS TaqMan HBV Test version 2 for Chinese HBV infections owing to a mismatch with the primer/probe. A duplex real-time PCR assay based on the S and C regions could solve this problem to some extent.
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Affiliation(s)
- Chao Liu
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Tingting Jia
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Fei Guo
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Lu Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Huimin Ji
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Junpeng Zhao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, No1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China. .,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China. .,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.
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