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Wang Z, Yuan Z, Liu M, Liu Z, Leng P, Ding S, Guo J, Zhang J. Soft interface confined DNA walker for sensitive and specific detection of SARS-CoV-2 variants. Talanta 2024; 274:126009. [PMID: 38579420 DOI: 10.1016/j.talanta.2024.126009] [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: 01/04/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Nucleic acid detection is conducive to preventing the spread of COVID-19 pandemic. In this work, we successfully designed a soft interface confined DNA walker by anchoring hairpin reporter probes on cell membranes for the detection of SARS-CoV-2 variants. In the presence of target RNA, the cyclic self-assembly reaction occurred between hairpin probes H1 and H2, and the continuous walking of target RNA on cell membranes led to the gradual amplification of fluorescence signal. The enrichment of H1 on membranes and the unique fluidity of membranes promoted the collision efficiency between DNA strands in the reaction process, endowing this method with high sensitivity. In addition, the double-blind test of synthetic RNA in 5% normal human serum demonstrated the good stability and anti-interference in complex environment of this method, which exhibited great potential in clinical diagnostics.
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Affiliation(s)
- Zhangmin Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zuowei Yuan
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Min Liu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhidong Liu
- Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Ping Leng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Juan Zhang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing, 400021, China.
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2
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Purba AKR, Rosyid AN, Handayani S, Rachman BE, Romdhoni AC, Al Farabi MJ, Wahyuhadi J, Prananingtias R, Rahayu AN, Alkaff FF, Azmi YA, Prasetyo S, Nadjib M, Gutjahr LP, Humaidy RF. Economic Evaluation of COVID-19 Screening Tests and Surveillance Strategies in Low-Income, Middle-Income, and High-Income Countries: A Systematic Review. Med Sci Monit 2024; 30:e943863. [PMID: 38643358 PMCID: PMC11044836 DOI: 10.12659/msm.943863] [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: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Economic evaluation of the testing strategies to control transmission and monitor the severity of COVID-19 after the pandemic is essential. This study aimed to review the economic evaluation of COVID-19 tests and to construct a model with outcomes in terms of cost and test acceptability for surveillance in the post-pandemic period in low-income, middle-income, and high-income countries. MATERIAL AND METHODS We performed the systematic review following PRISMA guidelines through MEDLINE and EMBASE databases. We included the relevant studies that reported the economic evaluation of COVID-19 tests for surveillance. Also, we input current probability, sensitivity, and specificity for COVID-19 surveillance in the post-pandemic period. RESULTS A total of 104 articles met the eligibility criteria, and 8 articles were reviewed and assessed for quality. The specificity and sensitivity of COVID-19 screening tests were reported as 80% to 90% and 40% to 90%, respectively. The target population presented a mortality rate between 0.2% and 19.2% in the post-pandemic period. The implementation model of COVID-19 screening tests for surveillance with a cost mean for molecular and antigen tests was US$ 46.64 (min-max US $0.25-$105.39) and US $6.15 (min-max US $2-$10), respectively. CONCLUSIONS For the allocation budget for the COVID-19 surveillance test, it is essential to consider the incidence and mortality of the post-pandemic period in low-income, middle-income, and high-income countries. A robust method to evaluate outcomes is needed to prevent increasing COVID-19 incidents earlier.
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Affiliation(s)
- Abdul Khairul Rizki Purba
- Division of Pharmacology and Therapy, Department of Anatomy Histology and Pharmacology, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
- Department of Health Science, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Medical Education Master Program, Faculty of Medicine, Universitas Airlangga, Surabaya, West Java, Indonesia
| | - Alfian Nur Rosyid
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Samsriyaningsih Handayani
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Brian Eka Rachman
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Achmad Chusnu Romdhoni
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Makhyan Jibril Al Farabi
- Department of Cardiology and Vascular Medicine, Universitas Airlangga/Soetomo General Hospital, Surabaya, Eest Java, Indonesia
| | - Joni Wahyuhadi
- Department of Neurosurgery, Faculty of medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Rosita Prananingtias
- Department of Medical Record, Universitas Airlangga Hospital, Surabaya, Eest Java, Indonesia
| | - Ainun Nitsa Rahayu
- Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Firas Farisi Alkaff
- Division of Pharmacology and Therapy, Department of Anatomy, Histology, and Pharmacology, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Yufi Aulia Azmi
- Department of Urology, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Academic Hospital, Surabaya, Eest Java, Indonesia
- Department Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sabarinah Prasetyo
- Department of Biostatistic and Population Studies, Faculty of Public Health, Universitas Indonesia, Depok, West Java, Indonesia
| | - Mardiati Nadjib
- Department of Health Administration and Health Policy, Faculty of Public Health, Universitas Indonesia, Depok, West Java, Indonesia
| | | | - Raudia Faridah Humaidy
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
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3
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Wang Q, Kline EC, Gilligan-Steinberg SD, Lai JJ, Hull IT, Olanrewaju AO, Panpradist N, Lutz BR. Sensitive Pathogen Detection and Drug Resistance Characterization Using Pathogen-Derived Enzyme Activity Amplified by LAMP or CRISPR-Cas. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.29.24305085. [PMID: 38633802 PMCID: PMC11023665 DOI: 10.1101/2024.03.29.24305085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Pathogens encapsulate or encode their own suite of enzymes to facilitate replication in the host. The pathogen-derived enzymes possess specialized activities that are essential for pathogen replication and have naturally been candidates for drug targets. Phenotypic assays detecting the activities of pathogen-derived enzymes and characterizing their inhibition under drugs offer an opportunity for pathogen detection, drug resistance testing for individual patients, and as a research tool for new drug development. Here, we used HIV as an example to develop assays targeting the reverse transcriptase (RT) enzyme encapsulated in HIV for sensitive detection and phenotypic characterization, with the potential for point-of-care (POC) applications. Specifically, we targeted the complementary (cDNA) generation activity of the HIV RT enzyme by adding engineered RNA as substrates for HIV RT enzyme to generate cDNA products, followed by cDNA amplification and detection facilitated by loop-mediated isothermal amplification (LAMP) or CRISPR-Cas systems. To guide the assay design, we first used qPCR to characterize the cDNA generation activity of HIV RT enzyme. In the LAMP-mediated Product-Amplified RT activity assay (LamPART), the cDNA generation and LAMP amplification were combined into one pot with novel assay designs. When coupled with direct immunocapture of HIV RT enzyme for sample preparation and endpoint lateral flow assays for detection, LamPART detected as few as 20 copies of HIV RT enzyme spiked into 25μL plasma (fingerstick volume), equivalent to a single virion. In the Cas-mediated Product-Amplified RT activity assay (CasPART), we tailored the substrate design to achieve a LoD of 2e4 copies (1.67fM) of HIV RT enzyme. Furthermore, with its phenotypic characterization capability, CasPART was used to characterize the inhibition of HIV RT enzyme under antiretroviral drugs and differentiate between wild-type and mutant HIV RT enzyme for potential phenotypic drug resistance testing. Moreover, the CasPART assay can be readily adapted to target the activity of other pathogen-derived enzymes. As a proof-of-concept, we successfully adapted CasPART to detect HIV integrase with a sensitivity of 83nM. We anticipate the developed approach of detecting enzyme activity with product amplification has the potential for a wide range of pathogen detection and phenotypic characterization.
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Affiliation(s)
- Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ayokunle O. Olanrewaju
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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4
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Kang M, Jeong E, Kim JY, Yun SA, Jang MA, Jang JH, Kim TY, Huh HJ, Lee NY. Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay. Sci Rep 2023; 13:20364. [PMID: 37990045 PMCID: PMC10663557 DOI: 10.1038/s41598-023-47645-0] [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: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
In the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
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Affiliation(s)
- Minhee Kang
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Eunjung Jeong
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji-Yeon Kim
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Sun Ae Yun
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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5
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Miyamura S, Oe R, Nakahara T, Koresawa H, Okada S, Taue S, Tokizane Y, Minamikawa T, Yano TA, Otsuka K, Sakane A, Sasaki T, Yasutomo K, Kajisa T, Yasui T. Rapid, high-sensitivity detection of biomolecules using dual-comb biosensing. Sci Rep 2023; 13:14541. [PMID: 37752134 PMCID: PMC10522648 DOI: 10.1038/s41598-023-41436-3] [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: 04/09/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023] Open
Abstract
Rapid, sensitive detection of biomolecules is important for biosensing of infectious pathogens as well as biomarkers and pollutants. For example, biosensing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still strongly required for the fight against coronavirus disease 2019 (COVID-19) pandemic. Here, we aim to achieve the rapid and sensitive detection of SARS-CoV-2 nucleocapsid protein antigen by enhancing the performance of optical biosensing based on optical frequency combs (OFC). The virus-concentration-dependent optical spectrum shift produced by antigen-antibody interactions is transformed into a photonic radio-frequency (RF) shift by a frequency conversion between the optical and RF regions in the OFC, facilitating rapid and sensitive detection with well-established electrical frequency measurements. Furthermore, active-dummy temperature-drift compensation with a dual-comb configuration enables the very small change in the virus-concentration-dependent signal to be extracted from the large, variable background signal caused by temperature disturbance. The achieved performance of dual-comb biosensing will greatly enhance the applicability of biosensors to viruses, biomarkers, environmental hormones, and so on.
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Affiliation(s)
- Shogo Miyamura
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Ryo Oe
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Takuya Nakahara
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Hidenori Koresawa
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Shota Okada
- Graduate School of Sciences and Technology for Innovation, Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Shuji Taue
- School of System Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami, Kochi, 782-8502, Japan
| | - Yu Tokizane
- Division of Next-Generation Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Takeo Minamikawa
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Taka-Aki Yano
- Division of Next-Generation Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
| | - Kunihiro Otsuka
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Ayuko Sakane
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
- Department of Biochemistry, Graduate School of Medicine, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Takuya Sasaki
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
- Department of Biochemistry, Graduate School of Medicine, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Koji Yasutomo
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan
- Department of Immunology and Parasitology, Graduate School of Medicine, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Taira Kajisa
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan.
- Graduate School of Interdisciplinary New Science, Toyo University, 2100 Kujirai, Kawagoe, Saitama, 350-8585, Japan.
| | - Takeshi Yasui
- Division of Next-Generation Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima, 770-8506, Japan.
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6
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Lee S, Kim S, Kim S. A novel paper-based lysis strip for SARS-CoV-2 RNA detection at low resource settings. Anal Biochem 2023; 664:115037. [PMID: 36623679 PMCID: PMC9817428 DOI: 10.1016/j.ab.2023.115037] [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: 10/31/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Infectious respiratory diseases such as COVID-19 are serious and global concerns from the past to the present. To isolate the spread of infectious diseases even in the absence of a health system, a simple, inexpensive, reliable, sensitive, and selective molecular diagnosis platform for Point of Care Test (POCT) is required. Especially, the nucleic acid extraction step is difficult to perform out of laboratory. Here, we propose a paper-based lysis (PBL) strip for nucleic acid extraction, especially in low-resource settings (LRS). PBL strips are suitable for isolating RNA from viruses with biological interference and inhibitors. We optimized the buffer compositions and membranes of the strip. A simple preparation method using a PBL strip could obtain an eluent for downstream inspection within 20 min. Overall, 104 copies/swaps were detected for 20 min for amplification in combination with Reverse Transcription Loop-Mediated Amplification (RT-LAMP).
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Affiliation(s)
| | | | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
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7
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Zhang L, Wang X, Liu D, Wu Y, Feng L, Han C, Liu J, Lu Y, Sotnikov DV, Xu Y, Cheng J. SMART: A Swing-Assisted Multiplexed Analyzer for Point-of-Care Respiratory Tract Infection Testing. BIOSENSORS 2023; 13:228. [PMID: 36831994 PMCID: PMC9954503 DOI: 10.3390/bios13020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Respiratory tract infections such as the ongoing coronavirus disease 2019 (COVID-19) has seriously threatened public health in the last decades. The experience of fighting against the epidemic highlights the importance of user-friendly and accessible point-of-care systems for nucleic acid (NA) detection. To realize low-cost and multiplexed point-of-care NA detection, a swing-assisted multiplexed analyzer for point-of-care respiratory tract infection testing (SMART) was proposed to detect multiple respiratory tract pathogens using visible loop-mediated isothermal amplification. By performing hand-swing movements to generate acceleration force to distribute samples into reaction chambers, the design of the SMART system was greatly simplified. By using different format of chips and integrating into a suitcase, this system can be applied to on-site multitarget and multi-sample testing. Three targets including the N and Orf genes of SARS-CoV-2 and the internal control were simultaneously analyzed (limit of detection: 2000 copies/mL for raw sample; 200 copies/mL for extracted sample). Twenty-three clinical samples with eight types of respiratory bacteria and twelve COVID-19 clinical samples were successfully detected. These results indicate that the SMART system has the potential to be further developed as a versatile tool in the diagnosis of respiratory tract infection.
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Affiliation(s)
- Li Zhang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xu Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dongchen Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yu Wu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing 101111, China
| | - Chunyan Han
- CapitalBiotech Technology, Beijing 101111, China
| | - Jiajia Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Dmitriy V. Sotnikov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Jing Cheng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
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8
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Wang A, Li Y, You X, Zhang S, Zhou J, Liu H, Ding P, Chen Y, Qi Y, Liu Y, Liang C, Zhu X, Zhang Y, Liu E, Zhang G. Electrochemical immunosensor nanoarchitectonics with the Ag-rGO nanocomposites for the detection of receptor-binding domain of SARS-CoV-2 spike protein. J Solid State Electrochem 2023; 27:489-499. [PMID: 36466035 PMCID: PMC9707143 DOI: 10.1007/s10008-022-05330-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022]
Abstract
As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a grave threat to human life and health, it is essential to develop an efficient and sensitive detection method to identify infected individuals. This study described an electrode platform immunosensor to detect SARS-CoV-2-specific spike receptor-binding domain (RBD) protein based on a bare gold electrode modified with Ag-rGO nanocomposites and the biotin-streptavidin interaction system. The Ag-rGO nanocomposites was obtained by chemical synthesis and characterized by electrochemistry and scanning electron microscope (SEM). Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to record the electrochemical signals in the electrode modification. The differential pulse voltammetry (DPV) results showed that the limit of detection (LOD) of the immunosensor was 7.2 fg mL-1 and the linear dynamic detection range was 0.015 ~ 158.5 pg mL-1. Furthermore, this sensitive immunosensor accurately detected RBD in artificial saliva with favorable stability, specificity, and reproducibility, indicating that it has the potential to be used as a practical method for the detection of SARS-CoV-2.
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Affiliation(s)
- Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yuya Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Xiaojuan You
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Jingming Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Hongliang Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yanhua Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yankai Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Chao Liang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Xifang Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Ying Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Enping Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Gaiping Zhang
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871 China
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan China
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002 Henan China
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9
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. Microbiol Spectr 2022; 10:e0158321. [PMID: 35708340 PMCID: PMC9430505 DOI: 10.1128/spectrum.01583-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/06/2022] [Indexed: 11/20/2022] Open
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high-throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false-negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multitarget redundancy and an internal amplification control. A convenient and cost-effective target-specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-CoV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high-frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multitarget redundancy. When challenged with extracted human samples the multiplex assay showed 87% or better sensitivity (of 30 positive samples), with 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction (of 21 positive samples), and 100% specificity (of 60 negative samples). These results are further evidence that conventional laboratory methodologies can be leveraged at the point of care for robust performance and diagnostic stability over time. IMPORTANCE The COVID-19 pandemic has had tremendous impact, and the ability to perform molecular diagnostics in resource limited settings has emerged as a key resource for mitigating spread of the disease. One challenge in COVID-19 diagnosis, as well as other viruses, is ongoing mutation that can allow viruses to evade detection by diagnostic tests. We developed a test that detects multiple parts of the virus genome in a single test to reduce the chance of missing a virus due to mutation, and it is designed to be simpler and faster than typical laboratory tests while maintaining high sensitivity. This capability is enabled by a novel fluorescent probe technology that works with a simple constant temperature reaction condition.
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Affiliation(s)
- Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health for Women Adolescents and Children, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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10
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Evaluation and Clinical Validation of Guanidine-Based Inactivation Transport Medium for Preservation of SARS-CoV-2. Adv Pharmacol Pharm Sci 2022; 2022:1677621. [PMID: 35873075 PMCID: PMC9301760 DOI: 10.1155/2022/1677621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 12/02/2022] Open
Abstract
WHO declared the outbreak of COVID-19, caused by SARS-CoV-2, a pandemic in March 2020. More than 223 million cases and approximately 4.6 million deaths have been confirmed. Early diagnosis and immediate treatment became a priority during this pandemic. However, COVID-19 diagnostic testing resources are limited, especially early in the pandemic. Apart from being limited, the COVID-19 diagnostic tests using reverse transcription polymerase chain reaction (RT-PCR) have encountered storage, transportation, and safety issues. These problems are mainly experienced by developing poor countries, countries in the equatorial region, and archipelagic countries. VITPAD® is a guanidine-based inactivation transport medium (ITM) formulated to maintain the RNA quality of SARS-CoV-2 during transportation without cold chains. This study, conducted from September 2020 to March 2021, performed clinical validation of VITPAD® by comparing its performance with a globally commercially available ITM from the NEST brand. Its stability at room temperature, safety, and resistance at high temperatures was also tested using RT-PCR analysis. VITPAD® can reduce the infectious nature of the specimen, preserve the SARS-CoV-2 for 18 days at an ambient temperature, and resist high temperatures (40°C for 3 hours). A guanidine-based transport medium, such as VITPAD®, is compatible and recommended for RT-PCR-based molecular diagnosis of COVID-19.
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11
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Hoffman JS, Hirano M, Panpradist N, Breda J, Ruth P, Xu Y, Lester J, Nguyen BH, Ceze L, Patel SN. Passively sensing SARS-CoV-2 RNA in public transit buses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:152790. [PMID: 35007574 PMCID: PMC8741327 DOI: 10.1016/j.scitotenv.2021.152790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/24/2021] [Accepted: 12/26/2021] [Indexed: 05/25/2023]
Abstract
Affordably tracking the transmission of respiratory infectious diseases in urban transport infrastructures can inform individuals about potential exposure to diseases and guide public policymakers to prepare timely responses based on geographical transmission in different areas in the city. Towards that end, we designed and tested a method to detect SARS-CoV-2 RNA in the air filters of public buses, revealing that air filters could be used as passive fabric sensors for the detection of viral presence. We placed and retrieved filters in the existing HVAC systems of public buses to test for the presence of trapped SARS-CoV-2 RNA using phenol-chloroform extraction and RT-qPCR. SARS-CoV-2 RNA was detected in 14% (5/37) of public bus filters tested in Seattle, Washington, from August 2020 to March 2021. These results indicate that this sensing system is feasible and that, if scaled, this method could provide a unique lens into the geographically relevant transmission of SARS-CoV-2 through public transit rider vectors, pooling samples of riders over time in a passive manner without installing any additional systems on transit vehicles.
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Affiliation(s)
- Jason S Hoffman
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA.
| | - Matthew Hirano
- Department of Electrical and Computer Engineering, University of Washington, 185 Stevens Way, Seattle 98195, WA, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle 98105, WA, USA
| | - Joseph Breda
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA
| | - Parker Ruth
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA; Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle 98105, WA, USA
| | - Yuanyi Xu
- Department of Microbiology, University of Washington, 1705 NE Pacific St, Seattle 98195, WA, USA; Department of Chemistry, University of Washington, 4000 15th Ave NE, Seattle 98195, WA, USA
| | - Jonathan Lester
- Microsoft Research, 14820 NE 36th St, Redmond 98052, WA, USA
| | | | - Luis Ceze
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA
| | - Shwetak N Patel
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 185 E. Stevens Way NE, Seattle 98195, WA, USA; Department of Electrical and Computer Engineering, University of Washington, 185 Stevens Way, Seattle 98195, WA, USA
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12
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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13
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Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B, Chung MH, Frenkel LM, Lutz BR, Klavins E, Beck IA. Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000185. [PMID: 36962187 PMCID: PMC10021139 DOI: 10.1371/journal.pgph.0000185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/09/2022] [Indexed: 04/24/2023]
Abstract
Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on "Aquarium", a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, "OLA-Simple", that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision. To evaluate the training by Aquarium software we conducted a feasibility study in a laboratory at Coptic Hope Center in Nairobi, Kenya. Twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit. None of the laboratory technicians had prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with genotyping results interpreted correctly by unaided-eye in 108/120 (90%) and by software in 116/120 (97%) of codons analyzed. In the surveys, participants favorably assessed the use of software guidance. The Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
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Affiliation(s)
- Justin D. Vrana
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Parker Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ruth Kanthula
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Samar R. Sakr
- Coptic Hope Center for Infectious Diseases, Nairobi, Kenya
| | - Bhavna Chohan
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Departments of Global Health, Medicine, Pediatrics, and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
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14
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Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B, Chung MH, Frenkel LM, Lutz BR, Klavins E, Beck IA. Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya. PLOS GLOBAL PUBLIC HEALTH 2022. [PMID: 36962187 DOI: 10.1101/2021.05.06.21256654v1.full.pdf+html] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on "Aquarium", a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, "OLA-Simple", that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision. To evaluate the training by Aquarium software we conducted a feasibility study in a laboratory at Coptic Hope Center in Nairobi, Kenya. Twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit. None of the laboratory technicians had prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with genotyping results interpreted correctly by unaided-eye in 108/120 (90%) and by software in 116/120 (97%) of codons analyzed. In the surveys, participants favorably assessed the use of software guidance. The Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
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Affiliation(s)
- Justin D Vrana
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Parker Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ruth Kanthula
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Samar R Sakr
- Coptic Hope Center for Infectious Diseases, Nairobi, Kenya
| | - Bhavna Chohan
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael H Chung
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- Departments of Global Health, Medicine, Pediatrics, and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
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15
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow. Analyst 2022; 147:3315-3327. [PMID: 35762367 PMCID: PMC10143869 DOI: 10.1039/d2an00405d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This new workflow enables co-extraction of HIV and SARS-CoV2 RNAs from clinical pooled plasma/nasal secretion samples that allows sensitive detection of SARS-CoV-2 and HIV infections in the patients-living with HIV.
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Affiliation(s)
- Gaurav K. Gulati
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, USA
| | - Samuel W. A. Stewart
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ceejay Boyce
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Santiago Avila-Ríos
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Peter D. Han
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gustavo Reyes-Terán
- Coordination of the Mexican National Institutes of Health and High Specialty Hospitals, Mexico City, Mexico
| | - Lea M. Starita
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Departments of Medicine, Pediatrics, Laboratory Medicine and Pathology, Global Health and Medicine, University of Washington, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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16
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Hull IT, Kline EC, Gulati GK, Kotnik JH, Panpradist N, Shah KG, Wang Q, Frenkel L, Lai J, Stekler J, Lutz BR. Isothermal Amplification with a Target-Mimicking Internal Control and Quantitative Lateral Flow Readout for Rapid HIV Viral Load Testing in Low-Resource Settings. Anal Chem 2021; 94:1011-1021. [PMID: 34920665 DOI: 10.1021/acs.analchem.1c03960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Point-of-care diagnostics often use isothermal nucleic acid amplification for qualitative detection of pathogens in low-resource healthcare settings but lack sufficient precision for quantitative applications such as HIV viral load monitoring. Although viral load (VL) monitoring is an essential component of HIV treatment, commercially available tests rely on relatively high-resource chemistries like real-time polymerase chain reaction and are thus used on an infrequent basis for millions of people living with HIV in low-income countries. To address the constraints of low-resource settings on nucleic acid quantification, we describe a recombinase polymerase amplification and lateral flow detection approach that quantifies HIV-1 DNA or RNA by comparison to a competitive internal amplification control (IAC) of a known copy number, which may be set to any useful threshold (in our case, a clinically relevant threshold for HIV treatment failure). The IAC is designed to amplify alongside the HIV target with a similar efficiency, allowing for normalization of the assay to variation or inhibition and enabling an endpoint readout that is compatible with commercially available kits for nucleic acid lateral flow detection and interpretable with minimal instrumentation or by the naked eye. We find that this approach can reliably differentiate ≤600 or ≥1400 copies of HIV DNA from a 1000-copy threshold when lateral flow strips are imaged with a conventional office scanner and analyzed with free densitometry software. We further demonstrate a user-friendly adaptation of this analysis to process cell phone photographs with an automated script. Alternatively, we show via a survey that 21 minimally trained volunteers could reliably resolve ≥10-fold (log10) differences of HIV DNA or RNA by naked eye interpretation of lateral flow results. This amplification and detection workflow requires minimal instrumentation, takes just 30 min to complete, and when combined with a suitable sample preparation method, may enable HIV VL testing while the patient waits or a self-test, which has the potential to improve care. This approach may be adapted for other applications that require quantitative analysis of a nucleic acid target in low-resource settings.
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Affiliation(s)
- Ian T Hull
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Gaurav K Gulati
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Jack Henry Kotnik
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Kamal G Shah
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Lisa Frenkel
- Department of Pediatrics, University of Washington, Seattle, Washington 98195-9300, United States.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195-7470, United States.,Department of Global Health, University of Washington, Seattle, Washington 98195-1620, United States.,Department of Medicine, University of Washington, Seattle, Washington 98195-6420, United States.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98145-5005, United States
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Joanne Stekler
- Department of Medicine, University of Washington, Seattle, Washington 98195-6420, United States
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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17
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Panpradist N, Kline EC, Atkinson RG, Roller M, Wang Q, Hull IT, Kotnik JH, Oreskovic AK, Bennett C, Leon D, Lyon V, Gilligan-Steinberg SD, Han PD, Drain PK, Starita LM, Thompson MJ, Lutz BR. Harmony COVID-19: A ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection. SCIENCE ADVANCES 2021; 7:eabj1281. [PMID: 34910507 PMCID: PMC8673764 DOI: 10.1126/sciadv.abj1281] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/26/2021] [Indexed: 05/22/2023]
Abstract
RNA amplification tests sensitively detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but their complexity and cost are prohibitive for expanding coronavirus disease 2019 (COVID-19) testing. We developed “Harmony COVID-19,” a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device. Our ready-to-use, multiplexed reverse transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/μl and can report in 17 min for high–viral load samples (5000 copies/μl). Harmony detected 97 or 83% of contrived samples with ≥0.5 viral particles/μl in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens (n = 101) showed 100% detection of RNA extracted from specimens with ≥0.5 SARS-CoV-2 RNA copies/μl, with 100% specificity in specimens positive for other respiratory pathogens. Extraction-free analysis (n = 29) had 95% success in specimens with ≥1 RNA copies/μl. Usability testing performed first time by health care workers showed 95% accuracy.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Global Health for Women, Adolescents, and Children, School of Public Health, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Robert G. Atkinson
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Michael Roller
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jack H. Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Crissa Bennett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Daniel Leon
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Victoria Lyon
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | | | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul K. Drain
- Departments of Global Health, Medicine, and Epidemiology, University of Washington, Seattle, WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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Wallner JJ, Beck IA, Panpradist N, Ruth PS, Valenzuela-Ponce H, Soto-Nava M, Ávila-Ríos S, Lutz BR, Frenkel LM. Rapid Near Point-of-Care Assay for HLA-B*57:01 Genotype Associated with Severe Hypersensitivity Reaction to Abacavir. AIDS Res Hum Retroviruses 2021; 37:930-935. [PMID: 34714103 DOI: 10.1089/aid.2021.0103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The nucleoside reverse transcriptase inhibitor abacavir (ABC) is used commonly to treat young children with HIV infection and is a component of the fixed-dose-combination Triumeq®. ABC can trigger a severe hypersensitivity reaction in people who are homozygous or heterozygous for HLA-B*57:01. Testing for HLA-B*57:01 before ABC initiation is standard-of-care in high-resource settings, but current tests are costly or difficult to access in resource-limited settings. To address these gaps, we developed an inexpensive simple-to-use rapid assay to detect HLA-B*57:01. We designed and optimized a multiplexed polymerase chain reaction (PCR) to amplify HLA-B*57 subtypes and the human beta-globin gene; employed probes and ligation to specifically tag the HLA-B*57:01 allele with biotin. Tagged-ligated products were detected by immunocapture in an enzyme-linked immunosorbent assay plate or lateral flow strip. Cell lines with known HLA genotypes were used to optimize the assay. The optimized assay was then compared with genotypes of clinical specimens (n = 60) determined by sequencing, with specimens enriched for individuals with HLA-B*57:01. The optimized assay utilizes 40-min 35-cycle multiplex PCR for B*57 and beta-globin; 20-min ligation reaction; and 15-min detection. Evaluation of the HLA-B*57:01 oligonucleotide ligation assay using clinical specimens had a sensitivity of 100% (n = 27/27 typed as B*57:01) and specificity of 100% (n = 33/33 typed as non-B*57:01) by visual interpretation of lateral flow strips. The cost is US$5.96/specimen. This rapid and economical assay accurately detects HLA-B*57:01 in clinical specimens. Use of this assay could expand access to HLA-B*57:01 genotyping and facilitate safe same-day initiation of ABC-based treatment.
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Affiliation(s)
- Jackson J. Wallner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, USA
| | - Parker S. Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
| | - Humberto Valenzuela-Ponce
- CIENI Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Maribel Soto-Nava
- CIENI Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Santiago Ávila-Ríos
- CIENI Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Laboratory Medicine and Pathology, Global Health, and Medicine, Departments of Pediatrics, University of Washington, Seattle, Washington, USA
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19
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He Y, Xie T, Tong Y. Rapid and highly sensitive one-tube colorimetric RT-LAMP assay for visual detection of SARS-CoV-2 RNA. Biosens Bioelectron 2021; 187:113330. [PMID: 34022500 PMCID: PMC8117486 DOI: 10.1016/j.bios.2021.113330] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a highly contagious disease. To tame the continuously raging outbreak of COVID-19, developing a cheap, rapid and sensitive testing assay is absolutely imperative. Herein, we developed a one-tube colorimetric RT-LAMP assay for the visual detection of SARS-CoV-2 RNA. The assay integrates Si-OH magnetic beads (MBs)-based fast RNA extraction and rapid isothermal amplification in a single tube, thus bypassing the RNA elution step and directly amplifying on-beads RNA molecules with the visualized results. This one-tube assay has a limit of detection (LOD) as low as 200 copies/mL for sample input volumes of up to 600 μL, and can be performed in less than 1 h from sample collection to result readout. This assay demonstrated a 100% concordance with the gold standard test RT-qPCR test by using 29 clinical specimens and showed high specificity. This one-tube colorimetric RT-LAMP assay can serve as an alternative platform for a rapid and sensitive diagnostic test for COVID-19 and is particularly suitable for use at community clinics or township hospitals.
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Affiliation(s)
- Yugan He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Tie Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, PR China.
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20
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Inexpensive workflow for simultaneous monitoring of HIV viral load and detection of SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.18.21256786. [PMID: 34462759 PMCID: PMC8404901 DOI: 10.1101/2021.08.18.21256786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
BACKGROUND COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are at high risk for exposure to SARS-CoV-2 infection and severe disease once infected. For this population, it is urgent to closely monitor HIV plasma viral load ( VL ) and screen for SARS-COV-2 infection. METHOD We have developed a non-proprietary method to isolate RNA from plasma, nasal secretions ( NS ), or both. HIV, SARS-CoV-2, and human RP targets in extracted RNA are then RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status ( i . e ., HIV as VL failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). We evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-seropositive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 pooled plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house extraction to those using a commercial extraction kit. RESULTS In-house extraction had a detection limit of 200-copies/mL for HIV and 100-copies/mL for SARS-CoV-2. In-house and commercial methods yielded positively correlated HIV VL (R 2 : 0.98 for contrived samples; 0.81 for seropositive plasma). SARS-CoV-2 detection had 100% concordant classifications in contrived samples, and in clinical NS extracted by in-house method, excluding indeterminate results, was 95% concordant (25 positives, 6 presumptive positives, and 31 negatives) to those using the commercial method. Analysis of pooled plasma/NS showed R 2 of 0.91 (contrived samples) and 0.71 (clinical specimens) for HIV VL correlations obtained by both extraction methods, while SARS-CoV-2 detection showed 100% concordance in contrived and clinical specimens. INTERPRETATION Our low-cost workflow for molecular testing of HIV and SARS-CoV-2 could serve as an alternative to current standard assays for laboratories in low-resource settings.
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21
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34462755 DOI: 10.1101/2021.08.13.21261995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multi-target redundancy and an internal amplification control. A convenient and cost-effective target specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-COV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multi-target redundancy. When challenged with extracted human samples the multiplexed assay showed 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction, and 100% specificity. These results are further evidence that conventional laboratory methodologies can be leveraged at the point-of-care for robust performance and diagnostic stability over time.
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22
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Akhtar MK, Leung RKK, Khan G. Rethinking COVID-19 test sensitivity-a strategy for improving the detection limit. Pan Afr Med J 2021; 39:244. [PMID: 34659617 PMCID: PMC8498663 DOI: 10.11604/pamj.2021.39.244.30131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/07/2021] [Indexed: 11/26/2022] Open
Abstract
Numerous genetic tests for the detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, including those based on the ever-popular real-time polymerase chain reaction (RT-qPCR) technique, have been reported. These diagnostic tests give false negatives particularly during the early and late stages of COVID-19 clearly indicating inadequate test sensitivity. The entire COVID-19 diagnostic workflow is often overlooked and given very little attention. Herein, we propose that volumetric modifications to COVID-19 workflows would significantly improve detection limits. We would therefore encourage researchers to adopt a holistic approach, in which all the steps of a COVID-19 diagnostic workflow, are carefully scrutinised, particularly those upstream factors at the viral sampling and pre-analytical stages.
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Affiliation(s)
- Mohammed Kalim Akhtar
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ross Ka-Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Gulfaraz Khan
- Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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