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Rashid SA, Rajendiran S, Nazakat R, Mohammad Sham N, Khairul Hasni NA, Anasir MI, Kamel KA, Muhamad Robat R. A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic. Heliyon 2024; 10:e30600. [PMID: 38765075 PMCID: PMC11098849 DOI: 10.1016/j.heliyon.2024.e30600] [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: 08/02/2023] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.
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Affiliation(s)
- Siti Aishah Rashid
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Sakshaleni Rajendiran
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Raheel Nazakat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Noraishah Mohammad Sham
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Nurul Amalina Khairul Hasni
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Mohd Ishtiaq Anasir
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Khayri Azizi Kamel
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Rosnawati Muhamad Robat
- Occupational & Environmental Health Unit, Public Health Division, Selangor State Health Department, Ministry of Health Malaysia, Malaysia
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Gulinaizhaer A, Yang C, Zou M, Ma S, Fan X, Wu G. Detection of monkeypox virus using helicase dependent amplification and recombinase polymerase amplification combined with lateral flow test. Virol J 2023; 20:274. [PMID: 37996921 PMCID: PMC10668421 DOI: 10.1186/s12985-023-02223-8] [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: 06/20/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
The monkeypox virus (MPXV) is a zoonotic DNA virus that belongs to the poxvirus family. Conventional laboratory methods for detecting MPXV are complex and expensive, making them unsuitable for detecting the virus in regions with limited resources. In this study, we using the Helicase dependent amplification (HDA) method and the Recombinase polymerase amplification (RPA) technique in combination with the lateral flow test (LFT), together with a self-designed qPCR technique for the detection of the MPXV specific conserved fragment F3L, to compare the sensitivity and specificity of the three assays. By analyzing the sensitivity detection results using Probit, it can be seen that the limit of detection (LOD) of the HDA-LFT detection target is 9.86 copies/µL (95% confidence interval, CI 7.52 copies/µL lower bound), the RPA-LFT detection target is 6.97 copies/µL (95% CI 3.90 copies/µL lower bound), and the qPCR detection target is 479.24 copies/mL (95% CI 273.81 copies/mL lower bound). The specificity test results showed that the specificity of the three methods mentioned above was higher than 90% in detecting pseudoviruses of the same genus of MPXV. The simple, highly sensitive, and specific MPXV assay developed in this study is anticipated to provide a solid foundation for future applications in the early screening, diagnosis, and evaluation of the efficacy of MPXV. This is the first time the HDA-LFT assay has been utilized to detect MPXV infection.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Chuankun Yang
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Mingyuan Zou
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Shuo Ma
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Xiaobo Fan
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China.
- Diagnostics Department, Medical School of Southeast University, Nanjing, 210009, People's Republic of China.
| | - Guoqiu Wu
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China.
- Diagnostics Department, Medical School of Southeast University, Nanjing, 210009, People's Republic of China.
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, People's Republic of China.
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Udeagu CCN, Gbedemah M, Pitiranggon M, Feldman S, Cordoba E, Goldenberg S, Keeley C, Blaney K, Vora NM, Long T. Integrating Contact Tracers Into Point-of-Care Testing Workflow to Accelerate the Tracing of People With Exposure to COVID-19, August-December 2020, New York City. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2023; 29:708-717. [PMID: 37290128 PMCID: PMC10373849 DOI: 10.1097/phh.0000000000001748] [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] [Indexed: 06/10/2023]
Abstract
OBJECTIVES We assessed the timeliness of contact tracing following rapid-positive COVID-19 test result at point-of-care testing (POCT) sites in New York City (NYC). DESIGN Interviewed case-patients to elicit exposed contacts and conducted COVID-19 exposure notifications. SETTINGS Twenty-two COVID-19 POCT sites in NYC, the 2 NYC international airports, and 1 ferry terminal. PARTICIPANTS Case-patients with rapid-positive COVID-19 test results and their named contacts. MAIN OUTCOME MEASURES We quantified the proportions of interviewed individuals with COVID-19 and notified contacts and assessed the timeliness between the dates of the rapid-positive COVID-19 test results and the interviews or notifications. RESULTS In total, 11 683 individuals with rapid-positive COVID-19 test results were referred for contact tracing on the day of their diagnosis; 8878 (76) of whom were interviewed within 1 day of diagnosis, of whom 5499 (62%) named 11 486 contacts. A median of 1.24 contacts were identified from each interview. The odds of eliciting contacts were significantly higher among individuals reporting COVID-19 symptoms than among persons with no symptoms (51% vs 36%; adjusted odds ratio [aOR] = 1.37; 95% confidence interval [CI], 1.11-1.70) or living with 1 or more persons than living alone (89% vs 38%; aOR = 12.11; 95% CI, 10.73-13.68). Among the 8878 interviewed case-patients, 8317 (94%) were interviewed within 1 day of their rapid-positive COVID-19 test results and 91% of contact notifications were completed within 1 day of contact identification. The median interval from test result to interview date and from case investigation interview to contact notification were both 0 days (IQR = 0). CONCLUSIONS The integration of contact tracers into COVID-19 POCT workflow achieved timely case investigation and contact notification. Accelerated contact tracing can be used to curb COVID-19 transmission during local outbreaks.
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Affiliation(s)
- Chi-Chi N. Udeagu
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Misato Gbedemah
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Masha Pitiranggon
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Samantha Feldman
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Evette Cordoba
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Shifra Goldenberg
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Chris Keeley
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Kathleen Blaney
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Neil M. Vora
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
| | - Theodore Long
- New York City Department of Health and Mental Hygiene, Queens, New York (Mss Udeagu, Pitiranggon, and Blaney and Dr Vora); New York City Test & Trace Corps, New York City, New York (Mss Udeagu, Gbedemah, Pitiranggon, Feldman, Goldenberg, Keeley, and Blaney and Drs Cordoba, Vora, and Long); and New York City Health + Hospitals Corporation, New York City, New York (Mss Gbedemah, Feldman, Goldenberg, and Keeley and Drs Cordoba and Long)
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McCloskey D, Boza J, Mason CE, Erickson D. MINI: A high-throughput point-of-care device for performing hundreds of nucleic acid tests per day. Biosens Bioelectron 2022; 216:114654. [PMID: 36084523 PMCID: PMC10960951 DOI: 10.1016/j.bios.2022.114654] [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: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022]
Abstract
There are a variety of infectious diseases with a high incidence and mortality in limited resource settings that could benefit from rapid point of care molecular diagnosis. Global health efforts have sought to implement mass-screening programs to provide earlier detection and subsequent treatment in an effort to control transmission and improve health outcomes. However, many of the current diagnostic technologies under development are limited to fewer than 10 samples per run, which inherently restricts the screening throughput of these devices. We have developed a high throughput device called "MINI" that is capable of testing hundreds of samples per day at the point-of-care. MINI can utilize multiple energy sources - electricity, flame, or solar - to perform loop-mediated isothermal amplification (LAMP) in a portable and robust device which is ideal for use in limited resource settings. The unique opto-electronic design of MINI minimizes the energy and space requirements of the device and maximizes the optical isolation and signal clarity, enabling point-of-care analysis of 96 unique samples at once. We show comparable performance to a commercial instrument using two different LAMP assays for Kaposi's sarcoma-associated herpesvirus and a common housekeeping gene, GAPDH. With a single device capable of running hundreds of samples per day, increased access to modern molecular diagnostics could improve health outcomes for a variety of diseases common in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Juan Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher E Mason
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - David Erickson
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
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Babler KM, Amirali A, Sharkey ME, Williams SL, Boone MM, Cosculluela GA, Currall BB, Grills GS, Laine J, Mason CE, Reding BD, Schürer SC, Stevenson M, Vidovic D, Solo-Gabriele HM. Comparison of Electronegative Filtration to Magnetic Bead-Based Concentration and V2G-qPCR to RT-qPCR for Quantifying Viral SARS-CoV-2 RNA from Wastewater. ACS ES&T WATER 2022; 2:2004-2013. [PMID: 37601294 PMCID: PMC10438908 DOI: 10.1021/acsestwater.2c00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Methods of wastewater concentration (electronegative filtration (ENF) versus magnetic bead-based concentration (MBC)) were compared for the analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), beta-2 microglobulin, and human-coronavirus OC43. Using ENF as the concentration method, two quantitative Polymerase Chain Reaction (qPCR) analytical methods were also compared: Volcano 2nd Generation (V2G)-qPCR and reverse transcriptase (RT)-qPCR measuring three different targets of the virus responsible for the COVID-19 illness (N1, modified N3, and ORF1ab). Correlations between concentration methods were strong and statistically significant for SARS-CoV-2 (r=0.77, p<0.001) and B2M (r=0.77, p<0.001). Comparison of qPCR analytical methods indicate that, on average, each method provided equivalent results with average ratios of 0.96, 0.96 and 1.02 for N3 to N1, N3 to ORF1ab, and N1 to ORF1ab and were supported by significant (p<0.001) correlation coefficients (r =0.67 for V2G (N3) to RT (N1), r =0.74 for V2G (N3) to RT (ORF1ab), r = 0.81 for RT (N1) to RT (ORF1ab)). Overall results suggest that the two concentration methods and qPCR methods provide equivalent results, although variability is observed for individual measurements. Given the equivalency of results, additional advantages and disadvantages, as described in the discussion, are to be considered when choosing an appropriate method.
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Affiliation(s)
- Kristina M. Babler
- Department of Chemical, Environmental and Materials Engineering, Coral Gables, FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental and Materials Engineering, Coral Gables, FL USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | | | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Jennifer Laine
- Department of Physiology and Biophysics and the WorldQuant Initiative, Weill Cornell Medicine, New York City, NY USA
| | | | - Brian D. Reding
- Department of Physiology and Biophysics and the WorldQuant Initiative, Weill Cornell Medicine, New York City, NY USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL USA
| | - Dusica Vidovic
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL USA
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