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Oyervides-Muñoz MA, Aguayo-Acosta A, de los Cobos-Vasconcelos D, Carrillo-Reyes J, Espinosa-García AC, Campos E, Driver EM, Lucero-Saucedo SL, Armenta-Castro A, de la Rosa O, Martínez-Ruiz M, Barragán-Trinidad M, Vázquez-Salvador N, Silva-Magaña MA, Zavala-Méndez M, Iqbal HM, Mazari-Hiriart M, Velazco H, Buitrón G, Noyola A, Halden RU, Sosa-Hernández JE, Parra-Saldívar R. Inter-institutional laboratory standardization for SARS-CoV-2 surveillance through wastewater-based epidemiology applied to Mexico City. IJID REGIONS 2024; 12:100429. [PMID: 39318545 PMCID: PMC11419891 DOI: 10.1016/j.ijregi.2024.100429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/26/2024]
Abstract
Objectives Wastewater-based surveillance applied to SARS-CoV-2 viral load quantification for COVID-19 has become one of the most relevant complementary tools in epidemiologic prevention programs worldwide. However, this valuable decision-making tool still requires fine-tuning to produce comparable results between laboratories, especially when applied to the surveillance of megacities. Methods Six laboratories across Mexico and one from the United States executed an interlaboratory study to set up a singular standardized protocol considering method cost, installed infrastructure, materials available, and supply availability for SARS-CoV-2 quantification from five Mexico City sampling sites across this megacity. Results Comparable data from processing outcomes in the Mexican laboratories and in the external international laboratory serve as a validating data source. The Bland-Altman comparison showed consistency, with cycle threshold values within ±1.96 SD of SARS-CoV-2 genetic copies for the standard curve quantification, with a mismatch of two laboratories. In addition, MS2 bacteriophage recovery rates varied between 35% and 67% among all participating laboratories. Finally, the efficiency of viral genetic material recovered from all participating laboratories varied between 65% and 93% for the participating laboratories. Conclusion This work lays the foundation for extensive and continuous wastewater-based surveillance application across independent Mexican laboratories in a time- and resource-effective manner.
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Affiliation(s)
- Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Alberto Aguayo-Acosta
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Daniel de los Cobos-Vasconcelos
- Grupo de Investigación en Procesos Anaerobios, Coordinación de Ingeniería Ambiental, Instituto de Ingeniería, Campus CU, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Julián Carrillo-Reyes
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Ana C. Espinosa-García
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eneida Campos
- Laboratorio de Ingeniería de Bioprocesos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, USA
| | | | - Arnoldo Armenta-Castro
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
| | - Orlando de la Rosa
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Martín Barragán-Trinidad
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Nallely Vázquez-Salvador
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miguel A Silva-Magaña
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Marcela Zavala-Méndez
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Marisa Mazari-Hiriart
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Velazco
- Laboratorio de Ingeniería de Bioprocesos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - German Buitrón
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Adalberto Noyola
- Grupo de Investigación en Procesos Anaerobios, Coordinación de Ingeniería Ambiental, Instituto de Ingeniería, Campus CU, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Rolf U. Halden
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, USA
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
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Huang W, Zhang Z, Lin D, Deng Y, Chen X, Huang J. RT-nestRPA is a new technology for the rapid and sensitive detection of nucleic acid detection of pathogens used for a variety of medical application scenarios. Anal Chim Acta 2023; 1262:341263. [PMID: 37179064 PMCID: PMC10123537 DOI: 10.1016/j.aca.2023.341263] [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: 02/20/2023] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND The effective detection of pathogens is of great importance for the diagnosis and treatment of infectious diseases. We have proposed the novel RT-nestRPA technique for SARS-CoV-2 detection, which is a rapid RNA detection technique with ultra-high sensitivity. RESULTS The RT-nestRPA technology has a sensitivity of 0.5 copies/uL of synthetic RNA targeting the ORF7a/7b/8 gene or 1 copy/uL synthetic RNA targeting the N gene of SARS-CoV-2. The entire detection process of RT-nestRPA only takes only 20 min, which is significantly shorter than RT-qPCR (nearly 100 min). Additionally, RT-nestRPA is capable of detecting dual genes of SARS-CoV-2 and human RPP30 simultaneously in one reaction tube. The excellent specificity of RT-nestRPA was verified by analyzing twenty-two SARS-CoV-2 unrelated pathogens. Furthermore, RT-nestRPA had great performance in detecting samples treated with cell lysis buffer without RNA extraction. The innovative double-layer reaction tube for RT-nestRPA can prevent aerosol contamination and simplify the reaction operation. Moreover, the ROC analysis revealed that RT-nestRPA had high diagnostic value (AUC = 0.98), while the AUC of RT-qPCR was 0.75. SIGNIFICANCE Our current findings suggested that RT-nestRPA could serve as a novel technology for nucleic acid detection of pathogens with rapid and ultrahigh sensitive features used in various medical application scenarios.
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Affiliation(s)
- Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhaoqi Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Dachuan Lin
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathology Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinchun Chen
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathology Biology, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng 2022; 6:944-956. [PMID: 35953650 PMCID: PMC10367768 DOI: 10.1038/s41551-022-00917-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/30/2022] [Indexed: 11/10/2022]
Abstract
Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies μl-1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13-35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23-31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.
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Affiliation(s)
- Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Aditya R Jangid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tina Y Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine Kogut
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Patrick D Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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