Article
Environmental Sciences
Emma J. Palmer, Juan P. Maestre, David Jarma, Alisa Lu, Elisabeth Willmann, Kerry A. Kinney, Mary Jo Kirisits
Summary: Monitoring SARS-CoV-2 RNA titers in wastewater is a promising strategy for tracking COVID-19 prevalence at a community scale, but the virus is found to be mainly present in suspended solids rather than the liquid phase. Samples taken from primary clarifier effluent show higher SARS-CoV-2 signal compared to those taken after preliminary treatment. Pasteurization and RNA extraction methods also affect the SARS-CoV-2 signal, with pasteurization at 60 degrees Celsius for 90 minutes reducing the signal by approximately 50-55%, and a magnetic bead RNA extraction method yielding a higher signal than a silica membrane approach.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Salmaan Sharif, Aamer Ikram, Adnan Khurshid, Muhammad Salman, Nayab Mehmood, Yasir Arshad, Jamal Ahmed, Rana Muhammad Safdar, Lubna Rehman, Ghulam Mujtaba, Jaffar Hussain, Johar Ali, Mehar Angez, Muhammad Masroor Alam, Ribqa Akthar, Muhammad Wasif Malik, Mirza Zeeshan Iqbal Baig, Muhammad Suleman Rana, Muhammad Usman, Muhammad Qaisar Ali, Abdul Ahad, Nazish Badar, Massab Umair, Sana Tamim, Asiya Ashraf, Faheem Tahir, Nida Ali
Summary: The study found 27% of wastewater samples tested positive for SARs-CoV-2, indicating the potential for monitoring viral spread through wastewater surveillance. Additionally, the detection of virus sequence data in wastewater highlights the importance of surveillance for early warning signs.
Article
Microbiology
Nicole C. Rondeau, Oliver J. Rose, Ellen R. Alt, Lina A. Ariyan, Annabelle B. Elikan, Jenna L. Everard, Abigail R. Schreier, Maya E. Tessler, Grace H. Tulinsky, Janet R. Vo, Caroline A. Ray, Cynthia Y. Yang, J. J. L. Miranda, Brian J. Mailloux
Summary: We established wastewater surveillance as part of our public health response to COVID-19 in a small urban college in New York City. Our results showed that wastewater monitoring could not accurately estimate the number of cases at the building level, but it was effective in detecting outbreak clusters. Our assay had a 60% positive predictive power, 90% negative predictive power, and 90% specificity, but the sensitivity was low at 40%.
MICROBIOLOGY SPECTRUM
(2023)
Article
Environmental Sciences
Yuanyuan Qiu, Jiaao Yu, Kanti Pabbaraju, Bonita E. Lee, Tiejun Gao, Nicholas J. Ashbolt, Steve E. Hrudey, Mathew Diggle, Graham Tipples, Rasha Maal-Bared, Xiaoli Pang
Summary: Wastewater surveillance of SARS-CoV-2 is a valuable tool for assessing population-level changes in community infections. This study validated a molecular testing method using ultrafiltration to concentrate viruses from wastewater and one-step RT-qPCR assay to detect SARS-CoV-2. The study optimized parameters such as sample storage condition, wastewater pH, RNA extraction, and RT-qPCR assay.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Mukhlid Yousif, Said Rachida, Setshaba Taukobong, Nkosenhle Ndlovu, Chinwe Iwu-Jaja, Wayne Howard, Shelina Moonsamy, Nompilo Mhlambi, Sipho Gwala, Joshua I. Levy, Kristian G. Andersen, Cathrine Scheepers, Anne von Gottberg, Nicole Wolter, Jinal N. Bhiman, Daniel Gyamfi Amoako, Arshad Ismail, Melinda Suchard, Kerrigan Mccarthy
Summary: Wastewater surveillance is an important tool to support clinical monitoring efforts, as it can identify and characterize SARS-CoV-2 variants not detected by clinical surveillance. Wastewater genomics can reliably recover the prevalence of local circulating variants and provide a signal of upcoming lineage transitions. This study demonstrates the utility of wastewater genomics in monitoring the evolution and spread of endemic viruses.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Maria Paola Tomasino, Miguel Semedo, Pedro Vieira e Moreira, Elza Ferraz, Adelaide Rocha, Maria F. Carvalho, Catarina Magalhaes, Ana P. Mucha
Summary: Research on wastewater infrastructures as public health observatories for virus circulation in communities, specifically focusing on SARS-CoV-2 surveillance, is being conducted globally. A continuous monitoring protocol was developed to track SARS-CoV-2 RNA concentrations in untreated wastewater from two treatment plants in Porto, Portugal, showing results that aligned with COVID-19 temporal trends in the region. The study supports the use of wastewater-based surveillance to complement clinical testing and assess pandemic trends.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Nicolette A. Zhou, Courtney Tharpe, John Scott Meschke, Christobel M. Ferguson
Summary: Environmental surveillance of SARS-CoV-2 in wastewater provides an early, cost-effective community-level indicator of COVID-19. Current research focuses on testing wastewater influent from large urban treatment plants using methods like polyethylene glycol precipitation, membrane filtration, and centrifugal ultrafiltration.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Nicolae Sapoval, Yunxi Liu, Esther G. G. Lou, Loren Hopkins, Katherine B. Ensor, Rebecca Schneider, Lauren B. Stadler, Todd J. Treangen
Summary: Sapoval et al. present QuaID, a novel bioinformatics tool for detecting SARS-CoV-2 variants based on quasi-unique mutations. QuaID leverages all mutations, including insertions and deletions, to accurately detect variants early in their spread. Wastewater monitoring is crucial for surveillance on the emergence of SARS-CoV-2 variants of concerns in communities, especially as clinical testing declines.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Diyar Mailepessov, Sathish Arivalan, Marcella Kong, Jane Griffiths, Swee Ling Low, Hongjie Chen, Hapuarachchige Chanditha Hapuarachchi, Xiaoqiong Gu, Wei Lin Lee, Eric J. Alm, Janelle Thompson, Stefan Wuertz, Karina Gin, Lee Ching Ng, Judith Chui Ching Wong
Summary: Wastewater-based surveillance is a widely used non-intrusive tool for monitoring population-level transmission of COVID-19. This study aimed to identify and evaluate SARS-CoV-2 virus concentration protocols for high-throughput wastewater testing. The results showed that optimal virus recovery was achieved by removing debris, incubating with 8% PEG at 4 degrees C, centrifugation, and column-based RNA extraction methods.
SCIENCE OF THE TOTAL ENVIRONMENT
(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
Environmental Sciences
Made Sandhyana Angga, Bikash Malla, Sunayana Raya, Ayame Kitano, Xiaomao Xie, Hiroshi Saitoh, Noriyuki Ohnishi, Eiji Haramoto
Summary: The sensitivity of detecting SARS-CoV-2 in wastewater is crucial in wastewater-based epidemiology. In this study, a PEG-based method called Pegcision, using magnetic nanoparticles, was developed and modified to increase its detection sensitivity and throughput. The performance of the Pegcision was compared to that of the PEG precipitation method, and it showed comparable results in detecting SARS-CoV-2 RNA concentration. This suggests that the Pegcision can be a viable virus concentration method.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Itay Bar-Or, Merav Weil, Victoria Indenbaum, Efrat Bucris, Dana Bar-Ilan, Michal Elul, Nofar Levi, Irina Aguvaev, Zvi Cohen, Rachel Shirazi, Oran Erster, Alin Sela-Brown, Danit Sofer, Orna Mor, Ella Mendelson, Neta S. Zuckerman
Summary: Monitoring SARS-CoV-2 variants in wastewater can accurately detect the prevalence of viral strains and assist in monitoring the diversity of circulating strains in the community, as well as pre-identify the emergence of relevant mutations or variants.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Sarmila Tandukar, Niva Sthapit, Ocean Thakali, Bikash Malla, Samendra P. Sherchan, Bijay Man Shakya, Laxman P. Shrestha, Jeevan B. Sherchand, Dev Raj Joshi, Bhupendra Lama, Eiji Haramoto
Summary: This study reports the presence and reduction of SARS-CoV-2 in wastewater from wastewater treatment plants and sewer lines in Nepal. It found a high prevalence of SARS-CoV-2 in wastewater, indicating that biological treatments at the treatment plants are not enough to eliminate the virus. The study suggests that wastewater-based epidemiology is a useful tool for estimating COVID-19 cases in developing countries.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Immunology
Yolanda M. Brooks, Bailey Gryskwicz, Shawn Sheehan, Sheri Piers, Parag Mahale, Susan McNeil, Jenna Chase, Doreen Webber, David Borys, Michael Hilton, Dion Robinson, Stephen Sears, Emer Smith, Emily K. Lesher, Robert Wilson, Matthew Goodwin, Michael Pardales
Summary: Wastewater surveillance was used to identify 2 coronavirus disease outbreaks at a college in Maine. Preceding the outbreaks, there were cumulative increases of >1 log(10) severe acute respiratory syndrome coronavirus 2 RNA in consecutive 24-hour composite samples. RNA was detected in grab samples from residence halls <= 7 days before case discovery in 76% of cases.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Elizabeth C. Stahl, Allan R. Gopez, Connor A. Tsuchida, Vinson B. Fan, Erica A. Moehle, Lea B. Witkowsky, Jennifer R. Hamilton, Enrique Lin-Shiao, Matthew McElroy, Shana L. McDevitt, Alison Ciling, C. Kimberly Tsui, Kathleen Pestal, Holly K. Gildea, Amanda Keller, Iman A. Sylvain, Clara Williams, Ariana Hirsh, Alexander J. Ehrenberg, Rose Kantor, Matthew Metzger, Kara L. Nelson, Fyodor D. Urnov, Bradley R. Ringeisen, Petros Giannikopoulos, Jennifer A. Doudna
Summary: The research developed a cost-effective RT-qPCR test capable of detecting SARS-CoV-2 N gene, E gene, and human RNase P in a single reaction, which saves time and cost, reduces the risk of false-negative results, and is suitable for large-scale clinical surveillance and wastewater monitoring efforts.
Article
Biochemical Research Methods
Mojca Milavec, Jernej Pavsic, Alexandra Bogozalec Kosir, Gerwyn M. Jones, Denise M. O'Sullivan, Alison S. Devonshire, Fran Van Heuverswyn, Maria Karczmarczyk, Jannika Neeb, Annabell Plauth, Philippe Corbisier, Heinz Schimmel, Andreas Kummrow, Joerg Neukammer, Carole A. Foy, Martin Kammel, Hans-Peter Grunert, Heinz Zeichhardt, Jim F. Huggett
Summary: The study evaluated a candidate digital PCR (dPCR)-based reference measurement procedure for quantification of human cytomegalovirus (hCMV) in multiple schemes, demonstrating high reproducibility and trueness of the method. The dPCR has the potential to act as a calibration independent reference measurement procedure for value assignment of hCMV calibration and support qPCR calibration.
Review
Biochemical Research Methods
Mojca Milavec, Megan H. Cleveland, Young-Kyung Bae, Robert Wielgosz, Maxim Vonsky, Jim F. Huggett
Summary: Nucleic acid analysis is widely used in various fields such as medicine, food safety, and environmental monitoring, but users are often unaware of the global metrological infrastructure. International efforts, particularly through the NAWG, focus on improving measurement capabilities and service dissemination to enhance the reliability, comparability, and traceability of nucleic acid measurement results.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Editorial Material
Plant Sciences
M. P. S. Rivarez, Z. Kogej, N. Jakos, A. Pecman, G. Seljak, A. Vucurovic, M. Ravnikar, N. Mehle, D. Kutnjak
Editorial Material
Plant Sciences
Dorotea Grbin, Anja Pecman, Martina Seruga Music, Denis Kutnjak, Dijana Skoric
Letter
Biotechnology & Applied Microbiology
Tim Mercer, Neil Almond, Michael A. Crone, Patrick S. G. Chain, Alina Deshpande, Deepa Eveleigh, Paul Freemont, Sebastien Fuchs, Russell Garlick, Jim Huggett, Martin Kammel, Po-E Li, Mojca Milavec, Elizabeth M. Marlowe, Denise M. O'Sullivan, Mark Page, Gary A. Pestano, Sara Suliman, Birgitte Simen, John J. Sninsky, Lynne Sopchak, Cristina M. Tato, Peter M. Vallone, Jo Vandesompele, Thomas J. White, Heinz Zeichhardt, Marc Salit
NATURE BIOTECHNOLOGY
(2022)
Article
Agronomy
Janja Zajc, Zala Kogej Zwitter, Sara Fiser, Cene Gostincar, Antonio Vicent, Anais Galvan Domenech, Luca Riccioni, Neil Boonham, Maja Ravnikar, Polona Kogovsek
Summary: This study developed a quantitative PCR (qPCR) assay based on the TEF1-alpha sequence for detecting the citrus black spot (CBS) pathogen. High-throughput sequencing (HTS) using DNA barcodes was also explored for detection and discrimination of the pathogen. The results of this study are important for improving the diagnostics of CBS and the surveillance and early detection of the pathogen.
Article
Microbiology
Mark Paul Selda Rivarez, Anja Pecman, Katarina Bacnik, Olivera Maksimovic, Ana Vucurovic, Gabrijel Seljak, Natasa Mehle, Ion Gutierrez-Aguirre, Maja Ravnikar, Denis Kutnjak
Summary: In agroecosystems, the diversity and role of viruses in non-crop plants is less known. This study used high-throughput sequencing to explore viral diversity in tomatoes and weeds at a nation-wide scale, detecting 125 viruses, including novel species. The presence of viruses in both tomatoes and weeds suggests possible exchange between the two, with implications for weed management and tomato health.
Article
Plant Sciences
Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z. A. Gaafar, Oscar P. Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovsek, Marie Lefebvre, Martha Malapi, Irena Mavric Plesko, Serkan Onder, Jean-Sebastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Cigdem Ulubas Serce, Inge van Duivenbode, David W. Waite, Xiaojun Hu, Heiko Ziebell, Sebastien Massart
Summary: High-throughput sequencing of plant tissues is a crucial tool for plant virologists to detect plant viruses. However, during the analysis of the data, researchers often neglect sequences without homologies to viruses, which may contain traces of other pathogens. In this study, we re-analyzed RNA-seq datasets and found non-viral plant pathogens, including fungi, insects, and mites. This highlights the potential of using total RNA-seq data for detecting various plant pathogens.