References
-
Gerrity, D., Crank, K., Steinle-Darling, E. & Pecson, B. M. Establishing pathogen log reduction value targets for direct potable reuse in the united States. AWWA Water Sci. 5, e1353 (2023).
-
Mehle, N. et al. Tomato brown rugose fruit virus in aqueous environments – survival and significance of water-mediated transmission. Front Plant. Sci 14, (2023).
-
Natarajan, A. et al. The tomato brown rugose fruit virus movement protein gene is a novel microbial source tracking marker. Appl. Environ. Microbiol. 89, e00583–e00523 (2023).
-
Rothman, J. A. & Whiteson, K. L. Sequencing and variant detection of eight abundant Plant-Infecting tobamoviruses across Southern California wastewater. Microbiol. Spectr. 10, e03050–e03022 (2022).
-
Sherchan, S. P., Malla, B. & Haramoto, E. First quantitative detection of tomato brown rugose fruit virus in wastewater in Louisiana. Sci. Total Environ. 888, 164001 (2023).
-
Salem, N., Mansour, A., Ciuffo, M. & Falk, B. W. Turina, M. A new tobamovirus infecting tomato crops in Jordan. Arch. Virol. 161, 503–506 (2016).
-
Luria, N. et al. A new Israeli tobamovirus isolate infects tomato plants harboring Tm-22 resistance genes. PLoS One. 12, e0170429 (2017).
-
Zhang, S., Griffiths, J. S., Marchand, G., Bernards, M. A. & Wang, A. Tomato brown rugose fruit virus: an emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide. Mol. Plant Pathol. 23, 1262–1277 (2022).
-
Eftim, S. E. et al. Occurrence of Norovirus in Raw sewage – A systematic literature review and meta-analysis. Water Res. 111, 366–374 (2017).
-
Hughes, B., Beale, D. J., Dennis, P. G., Cook, S. & Ahmed, W. Cross-Comparison of human Wastewater-Associated molecular markers in relation to fecal indicator bacteria and enteric viruses in recreational beach waters. Appl. Environ. Microbiol. 83, e00028–e00017 (2017).
-
Farkas, K. et al. Viral indicators for tracking domestic wastewater contamination in the aquatic environment. Water Res. 181, 115926 (2020).
-
Schmitz, B. W. et al. Virus surrogates throughout a full-scale advanced water reuse system. Water Res. 256, 121556 (2024).
-
Zhang, T. et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4, e3 (2005).
-
Kitajima, M., Sassi, H. P. & Torrey, J. R. Pepper mild mottle virus as a water quality indicator. Npj Clean. Water. 1, 1–9 (2018).
-
Symonds, E. M., Nguyen, K. H., Harwood, V. J. & Breitbart, M. Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management. Water Res. 144, 1–12 (2018).
-
Hamza, H., Rizk, N. M., Gad, M. A. & Hamza, I. A. Pepper mild mottle virus in wastewater in egypt: a potential indicator of wastewater pollution and the efficiency of the treatment process. Arch. Virol. 164, 2707–2713 (2019).
-
Gearhart, N. & Pagilla, K. Indicator and pathogenic virus removal in bench scale soil aquifer treatment. Sci. Total Environ. 945, 173997 (2024).
-
Bozkurt, H., D’Souza, D. H. & Davidson, P. M. Thermal inactivation of foodborne enteric viruses and their viral surrogates in foods. J. Food Prot. 78, 1597–1617 (2015).
-
Lau, M. et al. Selection of surrogate pathogens and process indicator organisms for pasteurisation of municipal wastewater—A survey of literature data on heat inactivation of pathogens. Process Saf. Environ. Prot. 133, 301–314 (2020).
-
Nasser, A., sasi, S. & Nitzan, Y. Coliphages as indicators for the microbial quality of treated wastewater effluents. Food Environ. Virol. 13, 170–178 (2021).
-
Teel, L. et al. Pathogen reduction by ozone–biological activated carbon-based advanced water reclamation for reuse. Water Environ. Res. 94, e10726 (2022).
-
Mikel, P., Vasickova, P. & Kralik, P. Methods for Preparation of MS2 Phage-Like particles and their utilization as process control viruses in RT-PCR and qRT-PCR detection of RNA viruses from food matrices and clinical specimens. Food Environ. Virol. 7, 96–111 (2015).
-
Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498 (2014).
-
Stachler, E., Akyon, B., de Carvalho, N. A., Ference, C. & Bibby, K. Correlation of crassphage qPCR markers with culturable and molecular indicators of human fecal pollution in an impacted urban watershed. Environ. Sci. Technol. 52, 7505–7512 (2018).
-
Haak, L. et al. Spatial and Temporal variability and data bias in wastewater surveillance of SARS-CoV-2 in a sewer system. Sci. Total Environ. 805, 150390 (2022).
-
Li, L. et al. Detecting SARS-CoV-2 variants in wastewater and their correlation with Circulating variants in the communities. Sci. Rep. 12, 16141 (2022).
-
Gharoon, N. et al. Removal of SARS-CoV-2 viral markers through a water reclamation facility. Water Environ. Res. https://doi.org/10.1002/wer.1641 (2021).
-
Li, L. et al. Longitudinal monitoring of SARS-CoV-2 in wastewater using viral genetic markers and the Estimation of unconfirmed COVID-19 cases. Sci. Total Environ. 817, 152958 (2022).
-
Panno, S. et al. Real-time reverse transcription polymerase chain reaction development for rapid detection of tomato brown rugose fruit virus and comparison with other techniques. PeerJ 7, e7928 (2019).
-
Khan, M. et al. Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community – A multi-site evaluation. One Health. 16, 100536 (2023).
-
Kalantar, K. L. et al. IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. GigaScience 9, giaa111 (2020).
-
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
-
Brumfield, K. D. et al. Microbiome Analysis for Wastewater Surveillance during COVID-19. mBio 13, e0059122 (2022).
-
Paisantham, P. et al. Evaluation of tomato brown rugose fruit virus as a microbial source tracking marker for human sewage in Thailand. Sci. Total Environ. 963, 178419 (2025).
-
Li, L., Haak, L., Carine, M. & Pagilla, K. R. Temporal assessment of SARS-CoV-2 detection in wastewater and its epidemiological implications in COVID-19 case dynamics. Heliyon 10, (2024).
-
Goitom, E. et al. Identification of environmental and methodological factors driving variability of pepper mild mottle virus (PMMoV) across three wastewater treatment plants in the City of Toronto. Sci. Total Environ. 932, 172917 (2024).
-
Wu, H., Brighton, K., Chen, J., Shuai, D. & Aw, T. G. Quantification of Particle-Associated viruses in secondary treated wastewater effluent. Food Environ. Virol. 17, 19 (2025).
