CDC, 2022
Sims, 2020, Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level, Environ. Int., 139, 10.1016/j.envint.2020.105689
Quer, 2022, Next-generation sequencing for confronting virus pandemics, Viruses, 14, 10.3390/v14030600
Wang, 2022, Detection of respiratory viruses directly from clinical samples using next-generation sequencing: a literature review of recent advances and potential for routine clinical use, Rev. Med. Virol., 32, 10.1002/rmv.2375
Fernandes, 2022, Recent advances in point of care testing for COVID-19 detection, Biomed. Pharmacother., 153, 10.1016/j.biopha.2022.113538
Rafieepoor, 2022, Detection of SARS-CoV-2 RNA in selected agricultural and food retail environments in Tehran, Iran, Front. Public Health, 10, 10.3389/fpubh.2022.823061
Brumfield, 2022, Microbiome analysis for wastewater surveillance during COVID-19, mBio, 13, 10.1128/mbio.00591-22
Kilaru, 2023, Wastewater surveillance for infectious disease: a systematic review, Am. J. Epidemiol., 192, 305, 10.1093/aje/kwac175
Dargahi, 2022, Investigating SARS-CoV-2 RNA in five municipal wastewater treatment plants, hospital wastewater and wastewater collection networks during the COVID-19 pandemic in Ardabil Province, Iran, Appl Water Sci, 12, 256, 10.1007/s13201-022-01773-6
Giacobbo, 2021, A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?, Sci. Total Environ., 774, 10.1016/j.scitotenv.2021.145721
LeChevallier, 2020, Protecting wastewater workers from disease risks: personal protective equipment guidelines, Water Environ. Res., 92, 524, 10.1002/wer.1249
Li, 2022, Longitudinal monitoring of SARS-CoV-2 in wastewater using viral genetic markers and the estimation of unconfirmed COVID-19 cases, Sci. Total Environ., 817, 10.1016/j.scitotenv.2022.152958
Ai, 2021, Wastewater SARS-CoV-2 monitoring as a community-level COVID-19 trend tracker and variants in Ohio, United States, Sci. Total Environ., 801, 10.1016/j.scitotenv.2021.149757
Haak, 2022, Spatial and temporal variability and data bias in wastewater surveillance of SARS-CoV-2 in a sewer system, Sci. Total Environ., 805, 10.1016/j.scitotenv.2021.150390
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., 71, 103, 10.15585/mmwr.mm7103a5
Rachmadi, 2016, Human polyomavirus: advantages and limitations as a human-specific viral marker in aquatic environments, Water Res., 105, 456, 10.1016/j.watres.2016.09.010
Fratini, 2014, Oncogenic papillomavirus and polyomavirus in water environments: is there a potential for waterborne transmission?, Food Environ. Virol., 6, 1, 10.1007/s12560-013-9134-0
Hrudey, 2022, The devil is in the details: emerging insights on the relevance of wastewater surveillance for SARS-CoV-2 to public health, J. Water Health, 20, 246, 10.2166/wh.2021.186
Soller, 2022, Modeling infection from SARS-CoV-2 wastewater concentrations: promise, limitations, and future directions, J. Water Health, 20, 1197, 10.2166/wh.2022.094
Li, 2022, Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities, Sci. Rep., 12, 16141, 10.1038/s41598-022-20219-2
CDC-Laboratories, 2020
Gharoon, 2021, Removal of SARS-CoV-2 viral markers through a water reclamation facility, Water Environ. Res., 93, 2819, 10.1002/wer.1641
Hartley, 2021, Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene, J. Genet. Genomics, 48, 40, 10.1016/j.jgg.2021.01.004
Kalantar, 2020, IDseq-an open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring, Gigascience, 9, 10.1093/gigascience/giaa111
Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635
Zhao, 2012, RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data, Bioinformatics, 28, 125, 10.1093/bioinformatics/btr595
Solo-Gabriele, 2023, Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples, Sci. Total Environ., 857, 10.1016/j.scitotenv.2022.159188
Reynolds, 2022, SARS-CoV-2 variant trends in Ireland: wastewater-based epidemiology and clinical surveillance, Sci. Total Environ., 838, 10.1016/j.scitotenv.2022.155828
Murni, 2022, The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia, PLoS One, 17, 10.1371/journal.pone.0274793
Lu, 2022, Wastewater surveillance of SARS-CoV-2 in dormitories as a part of comprehensive university campus COVID-19 monitoring, Environ. Res., 212, 10.1016/j.envres.2022.113580
Fontenele, 2021, High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants, Water Res., 205, 10.1016/j.watres.2021.117710
Scafetta, 2020, Distribution of the SARS-CoV-2 pandemic and its monthly forecast based on seasonal climate patterns, Int. J. Environ. Res. Public Health, 17, 10.3390/ijerph17103493
Wilder, 2021, Co-quantification of crAssphage increases confidence in wastewater-based epidemiology for SARS-CoV-2 in low prevalence areas, Water Res. X, 11, 10.1016/j.wroa.2021.100100
D’Aoust, 2021, COVID-19 wastewater surveillance in rural communities: comparison of lagoon and pumping station samples, Sci. Total Environ., 801
Wu, 2022, SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases, Sci. Total Environ., 805, 10.1016/j.scitotenv.2021.150121
CDC
WHO
Galani, 2023, Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region, Sci. Total Environ., 856, 10.1016/j.scitotenv.2022.159062
Maxmen, 2022, Why call it BA.2.12.1? A guide to the tangled omicron family, Nature, 606, 446, 10.1038/d41586-022-01466-9
Maxmen, 2022, Are new omicron subvariants a threat? Here’s how scientists are keeping watch, Nature, 604, 605, 10.1038/d41586-022-01069-4
Shiraz, 2022, Enhanced recombination among SARS-CoV-2 omicron variants contributes to viral immune escape, bioRxiv
CDC
WCHD, 2023
CDC
Qin, 2020, How does temperature play a role in the storage of extracellular vesicles?, J. Cell. Physiol., 235, 7663, 10.1002/jcp.29700
Huang, 2023, Cold exposure impairs extracellular vesicle swarm-mediated nasal antiviral immunity, J. Allergy Clin. Immunol., 151, 509, 10.1016/j.jaci.2022.09.037
Lowen, 2007, Influenza virus transmission is dependent on relative humidity and temperature, PLoS Pathog., 3, 1470, 10.1371/journal.ppat.0030151
Lowen, 2014, Roles of humidity and temperature in shaping influenza seasonality, J. Virol., 88, 7692, 10.1128/JVI.03544-13
Brumfield, 2021, Metagenomic sequencing and quantitative real-time PCR for fecal pollution assessment in an urban watershed, Front. Water, 3, 10.3389/frwa.2021.626849
Stamps, 2018, Characterization of the microbiome at the world’s largest potable water reuse facility, Front. Microbiol., 9, 2435, 10.3389/fmicb.2018.02435
Arias, 2009, Antibiotic-resistant bugs in the 21st century–a clinical super-challenge, N. Engl. J. Med., 360, 439, 10.1056/NEJMp0804651
Rezasoltani, 2020, Antimicrobial resistance as a hidden menace lurking behind the COVID-19 outbreak: the global impacts of too much hygiene on AMR, Front. Microbiol., 11, 10.3389/fmicb.2020.590683
Yao, 2021, Occurrence and removal of antibiotics, antibiotic resistance genes, and bacterial communities in hospital wastewater, Environ. Sci. Pollut. Res. Int., 28, 57321, 10.1007/s11356-021-14735-3
Nori, 2021, Bacterial and fungal coinfections in COVID-19 patients hospitalized during the new York City pandemic surge, Infect. Control Hosp. Epidemiol., 42, 84, 10.1017/ice.2020.368
Yamamoto, 2021, The human microbiome and COVID-19: a systematic review, PLoS One, 16, 10.1371/journal.pone.0253293