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do Nascimento MCA, Smith WJM, Gebrewold M, Liu Y, Simpson SL, Bivins A, Rahal P, Ahmed W. Development and evaluation of a colorimetric LAMP based-assay targeting the Bacteroides HF183 marker for tracking sewage pollution in environmental waters. WATER RESEARCH 2024; 264:122202. [PMID: 39146849 DOI: 10.1016/j.watres.2024.122202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024]
Abstract
Surface waters are vulnerable to contamination by human and animal feces, posing risks to human health due to potential exposure to enteric pathogens. This research developed a colorimetric loop-mediated isothermal amplification (cLAMP) assay to detect sewage associated Bacteroides dorei HF183/BacR287 (HF183) marker in wastewater and environmental water samples. The host sensitivity and host specificity of the assay were evaluated, and their performance was compared to the Bacteroides HF183 qPCR assay using control materials (gBlocks), environmental water samples seeded with untreated sewage, and ambient environmental water samples. In serial dilutions of control materials, qPCR produced quantifiable data across all dilutions, while cLAMP detected the marker down to 0.001 pg/µL of control materials, which was two orders of magnitude less sensitive than qPCR. All untreated sewage samples (n = 12) tested positive for HF183 by both the qPCR and cLAMP assays, demonstrating a host sensitivity value of 1.00 (maximum value of 1.00). The host specificity by analysing 70 non-human fecal nucleic acid samples revealed cLAMP's specificity value of 0.81 compared to qPCR's 0.64. When testing sewage-seeded environmental water samples, both methods detected HF183 for the lowest amount of sewage, indicating similar detection sensitivity. The application of cLAMP for tracking sewage pollution in environmental waters showed promising results, with moderate agreement between cLAMP and qPCR (κ = 0.510). However, cLAMP occasionally missed detections compared to qPCR, particularly in low-concentration samples. Overall, the cLAMP HF183 assay demonstrated promising potential as a rapid and sensitive method for detecting sewage pollution, offering a viable alternative to qPCR in certain environmental monitoring scenarios.
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Affiliation(s)
- Mariah C A do Nascimento
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia; Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | | | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia; State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Stuart L Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Paula Rahal
- Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
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2
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Jaroenram W, Teerapittayanon S, Suvannakad R, Pengpanich S, Kampeera J, Arunrut N, Dangtip S, Sirithammajak S, Tondee B, Khumwan P, Japakasetr S, Leaungwutiwong P, Chatnuntawech I, Kiatpathomchai W. Enhancing efficiency in detection of COVID-19 through AI-driven colorimetric isothermal detection with multiplex primers. Diagn Microbiol Infect Dis 2024; 110:116446. [PMID: 39096664 DOI: 10.1016/j.diagmicrobio.2024.116446] [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: 03/19/2024] [Revised: 06/27/2024] [Accepted: 07/14/2024] [Indexed: 08/05/2024]
Abstract
COVID-19 has afflicted millions of lives worldwide. Although there are many rapid methods to detect it based on colorimetric loop-mediated isothermal amplification, there remains room for improvement. This study aims to 1) integrate multiple primers into a singleplex assay to enhance the diagnostic sensitivity, and 2) utilize a high-throughput smartphone-operatable AI-driven color reading tool to enable a rapid result analysis. This setup can improve the sensitivity by 10-100 times and can analyze approximately 6700 samples per minute. The assay is simpler than RT-qPCR, with a turnaround time of less than 75 min. It can detect various types of SARS-CoV-2 by targeting 3 genes, increasing the likelihood that it will remain effective even if the virus undergoes mutations in any single target gene. In summary, it affords potential for adaptation to detection of new/re-emerging diseases with the visual readout for maximum assay simplicity and AI-operated mode for large-scale testing.
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Affiliation(s)
- Wansadaj Jaroenram
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Surat Teerapittayanon
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Rapheephat Suvannakad
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Sukanya Pengpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Jantana Kampeera
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Narong Arunrut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Sirintip Dangtip
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Sarawut Sirithammajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Benyatip Tondee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Pakapreud Khumwan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | | | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Itthi Chatnuntawech
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand
| | - Wansika Kiatpathomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani 12120, Thailand.
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3
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Sabateen A, Sadaqa D, Nino T, Zaghal G, Qumsieh G, Fakhori R, Rjoub H, Taha T, Zghari R, Abu Hanieh S, Al-Basha D, Qabaja M, Alsaid H, Hindiyeh MY. Evaluation of COVID-19 rapid antigen test against polymerase chain reaction test in immunocompromised patients. PLoS One 2024; 19:e0306396. [PMID: 39093858 PMCID: PMC11296623 DOI: 10.1371/journal.pone.0306396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 06/14/2024] [Indexed: 08/04/2024] Open
Abstract
On the 11th of March 2020, the world faced a new global pandemic, COVID-19 which is a disease caused by the novel coronavirus, it had multiple devastating outcomes on multiple sectors along with significant rates of mortality. These challenges encouraged the development of multiple testing methods, as well as anti-viral medications such as Molnupiravir, as well as evaluating the efficacy of available medications against it, like; Azithromycin, Ritonavir and Hydroxychloroquine. Vaccination against COVID-19 forged into a significant challenge, few months ensuing the first case of SARS-CoV-2, which was diagnosed in December 2019, in Wuhan-China, thus, multiple vaccines were approved for use around the world to combat this pandemic. Our study includes a sample of 556 oncology patients at Augusta Victoria Hospital in Jerusalem, all patients were tested using Panbio rapid antigen test and Allplex PCR Assay. The main objective was to study the sensitivity and specificity of Rapid antigen test, which contributes to a faster isolation call and management of infected patients, thus decreasing the risk on spread to other patients and health care. Patients were categorized based on two factors: Ct range and age group and studying their possible effect on false-negative results. Patients with Ct value less than 20, had the highest detection rate which is consistent with other studies in the literature. The sensitivity and specificity of Panbio Rapid Antigen testing were of 69.9% and 100%, respectively. A correlation between age group and false negative results could not be made, but a correlation between Ct value and false negative result was noticed, Ct value was directly related to false negative results. P-value of 0.007 indicated that results were statistically significant where PCR test is considered more sensitive compared to rapid antigen test.
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Affiliation(s)
- Ali Sabateen
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Dana Sadaqa
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Taleen Nino
- Molecular Laboratory, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Ghayd Zaghal
- Molecular Laboratory, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - George Qumsieh
- Molecular Laboratory, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Reena Fakhori
- Molecular Laboratory, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Hammam Rjoub
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Tahreer Taha
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Rami Zghari
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Sari Abu Hanieh
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Duaa Al-Basha
- Infectious Diseases Unit, Augusta Victoria Hospital, East Jerusalem, Palestine
- Pharmacy Department, Modern University College (MUC), Ramallah, Palestine
| | - Marwan Qabaja
- Pathology Laboratory, Augusta Victoria Hospital, East Jerusalem, Palestine
| | - Hamza Alsaid
- Internal Medicine Department, Hadassah University Hospital, Jerusalem, Israel
| | - Musa Y. Hindiyeh
- Molecular Laboratory, Augusta Victoria Hospital, East Jerusalem, Palestine
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Saifuddin SA, Rashid R, Nor Azmi NJ, Mohamad S. Colorimetric strategies applicable for loop-mediated isothermal amplification. J Microbiol Methods 2024; 223:106981. [PMID: 38945305 DOI: 10.1016/j.mimet.2024.106981] [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: 02/22/2023] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
In recent years, loop-mediated isothermal amplification (LAMP) has gained popularity for detecting various pathogen-specific genes due to its superior sensitivity and specificity compared to conventional polymerase chain reaction (PCR). The simplicity and flexibility of naked-eye detection of the amplicon make LAMP an ideal rapid and straightforward diagnostic tool, especially in resource-limited laboratories. Colorimetric detection is one of the simplest and most straightforward among all detection methods. This review will explore various colorimetric dyes used in LAMP techniques, examining their reaction mechanisms, advantages, limitations and latest applications.
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Affiliation(s)
- Syaidatul Akmal Saifuddin
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Roslina Rashid
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurin Jazlina Nor Azmi
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.
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5
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Nie C, Jeong H, Hyun KA, Park S, Jung HI. Capillary force-driven reverse-Tesla valve structure for microfluidic bioassays. Analyst 2024; 149:4072-4081. [PMID: 38980104 DOI: 10.1039/d4an00601a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Biological assays involve the lysis of biological particles, enzyme reactions, and gene amplification, and require a certain amount of time for completion. Microfluidic chips are regarded as powerful devices for biological assays and in vitro diagnostics; however, they cannot achieve a high mixing efficiency, particularly in some time-consuming biological reactions. Herein, we introduce a microfluidic reverse-Tesla (reTesla) valve structure in which the fluid is affected by vortices and branch flow convergence, resulting in flow retardation and a high degree of mixing. The reTesla is passively operated by a microfluidic capillary force without any pumping facility. Compared with our previously developed micromixers, this innovative pumpless microfluidic chip exhibited high performance, with a mixing efficiency of more than 93%. The versatility of our reTesla chip will play a pivotal role in the study of various biological and chemical reactions.
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Affiliation(s)
- Cheng Nie
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Hyorim Jeong
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Kyung-A Hyun
- Korea Electronics Technology Institute (KETI), 25 Saenari-ro Bundang-gu, Seongnam-si, Gyeonggi-do, 13509, Republic of Korea
| | - Sunyoung Park
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyo-Il Jung
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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6
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Alhamid G, Tombuloglu H, BenRashed HA, Almessiere MA, Rabaan AA. Ultra-sensitive colorimetric detection of SARS-CoV-2 by novel gold nanoparticle (AuNP)-assisted loop-mediated isothermal amplification (LAMP) and freezing methods. Mikrochim Acta 2024; 191:339. [PMID: 38789855 DOI: 10.1007/s00604-024-06422-0] [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: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a molecular diagnosis technology with the advantages of isothermal reaction conditions and high sensitivity. However, the LAMP reactions are prone to producing false-positive results and thus are usually less reliable. This study demonstrates a gold nanoparticle (AuNP)-assisted colorimetric LAMP technique for diagnosing SARS-CoV-2, which aims to overcome the false-positive results. The AuNPs were functionalized with E gene probes, specifically tailored to bind to the amplified E-gene LAMP product, using the freezing method. Varied salt concentration and AuNP/probe combinations were tested for the highest visual performance. The experiments were conducted on synthetic SARS-CoV-2 RNA (Omicron variant), as well as on clinical samples. The assay showed an exceptional sensitivity of 8.05 fg of LAMP amplicon mixture (0.537 fg/µL). The average reaction time was ~ 30 min. In conclusion, AuNP-assisted LAMP detection will not identify any potential unspecific amplification, which helps to improve the efficiency and reliability of LAMP assays in point-of-care applications. The freezing method to functionalize the AuNPs with probes simplifies the assay, which can be utilized in further diagnostic studies.
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Affiliation(s)
- Galyah Alhamid
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia.
| | - Hajar A BenRashed
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Munirah A Almessiere
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Ali A Rabaan
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia
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Almulla N, Soltane R, Alasiri A, Kamal Allayeh A, Alqadi T, Alshehri F, Hamad Alrokban A, Zaghlool SS, Zayan AZ, Abdalla KF, Sayed AM. Advancements in SARS-CoV-2 detection: Navigating the molecular landscape and diagnostic technologies. Heliyon 2024; 10:e29909. [PMID: 38707469 PMCID: PMC11068538 DOI: 10.1016/j.heliyon.2024.e29909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
According to information from the World Health Organization, the world has experienced about 430 million cases of COVID-19, a world-wide health crisis caused by the SARS-CoV-2 virus. This outbreak, originating from China in 2019, has led to nearly 6 million deaths worldwide. As the number of confirmed infections continues to rise, the need for cutting-edge techniques that can detect SARS-CoV-2 infections early and accurately has become more critical. To address this, the Federal Drug Administration (FDA) has issued emergency use authorizations (EUAs) for a wide range of diagnostic tools. These include tests based on detecting nucleic acids and antigen-antibody reactions. The quantitative real-time reverse transcription PCR (qRT-PCR) assay stands out as the gold standard for early virus detection. However, despite its accuracy, qRT-PCR has limitations, such as complex testing protocols and a risk of false negatives, which drive the continuous improvement in nucleic acid and serological testing approaches. The emergence of highly contagious variants of the coronavirus, such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529), has increased the need for tests that can specifically identify these mutations. This article explores both nucleic acid-based and antigen-antibody serological assays, assessing the performance of recently approved FDA tests and those documented in scientific research, especially in identifying new coronavirus strains.
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Affiliation(s)
- Nuha Almulla
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Ahlam Alasiri
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Abdou Kamal Allayeh
- Virology Lab 176, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Taha Alqadi
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ahlam Hamad Alrokban
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Sameh S. Zaghlool
- Department of Pharmacology and Toxicology, College of Pharmacy, Almaaqal University, 61014, Al-Maaqal, Basra, Iraq
| | - Abdallah Z. Zayan
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Karam F. Abdalla
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
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Changtor P, Rodriguez-Mateos P, Buddhachat K, Wattanachaiyingcharoen W, Iles A, Kerdphon S, Yimtragool N, Pamme N. Integration of IFAST-based nucleic acid extraction and LAMP for on-chip rapid detection of Agroathelia rolfsii in soil. Biosens Bioelectron 2024; 250:116051. [PMID: 38301544 DOI: 10.1016/j.bios.2024.116051] [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: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Agroathelia rolfsii (A. rolfsii) is a fungal infection and poses a significant threat to over 500 plant species worldwide. It can reduce crop yields drastically resulting in substantial economic losses. While conventional detection methods like PCR offer high sensitivity and specificity, they require specialized and expensive equipment, limiting their applicability in resource-limited settings and in the field. Herein, we present an integrated workflow with nucleic acid extraction and isothermal amplification in a lab-on-a-chip cartridge based on immiscible filtration assisted by surface tension (IFAST) to detect A. rolfsii fungi in soil for point-of-need application. Our approach enabled both DNA extraction of A. rolfsii from soil and subsequent colorimetric loop-mediated isothermal amplification (LAMP) to be completed on a single chip, termed IFAST-LAMP. LAMP primers targeting ITS region of A. rolfsii were newly designed and tested. Two DNA extraction methods based on silica paramagnetic particles (PMPs) and three LAMP assays were compared. The best-performing assay was selected for on-chip extraction and detection of A. rolfsii from soil samples inoculated with concentrations of 3.75, 0.375 and 0.0375 mg fresh weight per 100-g soil (%FW). The full on-chip workflow was achieved within a 1-h turnaround time. The platform was capable of detecting as low as 3.75 %FW at 2 days after inoculation and down to 0.0375 %FW at 3 days after inoculation. The IFAST-LAMP could be suitable for field-applicability for A. rolfsii detection in low-resource settings.
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Affiliation(s)
- Phanupong Changtor
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden; Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Pablo Rodriguez-Mateos
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Wandee Wattanachaiyingcharoen
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Alexander Iles
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Sutthichat Kerdphon
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Nonglak Yimtragool
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Biodiversity, Faculty of Science, Naresuan University, Phitsanulok, Thailand.
| | - Nicole Pamme
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
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Abugattas-Núñez del Prado J, Quintana Reyes A, Leon J, Blume La Torre J, Gutiérrez Loli R, Pinzón Olejua A, Chamorro Chirinos ER, Loza Mauricio FA, Maguiña JL, Rodriguez-Aliaga P, Málaga-Trillo E. Clinical validation of RCSMS: A rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva. PLoS One 2024; 19:e0290466. [PMID: 38527001 PMCID: PMC10962837 DOI: 10.1371/journal.pone.0290466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/08/2023] [Indexed: 03/27/2024] Open
Abstract
Peru's holds the highest COVID death rate per capita worldwide. Key to this outcome is the lack of robust, rapid, and accurate molecular tests to circumvent the elevated costs and logistics of SARS-CoV-2 detection via RT-qPCR. To facilitate massive and timely COVID-19 testing in rural and socioeconomically deprived contexts, we implemented and validated RCSMS, a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva. RCSMS uses the power of CRISPR-Cas technology and lateral flow strips to easily visualize the presence of SARS-CoV-2 even in laboratories with limited equipment. We show that a low-cost thermochemical treatment with TCEP/EDTA is sufficient to inactivate viral particles and cellular nucleases in saliva, eliminating the need to extract viral RNA with commercial kits, as well as the cumbersome nasopharyngeal swab procedure and the requirement of biosafety level 2 laboratories for molecular analyses. Notably, RCSMS performed outstandingly in a clinical validation done with 352 patients from two hospitals in Lima, detecting as low as 50 viral copies per 10 μl reaction in 40 min, with sensitivity and specificity of 96.5% and 99.0%, respectively, relative to RT-qPCR. The negative and positive predicted values obtained from this field validation indicate that RCSMS can be confidently deployed in both high and low prevalence settings. Like other CRISPR-Cas-based biosensors, RCSMS can be easily reprogrammed for the detection of new SARS-CoV-2 variants. We conclude that RCSMS is a fast, efficient and inexpensive alternative to RT-qPCR for expanding COVID-19 testing capacity in Peru and other low- and middle-income countries with precarious healthcare systems.
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Affiliation(s)
| | | | - Julio Leon
- IMS RIKEN Center for Integrative Medical Sciences, Japan
- University of California San Francisco, San Francisco, California, United States of America
| | - Juan Blume La Torre
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Renzo Gutiérrez Loli
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | | | | | - Jorge L. Maguiña
- Instituto de Evaluación de Tecnologías en Salud e Investigación (IETSI), EsSalud, Lima, Perú
| | - Piere Rodriguez-Aliaga
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Edward Málaga-Trillo
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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Liao C, Pan L, Tan M, Zhou Z, Long S, Yi X, Li X, Wei G, Liang L. A dual RPA-LFD assay for the simultaneous detection of Salmonella typhimurium and Salmonella enteritidis. Front Bioeng Biotechnol 2024; 12:1379939. [PMID: 38524195 PMCID: PMC10958489 DOI: 10.3389/fbioe.2024.1379939] [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: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction: Salmonella was one of the most common bacteria that caused foodborne illness, with S. typhimurium (Salmonella typhimurium) and S. enteritidis (Salmonella enteritidis) infections accounting for more than 75% of human salmonella infections. Methods: In this study, we developed a method of dual recombinase polymerase amplification (RPA) combined with a lateral flow dipstick for the rapid detection of S. typhimurium and S. enteritidis in clinical specimens (stool). Results: The entire reaction process, including amplification and result reading, could be completed within 65 min. The detection limits of S. typhimurium and S. enteritidis in pure culture samples were 5.23 × 101 CFU/mL and 3.59 × 101 CFU/mL, respectively. The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were 8.30 × 101 CFU/mL and 2.70 × 102 CFU/mL, respectively. In addition, the method had no cross-reaction with other pathogenic microorganisms. The results in clinical samples were fully consistent with those obtained using Bacterial Analysis Manual, with sensitivity and specificity were 100% (8/8) and 100% (17/17) for S. typhimurium and 100% (4/4) and 100% (21/21) for S. enteritidis, respectively. Discussion: The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were higher than those in pure culture samples, which might be attributed to the inherent complex composition of artificially contaminated samples. In addition, the detection limits of S. typhimurium and S. enteritidis in the same sample were also different, which might be attributed to different amplification efficiency of two target genes in the same reaction system. Conclusion: This assay had potential application outdoors, as it could be performed within 1 h at 38°C without a complex instrument, and the results could be observed with the naked eye. In conclusion, the dual RPA-LFD assay established in this study had practical significance for the rapid detection of S. typhimurium and S. enteritidis in the future.
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Affiliation(s)
- Chuan Liao
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Lele Pan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Meiying Tan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Zihan Zhou
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Shaoping Long
- Department of Clinical Laboratory, Baise People’s Hospital, Baise, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Xuebin Li
- Department of Neurology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Lina Liang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
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Pourakbari R, Gholami M, Shakerimoghaddam A, Khiavi FM, Mohammadimehr M, Khomartash MS. Comparison of RT-LAMP and RT-qPCR assays for detecting SARS-CoV-2 in the extracted RNA and direct swab samples. J Virol Methods 2024; 324:114871. [PMID: 38103738 DOI: 10.1016/j.jviromet.2023.114871] [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: 10/07/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infected patients is critical for infection control. Loop-mediated isothermal amplification (LAMP) has been demonstrated to be a rapid, simple, reliable, cost-effective and sensitive method to detect SARS-CoV-2 in a variety of samples in considerably less time than Real-Time PCR. In this study, we developed and optimized a rapid detection method for SARS-CoV-2 based on RT-LAMP method utilizing a specific primer set targeting the ORF1a gene and then examined its sensitivity and efficiency using a serially diluted viral RNA sample with a known concentration. Furthermore, the sensitivity of the RT-LAMP to detect SARS-CoV-2 in direct swab samples with varying Ct values were compared to a commercial molecular RT-qPCR based detection kit. According to our findings the optimal incubation time for RT-LAMP assay was 45 min. There was a complete agreement between RT-LAMP and RT-qPCR in diagnosing the viral genome in the diluted extracted RNA sample. However, it had a lower sensitivity (71%) to detect the viral genome in direct swab samples compared to RT-qPCR. In conclusion, due to its simplicity, rapidness, sensitivity, and specificity, RT-LAMP has tremendous potential as a point-of-care tool; nevertheless, more research is needed to utilize it for detecting SARS-CoV-2, particularly in direct swab samples.
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Affiliation(s)
- Ramin Pourakbari
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Mohammad Gholami
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Ali Shakerimoghaddam
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Farhad Motavalli Khiavi
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Mojgan Mohammadimehr
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Mehdi Shakouri Khomartash
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran..
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12
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Alsaeed M, Alhamid G, Tombuloglu H, Kabanja JH, Karagoz A, Tombuloglu G, Rabaan AA, Al-Suhaimi E, Unver T. Ultrasensitive and fast detection of SARS-CoV-2 using RT-LAMP without pH-dependent dye. Funct Integr Genomics 2024; 24:16. [PMID: 38242999 DOI: 10.1007/s10142-024-01297-z] [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: 11/28/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
This study investigates the performance of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the colorimetric detection of SARS-CoV-2 using fluorometric dye, namely, calcein. The detection limit (LoD) with the N-ID1 primer set resulted in superior performance, corresponding to ~ 2 copies/reaction or ~ 0.1 copies/μL of the RNA sample. The color development can be observed by the naked eye, using an ultraviolet (UV) transilluminator or a hand-UV light without the requirement of expensive devices. The average time-to-reaction (TTR) value was 26.2 min in high-copy number samples, while it was about 50 min in rRT-PCR. A mobile application was proposed to quantify the positive and negative results based on the three-color spaces (RGB, Lab, and HSB). Compared to rRT-PCR (n = 67), this assay allows fast and sensitive visual detection of SARS-CoV-2, with high sensitivity (90.9%), selectivity (100%), and accuracy (94.03%). Besides, the assay was sensitive regardless of variants. Since this assay uses a fluorescent dye for visual observation, it can be easily adapted in RT-LAMP assays with high sensitivity. Thus, it can be utilized in low-source centers and field testing such as conferences, sports meetings, refugee camps, companies, and schools.
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Affiliation(s)
- Moneerah Alsaeed
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Galyah Alhamid
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Juma H Kabanja
- Department of Pathology & Laboratory Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Aysel Karagoz
- Quality Assurance Department, Turk Pharmaceutical and Serum Ind. Inc., Ankara, Turkey
| | - Guzin Tombuloglu
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan
| | - Ebtesam Al-Suhaimi
- Vice Presidency for Scientific Research and Innovation, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Turgay Unver
- Ficus Biotechnology, Ankara, Turkey
- Faculty of Engineering, Ostim Technical University, 06374, Ankara, Turkey
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13
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Saejung W, Khumtong K, Rapichai W, Ratanabunyong S, Rattanasrisomporn A, Choowongkomon K, Rungsuriyawiboon O, Rattanasrisomporn J. Detection of feline immunodeficiency virus by neutral red-based loop-mediated isothermal amplification assay. Vet World 2024; 17:72-81. [PMID: 38406374 PMCID: PMC10884571 DOI: 10.14202/vetworld.2024.72-81] [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: 09/20/2023] [Accepted: 12/13/2023] [Indexed: 02/27/2024] Open
Abstract
Background and Aim Feline immunodeficiency virus (FIV) is a retroviral pathogen globally responsible for immunodeficiency disease in cats. However, the current diagnosis based on antibody detection has limitations and can also produce false-positive results. This study aimed to develop a one-pot loop-mediated isothermal amplification (LAMP) process integrated with neutral red (NR-LAMP) assay for detection of FIV proviral DNA. Materials and Methods We developed a one-pot, gag gene-based NR-LAMP for convenient, rapid, specific, and sensitive colorimetric inspection of FIV proviral DNA. Results The developed NR-LAMP was capable of amplifying at an optimum temperature of 65°C for 40 min. No cross-amplification was detected between FIV and other feline viruses tested, indicating the high specificity (98.44%) of the novel FIV-LAMP primer. Our NR-LAMP assay has a detection limit of 4.2 × 101 copies/μL. A total of 80 clinical samples with a background of FIV infection were collected and tested using the proposed method. The NR-LAMP assay showed a high sensitivity of 100% compared to conventional polymerase chain reaction assay. Conclusion These results support the suitability of NR-LAMP as a potential future alternative clinical molecular approach for further use in the diagnosis of FIV-infected cats.
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Affiliation(s)
- Wichayet Saejung
- Graduate Program in Animal Health and Biomedical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Kotchaporn Khumtong
- Graduate Program in Animal Health and Biomedical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Witsanu Rapichai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Amonpun Rattanasrisomporn
- Interdisciplinary of Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok, Thailand
| | | | - Oumaporn Rungsuriyawiboon
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Jatuporn Rattanasrisomporn
- Graduate Program in Animal Health and Biomedical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
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14
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Kashyap PL, Kumar S, Kumar RS, Sharma A, Khanna A, Raj S, Jasrotia P, Singh G. Molecular diagnostic assay for pre-harvest detection of Tilletia indica infection in wheat plants. Front Microbiol 2023; 14:1291000. [PMID: 38029161 PMCID: PMC10646428 DOI: 10.3389/fmicb.2023.1291000] [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: 09/08/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
The current study describes a new diagnostic method for the rapid and accurate detection of Tilletia indica, the pathogen accountable for causing Karnal bunt (KB) disease in wheat. This method uses quantitative real-time polymerase chain reaction (qPCR) and a primer set derived from glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of T. indica to identify the presence of the pathogen. The qPCR assay using this primer set was found highly sensitive, with a limit of detection (LOD) value of 4 pg of T. indica DNA. This level of sensitivity allows for the detection of the pathogen even in cases of different growth stages of wheat, where no visible symptoms of infection on the wheat plants can be seen by naked eyes. The study also validated the qPCR assay on ten different wheat cultivars. Overall, this study presents a valuable molecular tool for rapid, specific and sensitive detection of KB fungus in wheat host. This method has practical applications in disease management, screening of wheat genotypes against KB and can aid in the development of strategies to mitigate the impact of Karnal bunt disease on wheat production.
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Affiliation(s)
- Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
| | | | | | - Annie Khanna
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, India
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15
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Kost GJ. The Impact of Repeating COVID-19 Rapid Antigen Tests on Prevalence Boundary Performance and Missed Diagnoses. Diagnostics (Basel) 2023; 13:3223. [PMID: 37892044 PMCID: PMC10606553 DOI: 10.3390/diagnostics13203223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
A prevalence boundary (PB) marks the point in prevalence in which the false omission rate, RFO = FN/(TN + FN), exceeds the tolerance limit for missed diagnoses. The objectives were to mathematically analyze rapid antigen test (RAgT) performance, determine why PBs are breeched, and evaluate the merits of testing three times over five days, now required by the US Food and Drug Administration for asymptomatic persons. Equations were derived to compare test performance patterns, calculate PBs, and perform recursive computations. An independent July 2023 FDA-NIH-university-commercial evaluation of RAgTs provided performance data used in theoretical calculations. Tiered sensitivity/specificity comprise the following: tier (1) 90%, 95%; tier (2) 95%, 97.5%; and tier (3) 100%, ≥99%. Repeating a T2 test improves the PB from 44.6% to 95.2% (RFO 5%). In the FDA-NIH-university-commercial evaluation, RAgTs generated a sensitivity of 34.4%, which improved to 55.3% when repeated, and then improved to 68.5% with the third test. With RFO = 5%, PBs are 7.37/10.46/14.22%, respectively. PB analysis suggests that RAgTs should achieve a clinically proven sensitivity of 91.0-91.4%. When prevalence exceeds PBs, missed diagnoses can perpetuate virus transmission. Repeating low-sensitivity RAgTs delays diagnosis. In homes, high-risk settings, and hotspots, PB breaches may prolong contagion, defeat mitigation, facilitate new variants, and transform outbreaks into endemic disease. Molecular diagnostics can help avoid these potential vicious cycles.
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Affiliation(s)
- Gerald J. Kost
- Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA 95616, USA;
- Point-of-Care Testing Center for Teaching and Research (POCT•CTR), Knowledge Optimization, Davis, CA 95616, USA
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16
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Zhu W, Hussain M, Gao J, Mao R, An X. Development of Loop-Mediated Isothermal Amplification Method for Rapid and Sensitive Identification of Hermetia illucens (Diptera: Stratiomyidae). Methods Protoc 2023; 6:81. [PMID: 37736964 PMCID: PMC10514858 DOI: 10.3390/mps6050081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The black soldier fly (BSF) is well known for its ability to biologically convert organic waste into insect biomass, including protein and oil, which can be utilised as animal feed. Since raw BSF products, such as BSF powder, are difficult to differentiate from other biological raw materials, therefore new analytical approaches are required. In this study, we have developed a new and fast method based on loop-mediated isothermal AMPlification (LAMP) reaction that can diagnose black soldier fly larvae and BSF byproducts with high accuracy, specificity and sensitivity. Species-specific primers for BSF were designed based on targeting the mitochondrial cytochrome C oxidase I (COI) gene. The assay was able to detect as low as 820 fg/L of BSF DNA in 60 min at 65 °C, which was a hundredfold higher than the detection limit of classical polymerase chain reaction and did not show cross-reactivity. In conclusion, the LAMP assay demonstrated excellent sensitivity and specificity to detect BSF and BSF byproducts, with a sampling-to-result identification time of 60 min.
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Affiliation(s)
- Wenchao Zhu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
- Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Mubasher Hussain
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Jing Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Runqian Mao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Xincheng An
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Engineering Research Center for Mineral Oil Pesticides, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
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17
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Fernandez I Marti A, Parungao M, Hollin J, Selimotic B, Farrar G, Seyler T, Anand A, Ahmad R. A Novel, Precise and High-Throughput Technology for Viroid Detection in Cannabis (MFDetect TM). Viruses 2023; 15:1487. [PMID: 37515174 PMCID: PMC10385567 DOI: 10.3390/v15071487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Hop latent viroid (HLVd) is a severe disease of cannabis, causing substantial economic losses in plant yield and crop value for growers worldwide. The best way to control the disease is early detection to limit the spread of the viroid in grow facilities. This study describes MFDetectTM as a rapid, highly sensitive, and high-throughput tool for detecting HLVd in the early stages of plant development. Furthermore, in the largest research study conducted so far for HLVd detection in cannabis, we compared MFDetectTM with quantitative RT-PCR in a time course experiment using different plant tissues, leaves, petioles, and roots at different plant developmental stages to demonstrate both technologies are comparable. Our study found leaf tissue is a suitable plant material for HLVd detection, with the viroid titer increasing in the infected leaf tissue with the age of plants. The study showed that other tissue types, including petiole and roots, were equally sensitive to detection via MFDetectTM. The assay developed in this research allows the screening of thousands of plants in a week. The assay can be scaled easily to provide growers with a quick turnaround and a cost-effective diagnostic tool for screening many plants and tissue types at different stages of development.
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Affiliation(s)
- Angel Fernandez I Marti
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Marcus Parungao
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Jonathan Hollin
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Berin Selimotic
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Graham Farrar
- Glass House Farms, 645 W Laguna Road, Camarillo, CA 93012, USA
| | - Tristan Seyler
- Glass House Farms, 645 W Laguna Road, Camarillo, CA 93012, USA
| | - Ajith Anand
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Riaz Ahmad
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
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