Advances in virus detection methods for wastewater-based epidemiological applications

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Total Environ., 739, 10.1016/j.scitotenv.2020.139960 Zheng, 2022, Comparison of virus concentration methods and RNA extraction methods for SARS-CoV-2 wastewater surveillance, Sci. Total Environ., 824, 10.1016/j.scitotenv.2022.153687 La Rosa, 2021, SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring, Sci. Total Environ., 750, 10.1016/j.scitotenv.2020.141711 Ahmed, 2022, Wastewater surveillance demonstrates high predictive value for COVID-19 infection on board repatriation flights to Australia, Environ. Int., 158, 10.1016/j.envint.2021.106938 Ahmed, 2020, First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community, Sci. Total Environ., 728, 10.1016/j.scitotenv.2020.138764 Medema, 2020, Presence of SARS-coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in The Netherlands, Environ. Sci. Technol. Lett., 7, 511, 10.1021/acs.estlett.0c00357 Mautner, 2020, Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP), Virol. J., 17, 1, 10.1186/s12985-020-01435-6 Dzinamarira, 2022, Utilization of SARS-CoV-2 wastewater surveillance in Africa—a rapid review, International Journal of Environmental Research and Public Health, 19, 10.3390/ijerph19020969 Ahmed, 2022, Comparison of RT-qPCR and RT-dPCR platforms for the trace detection of SARS-CoV-2 RNA in wastewater, ACS EST Water, 10.1021/acsestwater.1c00387 Ciesielski, 2021, Assessing sensitivity and reproducibility of RT-ddPCR and RT-qPCR for the quantification of SARS-CoV-2 in wastewater, J. Virol. Methods, 297, 10.1016/j.jviromet.2021.114230 Kumar, 2021, Electrochemical sensing of SARS-CoV-2 amplicons with PCB electrodes, Sens. Actuators B Chem., 343, 10.1016/j.snb.2021.130169 Amoah, 2021, RT-LAMP: a cheaper, simpler and faster alternative for the detection of SARS-CoV-2 in wastewater, Food and Environmental Virology, 13, 447, 10.1007/s12560-021-09489-7 Zhu, 2022, Membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system for SARS-CoV-2 quantification in environmental waters, Environ. Sci. Technol., 56, 862, 10.1021/acs.est.1c04623 Ali, 2020, iSCAN: an RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2, Virus Res., 288, 10.1016/j.virusres.2020.198129 Chen, 2022, A rapid and label-free DNA-based interference reduction nucleic acid amplification strategy for viral RNA detection, Biosens. Bioelectron., 198, 10.1016/j.bios.2021.113829 Lara-jacobo, 2021, First detection of SARS-CoV-2 proteins in wastewater samples by mass spectrometry, Res. Sq, 1 Seo, 2020 Alafeef, 2022, Monitoring the viral transmission of SARS-CoV-2 in still waterbodies using a lanthanide-doped carbon nanoparticle-based sensor array, ACS Sustain. Chem. Eng., 10, 245, 10.1021/acssuschemeng.1c06066 Quan, 2018, DPCR: a technology review, Sensors (Switzerland), 18, 10.3390/s18041271 Barceló, 2020, Wastewater-Based Epidemiology to monitor COVID-19 outbreak: present and future diagnostic methods to be in your radar, Case Stud. Chem. Environ. Eng., 2, 10.1016/j.cscee.2020.100042 Suo, 2020, ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens, Emerg. Microbes Infect., 9, 1259, 10.1080/22221751.2020.1772678 Graham, 2020, SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 cases in a large urban sewershed, Environ. Sci. Technol. Heijnen, 2021, Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater, Sci. Total Environ., 799, 10.1016/j.scitotenv.2021.149456 Canh, 2021, Capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater, Sci. Total Environ., 791, 10.1016/j.scitotenv.2021.148342 Monteiro, 2022, Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR, Sci. Total Environ., 815, 10.1016/j.scitotenv.2022.152914 Wurtzer, 2021, Several forms of SARS-CoV-2 RNA can be detected in wastewaters: implication for wastewater-based epidemiology and risk assessment, Water Res., 198, 10.1016/j.watres.2021.117183 Leifels, 2021, Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications – a systematic review, Water Res. X, 11, 10.1016/j.wroa.2020.100080 Aoki, 2021, Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load, Sci. Rep., 11, 1, 10.1038/s41598-021-88506-y Haque, 2021, A novel RdRp-based colorimetric RT-LAMP assay for rapid and sensitive detection of SARS-CoV-2 in clinical and sewage samples from Pakistan, Virus Res., 302 Bivins, 2022, Building-level wastewater surveillance using tampon swabs and RT-LAMP for rapid SARS-CoV-2 RNA detection, Environ. Sci. Water Res. Technol., 8, 173, 10.1039/D1EW00496D Ganbaatar, 2021, CRISPR-based COVID-19 testing: toward next-generation point-of-care diagnostics, Frontiers in Cellular and Infection Microbiology, 11, 10.3389/fcimb.2021.663949 Tsou, 2021, Rapid and sensitive detection of SARS-CoV-2 using clustered regularly interspaced short palindromic Repeats, Biomedicines, 9, 10.3390/biomedicines9030239 Chaibun, 2021, Rapid electrochemical detection of coronavirus SARS-CoV-2, Nat. Commun., 12, 1, 10.1038/s41467-021-21121-7 Zhang, 2021, Rolling circle amplification as an efficient analytical tool for rapid detection of contaminants in aqueous environments, Biosensors, 11, 1, 10.3390/bios11100352 Chen, 2019, The interactions of algae-activated sludge symbiotic system and its effects on wastewater treatment and lipid accumulation, Bioresour. Technol., 292 Feng, 2020, Molecular diagnosis of COVID-19: challenges and research needs, Anal. Chem., 92, 10196, 10.1021/acs.analchem.0c02060 Neault, 2020 Ihling, 2020, Mass spectrometric identification of SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients, J. Proteome Res., 10.1021/acs.jproteome.0c00280 Cardozo, 2020, Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts, Nat. Commun., 11, 1, 10.1038/s41467-020-19925-0 Mann, 2021, Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry, Anal. Bioanal. Chem., 413, 7241, 10.1007/s00216-021-03649-1 Lara-Jacobo, 2022, Detection of SARS-CoV-2 proteins in wastewater samples by mass spectrometry, Environ. Sci. Technol., 56, 5062, 10.1021/acs.est.1c04705 Griffin, 2021, Mass spectrometry analytical responses to the SARS-CoV2 coronavirus in review, TrAC - Trends Anal. Chem., 142, 10.1016/j.trac.2021.116328 Ye, 2019, Integrated cell culture-mass spectrometry method for infectious human virus monitoring, Environ. Sci. Technol. Lett., 6, 407, 10.1021/acs.estlett.9b00226 Buonerba, 2021, Coronavirus in water media: analysis, fate, disinfection and epidemiological applications, J. Hazard. Mater., 415, 10.1016/j.jhazmat.2021.125580 Picó, 2021, Mass spectrometry in wastewater-based epidemiology for the determination of small and large molecules as biomarkers of exposure: toward a global view of environment and human health under the COVID-19 outbreak, ACS Omega, 6, 30865, 10.1021/acsomega.1c04362 Mavrikou, 2020, Development of a portable, ultra-rapid and ultra-sensitive cell-based biosensor for the direct detection of the SARS-CoV-2 S1 spike protein antigen, Sensors, 20, 10.3390/s20113121 Cho, 2021, Antibody-Free rapid detection of SARS-CoV-2 proteins using corona phase molecular recognition to accelerate development time, Anal. Chem., 93, 14685, 10.1021/acs.analchem.1c02889 Nag, 2022, Monitoring of SARS-CoV-2 variants by wastewater-based surveillance as a sustainable and pragmatic approach—a case study of Jaipur (India), Water Switz., 14, 1 Bar-Or, 2021, Detection of SARS-CoV-2 variants by genomic analysis of wastewater samples in Israel, Sci. Total Environ., 789, 10.1016/j.scitotenv.2021.148002 Crits-Christoph, 2021, Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants, mBio, 12, 1, 10.1128/mBio.02703-20 Smyth, 2022, Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater, Nat. Commun., 13, 1 Johnson, 2022, Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology, Sci. Rep., 12, 10.1038/s41598-022-05110-4 Kirby, 2022, Notes from the field: early evidence of the SARS-CoV-2 B.1.1.529 (Omicron) variant in community wastewater — United States, november–december 2021, MMWR Morb. Mortal. Wkly. Rep., 71, 103, 10.15585/mmwr.mm7103a5 Ahmed, 2020, Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers, J. Travel Med., 27, 1, 10.1093/jtm/taaa116 La Rosa, 2021, Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein, Water Res., 197, 10.1016/j.watres.2021.117104 La Rosa, 2022, The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance, Sci. Total Environ., 837, 10.1016/j.scitotenv.2022.155767 Bedotto, 2021, Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant, J. Clin. Virol., 139, 19, 10.1016/j.jcv.2021.104814 Lee, 2021, Quantitative SARS-CoV-2 Alpha variant B.1.1.7 tracking in wastewater by allele-specific RT-qPCR, Environ. Sci. Technol. Lett., 8, 675, 10.1021/acs.estlett.1c00375 D'Agostino, 2022, Rapid and sensitive detection of SARS-CoV-2 variants in nasopharyngeal swabs and wastewaters, Diagn. Microbiol. Infect. Dis., 102, 10.1016/j.diagmicrobio.2021.115632 Xu, 2022, Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance, Water Res., 220, 10.1016/j.watres.2022.118686 Peng, 2022, Early warning measurement of SARS-CoV-2 variants of concern in wastewaters by mass spectrometry, Environ. Sci. Technol. Lett., 9, 638, 10.1021/acs.estlett.2c00280 Nourinejad, 2021, Placing sensors in sewer networks: a system to pinpoint new cases of coronavirus, PLoS ONE, 16, 10.1371/journal.pone.0248893 Larson, 2020, Sampling manholes to home in on SARS-CoV-2 infections, PLoS ONE, 15, 10.1371/journal.pone.0240007 McMahan, 2021, COVID-19 wastewater epidemiology: a model to estimate infected populations, Lancet Planet. Health, 5, e874, 10.1016/S2542-5196(21)00230-8