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Baron A, Moisan A, Unal G, Lemée V, Etienne M, Plantier JC. Evaluation of the ELITechGroup solution for plasma HIV-1 RNA quantification. J Clin Virol 2024; 173:105663. [PMID: 38471301 DOI: 10.1016/j.jcv.2024.105663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
In the last few years, many manufacturers have developed new kits for plasma HIV-1 RNA quantification. Recently, a solution consisting of the ELITe InGenius® instrument and the HIV1 ELITe MGB®kit has been commercialized worldwide. Our aim was to compare its clinical performance with the Aptima® HIV-1 Quant Dx kit by Hologic, on a panel of HIV-1 group M circulating variants, representative of viral load levels found during the pre- and post-treatment follow-up of patients. The linearity was evaluated on the AcroMetrix® HIV-1 Panel. Clinical specificity was evaluated on 100 plasma samples negative for HIV; and clinical sensitivity and sequential follow-up were evaluated on 166 HIV-1 positive plasma samples from 126 patients. The linearity data showed a difference obtained for each point of less than 0.2 Log cp/mL. No amplification was found for the 100 HIV negative clinical specimens. The overall agreement between the two kits was 83.7 %; the differences corresponded to a slightly higher detection for the Aptima kit (with more samples detected below the lower limit of quantification). A Bland & Altman analysis of the quantifiable samples showed a mean difference of -0.05 Log and Spearman's coefficient was 0.975. Only six samples presented discrepancies (above 0.5 Log), but these differences were overall similar between the two kits. Our study has shown that the HIV1 ELITe MGB® Kit can be successfully used for the monitoring of patients infected with various epidemic HIV-1 strains, and for the precise quantification of the viral load.
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Affiliation(s)
- Adeline Baron
- CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - Alice Moisan
- Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - Guillemette Unal
- Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - Véronique Lemée
- Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - Manuel Etienne
- Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Tropical and Infectious Diseases, F-76000 Rouen, France
| | - Jean-Christophe Plantier
- Univ Rouen Normandie, Univ de Caen, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France.
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Jeong S, Lee SK, Cho EJ, Kim HS, Lee YK, Kim JS, Song W, Kim HS. Performance Evaluation of the Roche Cobas 5800 HBV and HCV Tests: Comparison of the 200 and 500 μL Protocols. Ann Lab Med 2024; 44:253-261. [PMID: 38098301 PMCID: PMC10813821 DOI: 10.3343/alm.2023.0306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 11/29/2023] [Indexed: 01/26/2024] Open
Abstract
Background Clinical management of patients infected with hepatitis B virus (HBV) or hepatitis C virus (HCV) relies on the viral load (VL). The Cobas 5800 system (Roche Diagnostics) can determine VLs in 200 and 500 μL samples, but the performance of each protocol has not been compared. We evaluated the performance of both protocols for the HBV and HCV tests. Methods Precision and linearity were verified using commercial panels. Probit analyses were used to determine limits of detection (LoDs). The results obtained with 336 samples were compared using the 200 and 500 μL protocols. Data from 6,737 retrospective HBV and 768 HCV samples were compared to estimate the effects of the different LoDs on the diagnostic results of the protocols. Correlations between protocols were tested with Spearman's rank correlation coefficients (rho). Results The precision and linearity of both protocols were verified. The LoDs for the 200 and 500 μL protocols were 6.5 and 2.7 IU/mL for HBV and 29.7 and 8.2 IU/mL for HCV, respectively. The agreement between the protocols ranged from 0.8 to 1.0. The results obtained with the HBV and HCV tests showed a strong correlation (rho=0.994). Only 0.4% of HBV and 0.4% of HCV test results were affected by the LoDs of the 200 μL protocol. Conclusions The Cobas 5800 200 and 500 μL protocols for the HBV DNA and HCV RNA tests demonstrated excellent performance. These findings establish the 200 μL protocol as a new option for low-volume samples, especially for pediatric and difficult-to-bleed patients.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Su Kyung Lee
- Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Korea
| | - Eun-Jung Cho
- Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Korea
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Shigemori H, Fujita S, Tamiya E, Nagai H. Miniaturization of CRISPR/Cas12-Based DNA Sensor Array by Non-Contact Printing. MICROMACHINES 2024; 15:144. [PMID: 38258263 PMCID: PMC10818962 DOI: 10.3390/mi15010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
DNA microarrays have been applied for comprehensive genotyping, but remain a drawback in complicated operations. As a solution, we previously reported the solid-phase collateral cleavage (SPCC) system based on the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 12 (CRISPR/Cas12). Surface-immobilized Cas12-CRISPR RNA (crRNA) can directly hybridize target double-stranded DNA (dsDNA) and subsequently produce a signal via the cleavage of single-stranded DNA (ssDNA) reporter immobilized on the same spot. Therefore, SPCC-based multiplex dsDNA detection can be performed easily. This study reports the miniaturization of SPCC-based spots patterned by a non-contact printer and its performance in comprehensive genotyping on a massively accumulated array. Initially, printing, immobilization, and washing processes of Cas12-crRNA were established to fabricate the non-contact-patterned SPCC-based sensor array. A target dsDNA concentration response was obtained based on the developed sensor array, even with a spot diameter of 0.64 ± 0.05 mm. Also, the limit of detection was 572 pM, 531 pM, and 3.04 nM with 40, 20, and 10 nL-printing of Cas12-crRNA, respectively. Furthermore, the sensor array specifically detected three dsDNA sequences in one-pot multiplexing; therefore, the feasibility of comprehensive genotyping was confirmed. These results demonstrate that our technology can be miniaturized as a CRISPR/Cas12-based microarray by using non-contact printing. In the future, the non-contact-patterned SPCC-based sensor array can be applied as an alternative tool to DNA microarrays.
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Affiliation(s)
- Hiroki Shigemori
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-0011, Hyogo, Japan
| | - Satoshi Fujita
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
| | - Eiichi Tamiya
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Osaka, Japan
| | - Hidenori Nagai
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-0011, Hyogo, Japan
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Bwire GM, Aiko BG, Mosha IH, Kilapilo MS, Mangara A, Kazonda P, Swai JP, Swalehe O, Jordan MR, Vercauteren J, Sando D, Temba D, Shao A, Mauka W, Decouttere C, Vandaele N, Sangeda RZ, Killewo J, Vandamme AM. High viral suppression and detection of dolutegravir-resistance associated mutations in treatment-experienced Tanzanian adults living with HIV-1 in Dar es Salaam. Sci Rep 2023; 13:20493. [PMID: 37993493 PMCID: PMC10665358 DOI: 10.1038/s41598-023-47795-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023] Open
Abstract
To curb HIV infection rate in Tanzania, antiretroviral therapy (ART) has been scaled up since 2006, and in 2019, the country shifted to regimen including dolutegravir as a default first line. We assessed the success of ART and the contribution of HIV drug resistance (HIVDR) to unsuppressed viral loads. Between February and May 2023 a cross-sectional survey with random sampling was conducted in the six clinics in an urban cohort in Dar es Salaam. Patients with unsuppresed viral loads (local criteria viral load (VL) ≥ 1000 copies/mL) were tested for HIVDR mutations using the WHO adapted protocol for plasma samples. Mutations were interpreted using the Stanford HIVDR database. In total 600 individuals participated in this survey, the majority were female (76.83%), mean age ([Formula: see text] standard deviation) was 44.0 ([Formula: see text] 11.6) years. The median duration on ART (interquartile range) was 6.5 (3.9-10.2) years. Approximately 99% were receiving tenofovir + lamivudine + dolutegravir as a fixed dose combination. VL testing was successful in 99.67% (598/600) of survey patients and only 33 had VL ≥ 1000 copies/mL, resulting in a viral suppression level of 94.48% (565/598, 95% CI 92.34-96.17%). For 23 samples, protease and reverse transcriptase (RT) genotyping were successful, with 13 sequences containing RT inhibitor surveillance drug resistance mutations (SDRMs) (56.5%). No SDRM against protease inhibitors were detected. Thirty samples were successfully genotyped for integrase with 3 sequences (10.08%) containing integrase strand transfer inhibitor (INSTI) SDRMs. In samples successfully genotyped in the three genetic regions, 68.18% (16/22) had a genotypic susceptibility score (GSS) ≥ 2.5 for the concurrent regimen, implying factors beyond drug resistance caused the unsuppressed viral load. For five patients, GSS indicated that HIVDR may have caused the unsuppressed viral load. All three patients with INSTI resistance mutations were highly resistant to dolutegravir and accumulated nucleoside and non-nucleoside RT inhibitor HIVDR mutations. Although in this cohort the last 95 UNAIDS target was almost achieved, HIVDR mutations, including INSTIs resistance mutations were detected in HIV-positive individuals taking ART for at least one year. We recommend the design and implementation of high-impact interventions to prevent the increase of HIVDR, failure of dolutegravir and address the non-resistance factors in the study area.
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Affiliation(s)
- George M Bwire
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research Clinical and Epidemiological Virology, Institute for the Future, KU Leuven, Rega-Herestraat 49-Bus 1040, 3000, Leuven, Belgium.
- Department of Pharmaceutical Microbiology, School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, 65013, Tanzania.
| | - Beatrice Godwin Aiko
- Department of Pharmaceutics and Pharmacy Practice, School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, 65013, Tanzania
- Faculty of Economics and Business, Access to Medicine Research Center, KU Leuven, 3000, Leuven, Belgium
| | - Idda H Mosha
- Department of Behavioural Sciences, School of Public Health and Social Sciences, Muhimbili University of Health and Allied Sciences, Dar es Salaam, 65015, Tanzania
| | - Mary S Kilapilo
- Department of Pharmaceutical Microbiology, School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, 65013, Tanzania
| | - Alli Mangara
- Department of Epidemiology and Biostatistics, School of Public Health and Social Sciences, Dar es Salaam Urban Cohort Study, Dar es Salaam, 65013, Tanzania
| | - Patrick Kazonda
- Department of Epidemiology and Biostatistics, School of Public Health and Social Sciences, Dar es Salaam Urban Cohort Study, Dar es Salaam, 65013, Tanzania
| | - Janeth P Swai
- Department of Business Studies, School of Business, Mzumbe University, Dar es Salaam, 20266, Tanzania
| | - Omary Swalehe
- Department of Business Studies, School of Business, Mzumbe University, Dar es Salaam, 20266, Tanzania
| | | | - Jurgen Vercauteren
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research Clinical and Epidemiological Virology, Institute for the Future, KU Leuven, Rega-Herestraat 49-Bus 1040, 3000, Leuven, Belgium
| | - David Sando
- Managament and Development for Health, Mwai Kibaki Road, Dar es Salaam, Tanzania
| | - David Temba
- Managament and Development for Health, Mwai Kibaki Road, Dar es Salaam, Tanzania
| | - Amani Shao
- Managament and Development for Health, Mwai Kibaki Road, Dar es Salaam, Tanzania
| | - Wilhellmuss Mauka
- Managament and Development for Health, Mwai Kibaki Road, Dar es Salaam, Tanzania
| | - Catherine Decouttere
- Faculty of Economics and Business, Access to Medicine Research Center, KU Leuven, 3000, Leuven, Belgium
| | - Nico Vandaele
- Faculty of Economics and Business, Access to Medicine Research Center, KU Leuven, 3000, Leuven, Belgium
| | - Raphael Z Sangeda
- Department of Pharmaceutical Microbiology, School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, 65013, Tanzania
| | - Japhet Killewo
- Department of Epidemiology and Biostatistics, School of Public Health and Social Sciences, Muhimbili University of Health and Allied Sciences, Dar es Salaam, 65015, Tanzania
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research Clinical and Epidemiological Virology, Institute for the Future, KU Leuven, Rega-Herestraat 49-Bus 1040, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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Shigemori H, Fujita S, Tamiya E, Wakida SI, Nagai H. Solid-Phase Collateral Cleavage System Based on CRISPR/Cas12 and Its Application toward Facile One-Pot Multiplex Double-Stranded DNA Detection. Bioconjug Chem 2023; 34:1754-1765. [PMID: 37782626 PMCID: PMC10587867 DOI: 10.1021/acs.bioconjchem.3c00294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/31/2023] [Indexed: 10/04/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 12 (Cas12) system is attracting interest for its potential as a next-generation nucleic acid detection tool. The system can recognize double-stranded DNA (dsDNA) based on Cas12-CRISPR RNA (crRNA) and induce signal transduction by collateral cleavage. This property is expected to simplify comprehensive genotyping. Here, we report a solid-phase collateral cleavage (SPCC) reaction by CRISPR/Cas12 and its application toward one-pot multiplex dsDNA detection with minimal operational steps. In the sensor, Cas12-crRNA and single-stranded DNA (ssDNA) are immobilized on the sensing surface and act as enzyme and reporter substrates, respectively. We also report a dual-target dsDNA sensor prepared by immobilizing Cas12-crRNA and a fluorophore-labeled ssDNA reporter on separate spots. When a spot captures a target dsDNA sequence, it cleaves the ssDNA reporter on the same spot and reduces its fluorescence by 42.1-57.3%. Crucially, spots targeting different sequences do not show a reduction in fluorescence, thus confirming the one-pot multiplex dsDNA detection by SPCC. Furthermore, the sequence specificity has a two-base resolution, and the detectable concentration for the target dsDNA is at least 10-9 M. In the future, the SPCC-based sensor array could achieve one-pot comprehensive genotyping by using an array spotter as a reagent-immobilizing method.
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Affiliation(s)
- Hiroki Shigemori
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo 657-0011, Japan
| | - Satoshi Fujita
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Eiichi Tamiya
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Institute
of Scientific and Industrial Research (SANKEN), Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shin-ichi Wakida
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Institute
of Scientific and Industrial Research (SANKEN), Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Hidenori Nagai
- Advanced
Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL),
National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Graduate
School of Human Development and Environment, Kobe University, 3-11
Tsurukabuto, Nada-ku, Kobe, Hyogo 657-0011, Japan
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