Article
Medicine, General & Internal
Xin Huang, Gongyu Tang, Nahed Ismail, Xiaowei Wang
Summary: This study improved the rapid diagnostic method for COVID-19 through a combination of bioinformatics and experimental analysis. The validated method showed comparable sensitivity and specificity to the standard RT-qPCR, providing a reliable option for diagnosing COVID-19 cases.
Article
Microbiology
Mariana Fernandez-Pittol, Juan Carlos Hurtado, Maryam Ali, Alvar Simarro, Fadiana Proano, Maria Sierra, Jordi Vila
Summary: In various healthcare settings, such as emergency surgery patients, there is a need for rapid detection of SARS-CoV-2. The QuantuMDx Q-POC is an automated fast workflow platform that detects three genes, allowing differentiation between SARS-CoV-2 and other coronaviruses. This study compared QuantuMDx Q-POC with the Cobas 6800 algorithm for SARS-CoV-2 detection, showing high sensitivity and a short detection time of 30 minutes. Overall, the QuantuMDx Q-POC system is a reliable option for rapid SARS-CoV-2 detection.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Galyah Alhamid, Huseyin Tombuloglu, Ebtesam Al-Suhaimi
Summary: The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. We developed colorimetric and fluorometric RT-LAMP assays using five LAMP primers instead of six to overcome misamplifications and verified their performance with the gold-standard RT-PCR technique. The E-ID1 primer set, including five primers, performed superbly on both colorimetric and fluorometric assays, with high sensitivity, specificity, and accuracy.
SCIENTIFIC REPORTS
(2023)
Article
Engineering, Environmental
Wei Lin Lee, Federica Armas, Flavia Guarneri, Xiaoqiong Gu, Nicoletta Formenti, Fuqing Wu, Franciscus Chandra, Giovanni Parisio, Hongjie Chen, Amy Xiao, Claudia Romeo, Federico Scali, Matteo Tonni, Mats Leifels, Feng Jun Desmond Chua, Germaine W. C. Kwok, Joey Y. R. Tay, Paolo Pasquali, Janelle Thompson, Giovanni Loris Alborali, Eric J. Aim
Summary: The study successfully validated a new method for detecting the Omicron variant using wastewater-based monitoring at a wastewater treatment plant in Italy, revealing a rapid displacement trend of the Omicron variant over the Delta variant in wastewater. These data support clinical studies that found the Omicron variant to have an infection advantage in vaccinated populations.
Article
Engineering, Environmental
Wei Lin Lee, Federica Armas, Flavia Guarneri, Xiaoqiong Gu, Nicoletta Formenti, Fuqing Wu, Franciscus Chandra, Giovanni Parisio, Hongjie Chen, Amy Xiao, Claudia Romeo, Federico Scali, Matteo Tonni, Mats Leifels, Feng Jun Desmond Chua, Germaine Wc Kwok, Joey Yr Tay, Paolo Pasquali, Janelle Thompson, Giovanni Loris Alborali, Eric J. Alm
Summary: This article introduces a wastewater monitoring method for tracking the dynamics of SARS-CoV-2 variants in communities. The authors developed an RT-qPCR assay that can quantitatively detect the presence of the Omicron variant in wastewater and validated it through experiments. They found that the Omicron variant rapidly displaced the Delta variant within a short period of time, which is consistent with previous clinical studies and vaccination rates.
Article
Engineering, Environmental
Haorui Cao, Kang Mao, Fang Ran, Pengqi Xu, Yirong Zhao, Xiangyan Zhang, Hourong Zhou, Zhugen Yang, Hua Zhang, Guibin Jiang
Summary: A portable paper device based on CRISPR/Cas12a and RT-LAMP was developed for the detection of SARS-CoV-2 in wastewater, offering high sensitivity and specificity. The device enables simultaneous detection of the N, E, and S genes through different visualization pathways, and provides semi-quantitative analysis. This study demonstrates a promising point-of-use method for wastewater-based surveillance.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Medicine, General & Internal
Juan Garcia-Bernalt Diego, Pedro Fernandez-Soto, Marta Dominguez-Gil, Moncef Belhassen-Garcia, Juan Luis Munoz Bellido, Antonio Muro
Summary: The global SARS-CoV-2 pandemic has brought about a need for widespread testing for COVID-19, with RT-qPCR as the gold standard method, but facing challenges. A novel RT-LAMP method has been developed, showing promise for cost-effective, rapid, and stable detection of SARS-CoV-2.
Article
Engineering, Environmental
Roberto G. Ramirez-Chavarria, Elizabeth Castillo-Villanueva, Bryan E. Alvarez-Serna, Julian Carrillo-Reyes, Rosa Maria Ramirez-Zamora, German Buitron, Luis Alvarez-Icaza
Summary: The study introduces a simple, low-cost, and affordable electrochemical sensor for specific detection of the genes of the novel coronavirus. Testing with wastewater samples demonstrates the sensor's performance and reliability.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Zhu Yang, Nicole Y. Liu, Zhiwei Zhu, Minmin Xiao, Shuzhi Zhong, Qiqi Xue, Lina Nie, Jinhong Zhao
Summary: In this study, a triple-target RT-LAMP assay was developed for the detection of SARS-CoV-2. It showed higher sensitivity compared to singleplex or duplex RT-LAMP assays and could detect as low as 11 copies of SARS-CoV-2 RNA per 25 mL reaction. The study also investigated the use of two different color indicators, hydroxy naphthol blue (HNB) and cresol red, in the colorimetric RT-LAMP assay.
Article
Multidisciplinary Sciences
Francisco Santos Schneider, Laurence Molina, Marie-Christine Picot, Nicolas L'Helgoualch, Julien Espeut, Pierre Champigneux, Mellis Alali, Julie Baptiste, Lise Cardeur, Christophe Carniel, Martin Davy, Daniel Dedisse, Benjamin Dubuc, Hugo Fenech, Vincent Foulongne, Carole Fruchart Gaillard, Florence Galtier, Alain Makinson, Gregory Marin, Raissa Medina Santos, David Morquin, Alimata Ouedraogo, Alexandra Prieux Lejeune, Marine Quenot, Pierre Keiflin, Francisco Checa Robles, Carolina Rodrigues Rego, Nicolas Salvetat, Charline Trento, Diana Vetter, Franck Molina, Jacques Reynes
Summary: The study evaluated the diagnostic performance of a rapid, extraction-free and connected RT-LAMP assay on saliva for detecting SARS-CoV-2. The test showed high sensitivity and specificity, and performed similarly for symptomatic and asymptomatic individuals. No dominant mutation in the RT-LAMP primer region was observed. This reliable and simple connected test could facilitate the restart of professional and social events in the current economic context.
SCIENTIFIC REPORTS
(2022)
Article
Environmental Sciences
Anna Navarro, Livia Gomez, Isabella Sanseverino, Magdalena Niegowska, Eszter Roka, Rosalba Pedraccini, Marta Vargha, Teresa Lettieri
Summary: A multiplex RT-qPCR method was developed for simultaneous detection of different SARS-CoV-2 genes. The results showed that the multiplex assay was comparable to single assay in detecting SARS-CoV-2, but faster and cost-effective.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Virology
Ali Bektas, Michael F. Covington, Guy Aidelberg, Anibal Arce, Tamara Matute, Isaac Nunez, Julia Walsh, David Boutboul, Constance Delaugerre, Ariel B. Lindner, Fernan Federici, Anitha D. Jayaprakash
Summary: The COVID-19 pandemic has highlighted the challenges in large-scale testing, leading to the development of a DIY workflow for rapid and accurate detection of viral RNA with high sensitivity and specificity. This method improves efficiency and accuracy of testing through various techniques, allowing for quick testing at home or in healthcare settings.
Article
Biophysics
Zifan Tang, Reza Nouri, Ming Dong, Jianbo Yang, Wallace Greene, Yusheng Zhu, Michele Yon, Meera Surendran Nair, Suresh Kuchipudi, Weihua Guan
Summary: The study introduces an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2, with a focus on the nucleocapsid assay for its quick and sensitive performance, showing excellent agreement with the gold standard RT-PCR assay.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Virology
Eline Meyers, Jeongho Park, Anja Coen, Leen Raman, Stefan Heytens, Joowon Rhee, Elizaveta Padalko, Piet Cools
Summary: During the SARS-CoV-2 pandemic, rapid and sensitive detection of the virus is crucial. A new point-of-care test system based on LAMP technology was evaluated, and it showed high clinical sensitivity and specificity for SARS-CoV-2 detection. The system's easy operation and ready-to-use reagents make it suitable for various settings, contributing to more efficient outbreak control and quarantine policies.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Francesco Elia Marino, Eric Proffitt, Eugene Joseph, Arun Manoharan
Summary: This study describes an extraction-less method for the rapid qualitative detection of SARS-CoV-2 nucleic acid in upper respiratory specimens using reverse transcriptase loop-mediated isothermal amplification (RT-LAMP). The test exhibits high sensitivity, specificity, and does not require RNA extraction, making it suitable for use in various laboratory and remote settings.
Article
Public, Environmental & Occupational Health
Drew Capone, Aaron Bivins, Joe Brown
Summary: This paper discusses the importance of estimating the risk of pathogen exposure in quantitative microbial risk assessment (QMRA) and proposes a general method for calculating ratio measures of effect. These ratio estimates can be used for evaluating interventions and conducting systematic reviews and meta-analyses.
Article
Polymer Science
Madeline G. Jensen, Patrick T. O'Shaughnessy, Marlee Shaffer, Sooyoun Yu, Yun Young Choi, Megan Christiansen, Charles O. Stanier, Michael Hartley, Joey Huddle, Jed Johnson, Kyle Bibby, Nosang V. Myung, David M. Cwiertny
Summary: During the global spread of COVID-19, the high demand and limited availability of melt-blown filtration material led to a manufacturing backlog of N95 Filtering Facepiece Respirators (FFRs). An alternative filter material, consisting of electrospun polystyrene (PS) microfibers, showed favorable performance in terms of filtration efficiency and antibacterial activity, potentially making it a suitable option for use in N95 FFRs.
JOURNAL OF APPLIED POLYMER SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Pedro F. P. Brandao-Dias, Daniel M. C. Hallack, Elise D. D. Snyder, Jennifer L. L. Tank, Diogo Bolster, Sabrina Volponi, Arial J. J. Shogren, Gary A. A. Lamberti, Kyle Bibby, Scott P. P. Egan
Summary: Environmental DNA (eDNA) analysis is a powerful tool for detecting target organisms remotely. This study explores the possibility of obtaining longitudinal dynamics information on targets by separating different size components of eDNA within a sample. The results show that medium-sized particles decay more slowly and increase in proportion over time. Different sizes of eDNA particles do not decay independently, but a parsimonious mathematical model best explains the data. A framework for discerning target distance and abundance with eDNA data is proposed.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Environmental Sciences
Ananda Tiwari, Sangeet Adhikari, Devrim Kaya, Md. Aminul Islam, Bikash Malla, Samendra P. Sherchan, Ahmad I. Al-Mustapha, Manish Kumar, Srijan Aggarwal, Prosun Bhattacharya, Kyle Bibby, Rolf U. Halden, Aaron Bivins, Eiji Haramoto, Sami Oikarinen, Annamari Heikinheimo, Tarja Pitkaenen
Summary: Monkeypox disease, caused by the monkeypox virus, has become a global concern. Wastewater-based surveillance can be a useful tool for early detection of the virus, but there are challenges to overcome.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
William A. Norfolk, Carolina Melendez-Declet, Erin K. Lipp
Summary: The mucus membrane is the front line of defense against pathogens in corals. Understanding disease transmission in corals is complicated, but most of the established transmission pathways are associated with damage rather than evasion of immune defenses. However, this study suggests that ingestion may be an important pathway for the transmission of coral pathogens that bypasses the mucus membrane.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
William M. Baldwin, Robert D. Dayton, Aaron W. Bivins, Rona S. Scott, Andrew D. Yurochko, John A. Vanchiere, Terry Davis, Connie L. Arnold, Jose. E. T. Asuncion, Mohammad A. N. Bhuiyan, Brandon Snead, William Daniel, Deborah G. Smith, Nicholas E. Goeders, Christopher G. Kevil, Jennifer Carroll, Kevin S. Murnane
Summary: Wastewater surveillance is a useful tool in fighting against the SARS-CoV-2 virus, especially at the population level. In this study, wastewater samples were collected from three communities with different social vulnerability indices in Shreveport, Louisiana, to monitor the spread of the virus. The results showed that communities with higher social vulnerability had higher viral loads in wastewater.
ENVIRONMENTAL RESEARCH
(2023)
Article
Engineering, Environmental
Olivia Ginn, Jennifer L. Tank, Andrei Badilla-Aguilar, Elise Snyder, Pedro F. P. Brandao-Dias, Emma Thrift, Diogo Bolster, Kyle Bibby
Summary: Environmental factors play a critical role in understanding the fate and transport of antibiotic resistance in impacted streams. This study examines the impact of stream characteristics and particle size association on the removal of antimicrobial resistance genes over time. The findings suggest that both substrate and particle size influence the behavior and removal rates of antibiotic resistance genes in surface waters.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Environmental Sciences
Warish Ahmed, Aaron Bivins, Mikayla Stephens, Suzanne Metcalfe, Wendy J. M. Smith, Kwanrawee Sirikanchana, Masaaki Kitajima, Stuart L. Simpson
Summary: This study analyzed wastewater samples from four wastewater treatment plants in Queensland, Australia, and found the presence of 13 respiratory viruses. The results were compared with clinical cases, showing the potential of wastewater surveillance in viral disease monitoring. The most commonly detected viruses were bocavirus, parechovirus, rhinovirus A, and rhinovirus B.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
William Chen, Kyle Bibby
Summary: Wastewater-based epidemiology (WBE) is a community-level monitoring technique used to track diseases, but its feasibility for monitoring vector-borne pathogens like Zika virus is uncertain. Monte Carlo simulation was used to generate distributions for total Zika RNA shedding and the process limit of detection (PLOD), and the probability of detecting Zika RNA in wastewater was calculated. Results suggest that successful Zika WBE application is unlikely in the United States but likely in Zika-endemic countries with decreased wastewater treatment plant (WWTP) per capita flows. However, the great discrepancy between true and reported clinical cases suggests that Zika WBE may be feasible even in the absence of outbreaks in endemic countries.
Review
Environmental Sciences
Aaron Bivins, Robert Morfino, Andrew Franklin, Stuart Simpson, Warish Ahmed
Summary: Commercial air travel connects people but also facilitates the spread of infectious diseases. During the COVID-19 pandemic, public health agencies used control strategies to manage the risk of transmission associated with air travel, and aircraft wastewater surveillance emerged as a promising method to screen for COVID-19. By sampling aircraft wastewater, the global circulation of human pathogens can be monitored, leading to better targeted public health control measures during epidemics.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
Article
Engineering, Environmental
Pedro F. P. Brandao-Dias, Jennifer L. Tank, Elise D. Snyder, Ursula H. Mahl, Brett Peters, Diogo Bolster, Arial J. Shogren, Gary A. Lamberti, Kyle Bibby, Scott P. Egan
Summary: eDNA in aquatic systems is a complex mixture that includes dissolved DNA, intracellular DNA, and particle-adsorbed DNA. Understanding the composition and interactions of eDNA is crucial for determining the abundance and location of target organisms. This study found that eDNA rapidly adsorbs to other materials in the water column, affecting its concentration and particle size distribution. Only particulate organic matter affected the removal rate of eDNA. The removal of larger eDNA components was influenced by physical processes, while the removal of smaller eDNA components was driven by biological degradation.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Warish Ahmed, Wendy J. M. Smith, Kwanrawee Sirikanchana, Masaaki Kitajima, Aaron Bivins, Stuart L. Simpson
Summary: The ongoing COVID-19 pandemic has highlighted the importance of wastewater surveillance in monitoring and tracking the spread of infectious diseases, such as SARS-CoV-2. This study used the adsorption-extraction (AE) method with different pore size membranes to determine the concentrations of four types of endogenous viruses in wastewater samples. The results showed that the larger pore size membrane performed comparably to the smaller pore size membrane for virus detection/quantitation. The study provides valuable insights into the application of the AE method for virus recovery from wastewater, which is crucial for monitoring and tracking infectious diseases in communities.
JOURNAL OF VIROLOGICAL METHODS
(2023)
Article
Engineering, Environmental
William Chen, Kyle Bibby
Summary: This paper discusses the importance of wastewater-based surveillance in understanding the occurrence and spread of infectious diseases and proposes a framework to assess the suitability of novel diseases for wastewater monitoring. The paper also explores five primary factors that influence the detection probability in wastewater-based surveillance and emphasizes the need for further research on these factors.
Article
Public, Environmental & Occupational Health
Aparna Keshaviah, Megan B. Diamond, Matthew J. Wade, Samuel V. Scarpino
Summary: We surveyed wastewater monitoring programmes in 43 countries to inform the development of global monitoring systems. Most programmes focused on urban populations. High-income countries primarily used composite sampling at treatment plants, while low-income and middle-income countries often used grab sampling from surface waters, drains, and latrines. Though most programmes analyzed samples domestically, there was a longer processing time in low-income and middle-income countries. While SARS-CoV-2 variant monitoring was common in high-income countries, it was less frequent in low-income and middle-income countries. Most programmes shared data internally, but not publicly. These findings emphasize the importance of integrating and expanding wastewater initiatives for global disease surveillance.
LANCET GLOBAL HEALTH
(2023)
Article
Environmental Sciences
Elise D. Snyder, Jennifer L. Tank, Pedro F. P. Branda, Kyle Bibby, Arial J. Shogren, Aaron W. Bivins, Brett Peters, Erik M. Curtis, Diogo Bolster, Scott P. Egan, Gary A. Lamberti
Summary: The use of environmental DNA (eDNA) as a sampling tool allows for the detection of invasive and/or rare aquatic species and enables biodiversity assessment without labor-intensive traditional sampling approaches. However, there is limited understanding of the environmental factors that impact the removal of eDNA in flowing waters. This study investigates the impact of light and substrate conditions on eDNA removal rates and suggests that changes in eDNA size classes over time and with differing environmental conditions could be used to predict the location of target organisms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)