{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T22:13:33Z","timestamp":1790547213627,"version":"4.1.0"},"reference-count":64,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,24]],"date-time":"2025-05-24T00:00:00Z","timestamp":1748044800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute for Infectious Diseases \u201cLazzaro Spallanzani\u201d, IRCCS","award":["Missione 4-Componente 2-LI 1.4-CUP F53C24001620001"],"award-info":[{"award-number":["Missione 4-Componente 2-LI 1.4-CUP F53C24001620001"]}]},{"name":"Italian Ministry of Health","award":["Missione 4-Componente 2-LI 1.4-CUP F53C24001620001"],"award-info":[{"award-number":["Missione 4-Componente 2-LI 1.4-CUP F53C24001620001"]}]},{"name":"dall\u2019Unione Europea-Next Generation EU","award":["Missione 4-Componente 2-LI 1.4-CUP F53C24001620001"],"award-info":[{"award-number":["Missione 4-Componente 2-LI 1.4-CUP F53C24001620001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>Wastewater surveillance has proven to be a cost-effective, non-invasive method for monitoring the spread and evolution of SARS-CoV-2, yet its value during today\u2019s low-incidence phase is still being defined. Between August 2023 and July 2024, 42 composite wastewater samples were collected in Perugia, Italy and analyzed using RT-qPCR and whole-genome sequencing to identify circulating SARS-CoV-2 lineages. In parallel, clinical samples (respiratory tract samples) were collected and analyzed, allowing for direct comparisons to confirm the robustness of the wastewater findings. The sewage viral loads ranged from 8.9 \u00d7 105 to 4.9 \u00d7 107 genome copies inhabitant\u22121 day\u22121, outlining two modest community waves (September\u2013December 2023 and May\u2013July 2024). Sequencing resolved 403 Omicron lineages and revealed three successive subvariant phases: (i) XBB.* dominance (August\u2013October 2023), when late-Omicron XBB subvariants (mainly EG.5.* and XBB.1.5) accounted for almost all genomes; (ii) a BA.2.86\/JN surge (November 2023\u2013March 2024), during which the BA.2.86 subvariant, driven mainly by its JN descendants (especially JN.1), rapidly displaced XBB.* and peaked at 89% in February 2024; and (iii) KP.* takeover (April\u2013July 2024), with JN.1-derived KP subvariants rising steadily and KP.3 reaching 81% by July 2024, thereby becoming the dominant lineage. Comparisons of data from wastewater and clinical surveillance demonstrated how the former presented a much higher diversity of circulating viral lineages. Importantly, some subvariants (including BA.2.86*) were detected in wastewater weeks to months prior to clinical identification, and for longer periods. Taken together, the obtained data validated wastewater surveillance as an effective early warning system, especially during periods of low infection prevalence and\/or limited molecular testing efforts. This methodology can thus complement clinical surveillance by offering valuable insights into viral dynamics at the community level and enhancing pandemic preparedness.<\/jats:p>","DOI":"10.3390\/life15060850","type":"journal-article","created":{"date-parts":[[2025,5,25]],"date-time":"2025-05-25T20:39:36Z","timestamp":1748205576000},"page":"850","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["One-Year Monitoring of the Evolution of SARS-CoV-2 Omicron Subvariants Through Wastewater Analysis (Central Italy, August 2023\u2013July 2024)"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3036-7597","authenticated-orcid":false,"given":"Alessandra","family":"Nappo","sequence":"first","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"},{"name":"Bioinformatics Research Unit in Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2837-4517","authenticated-orcid":false,"given":"Maya","family":"Petricciuolo","sequence":"additional","affiliation":[{"name":"Laboratory of Applied and Environmental Microbiology, Department of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0331-2627","authenticated-orcid":false,"given":"Giulia","family":"Berno","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnese","family":"Carnevali","sequence":"additional","affiliation":[{"name":"Laboratory of Applied and Environmental Microbiology, Department of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8831-3380","authenticated-orcid":false,"given":"Cesare Ernesto Maria","family":"Gruber","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"},{"name":"Bioinformatics Research Unit in Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Bicchieraro","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery and Center of Functional Genomics (C.U.R.Ge.F), University of Perugia, 06132 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2100-6172","authenticated-orcid":false,"given":"Roberta","family":"Spaccapelo","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery and Center of Functional Genomics (C.U.R.Ge.F), University of Perugia, 06132 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5162-046X","authenticated-orcid":false,"given":"Martina","family":"Rueca","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1952-5117","authenticated-orcid":false,"given":"Fabrizio","family":"Carletti","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6743-014X","authenticated-orcid":false,"given":"Pietro Giorgio","family":"Spezia","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina","family":"Veneri","sequence":"additional","affiliation":[{"name":"National Center for Water Safety (CeNSia), Istituto Superiore di Sanit\u00e0, 00161 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2657-100X","authenticated-orcid":false,"given":"Giuseppina","family":"La Rosa","sequence":"additional","affiliation":[{"name":"National Center for Water Safety (CeNSia), Istituto Superiore di Sanit\u00e0, 00161 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7605-0539","authenticated-orcid":false,"given":"Elisabetta","family":"Suffredini","sequence":"additional","affiliation":[{"name":"Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanit\u00e0, 00161 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8811-195X","authenticated-orcid":false,"given":"Daniele","family":"Focosi","sequence":"additional","affiliation":[{"name":"North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3901-6926","authenticated-orcid":false,"given":"Giovanni","family":"Chillemi","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Unit in Infectious Diseases, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"},{"name":"Department of Experimental Medicine, University of Rome \u201cTor Vergata\u201d, 00133 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4983-1967","authenticated-orcid":false,"given":"Ermanno","family":"Federici","sequence":"additional","affiliation":[{"name":"Laboratory of Applied and Environmental Microbiology, Department of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7489-5271","authenticated-orcid":false,"given":"Fabrizio","family":"Maggi","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani\u2014IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s12982-024-00140-x","article-title":"Evolution and Implications of SARS-CoV-2 Variants in the Post-Pandemic Era","volume":"21","author":"Manirambona","year":"2024","journal-title":"Discov. Public Health"},{"key":"ref_2","unstructured":"Aggiornamento Dei Dati (2025, April 24). Del Bollettino Della Sorveglianza Integrata COVID-19 in Italia. Available online: https:\/\/www.epicentro.iss.it\/coronavirus\/aggiornamenti."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Shanmugam, B.K., Alqaydi, M., Abdisalam, D., Shukla, M., Santos, H., Samour, R., Petalidis, L., Oliver, C.M., Brudecki, G., and Bin Salem, S. (2024). A Narrative Review of High Throughput Wastewater Sample Processing for Infectious Disease Surveillance: Challenges, Progress, and Future Opportunities. Int. J. Env. Res. Public Health, 21.","DOI":"10.3390\/ijerph21111432"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Zhao, L., Xu, J., Guo, J., Zhang, P., Guo, X., Zuo, Z., Gao, L., Jia, Z., Xue, P., and Wang, J. (2024). An Epidemiologic Surveillance Study Based on Wastewater and Respiratory Specimens Reveals Influenza a Virus Prevalence and Mutations in Taiyuan, China during 2023\u20132024. BMC Infect. Dis., 24.","DOI":"10.1186\/s12879-024-10169-7"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Annan, J., Henderson, R., Gray, M., Clark, R.G., Sarin, C., and Black, K. (2024). A Review of Wastewater-Based Epidemiology for the SARS-CoV-2 Virus in Rural, Remote, and Resource-Constrained Settings Internationally: Insights for Implementation, Research, and Policy for First Nations in Canada. Int. J. Env. Res. Public Health, 21.","DOI":"10.3390\/ijerph21111429"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s12560-024-09616-0","article-title":"Harnessing the Power of Next-Generation Sequencing in Wastewater-Based Epidemiology and Global Disease Surveillance","volume":"17","author":"Farkas","year":"2025","journal-title":"Food Environ. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Chukwu, E.E., Okwuraiwe, A., Kunle-Ope, C.N., Igbasi, U.T., Onyejepu, N., Osuolale, K., Shaibu, J.O., Ojogbede, A., Abuh, D., and Afocha, E. (2024). Surveillance of Public Health Pathogens in Lagos Wastewater Canals: A Cross-Sectional Study. BMC Public Health, 24.","DOI":"10.1186\/s12889-024-21157-6"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Nkambule, S., Street, R., Surujlal-Naicker, S., Johnson, R., and Mathee, A. (2024). Wastewater Surveillance for SARS-CoV-2 during a Mass Sporting Event in the City of Cape Town, Western Cape. Front. Public Health, 12.","DOI":"10.3389\/fpubh.2024.1462629"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Jones, G., Nelson, A., Chadwick, D.R., Cobley, S., Jones, D.L., Perrett, S., Perry, W.B., Weightman, A.J., Williams, R.C., and Thomas, D.R. (2024). Evaluation of Wastewater Surveillance for SARS-CoV-2 in a Prison Population: A Mixed-Methods Approach. Front. Public Health, 12.","DOI":"10.3389\/fpubh.2024.1462186"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1007\/s10661-024-13341-3","article-title":"Dengue and Chikungunya Virus Dynamics, Identification, and Monitoring in Wastewater","volume":"196","author":"Haldar","year":"2024","journal-title":"Env. Monit. Assess."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Gir\u00f3n-Guzm\u00e1n, I., S\u00e1nchez, G., and P\u00e9rez-Catalu\u00f1a, A. (2024). Tracking Epidemic Viruses in Wastewaters. Microb. Biotechnol., 17.","DOI":"10.1111\/1751-7915.70020"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"100939","DOI":"10.1016\/j.lanmic.2024.07.002","article-title":"Global Wastewater Surveillance for Pathogens with Pandemic Potential: Opportunities and Challenges","volume":"6","author":"Grassly","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Saravia, C.J., P\u00fctz, P., Wurzbacher, C., Uchaikina, A., Drewes, J.E., Braun, U., Bannick, C.G., and Obermaier, N. (2024). Wastewater-Based Epidemiology: Deriving a SARS-CoV-2 Data Validation Method to Assess Data Quality and to Improve Trend Recognition. Front. Public Health, 12.","DOI":"10.3389\/fpubh.2024.1497100"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2171","DOI":"10.2166\/wh.2024.285","article-title":"Unveiling the Silent Information of Wastewater-Based Epidemiology of SARS-CoV-2 at Community and Sanitary Zone Levels: Experience in C\u00f3rdoba City, Argentina","volume":"22","author":"Masachessi","year":"2024","journal-title":"J. Water Health"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Schenk, H., Rauch, W., Zulli, A., and Boehm, A.B. (2024). SARS-CoV-2 Surveillance in US Wastewater: Leading Indicators and Data Variability Analysis in 2023\u20132024. PLoS ONE, 19.","DOI":"10.1101\/2024.08.28.24312739"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Parkins, M.D., Lee, B.E., Acosta, N., Bautista, M., Hubert, C.R.J., Hrudey, S.E., Frankowski, K., and Pang, X.L. (2024). Wastewater-Based Surveillance as a Tool for Public Health Action: SARS-CoV-2 and Beyond. Clin. Microbiol. Rev., 37.","DOI":"10.1128\/cmr.00103-22"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1001\/jama.2022.12563","article-title":"Study: New Wastewater Surveillance Method Detected SARS-CoV-2 Variants of Concern Up to 2 Weeks Before Clinical Tests","volume":"328","year":"2022","journal-title":"JAMA"},{"key":"ref_18","unstructured":"(2025, April 24). WHO Coronavirus Network (CoViNet). Available online: https:\/\/www.who.int\/groups\/who-coronavirus-network."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1016\/S0140-6736(21)02758-6","article-title":"Omicron SARS-CoV-2 Variant: A New Chapter in the COVID-19 Pandemic","volume":"398","author":"Karim","year":"2021","journal-title":"Lancet"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/s41586-021-04385-3","article-title":"Omicron Escapes the Majority of Existing SARS-CoV-2 Neutralizing Antibodies","volume":"602","author":"Cao","year":"2022","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"105699","DOI":"10.1016\/j.micpath.2022.105699","article-title":"Unique Mutations in SARS-CoV-2 Omicron Subvariants\u2019 Non-Spike Proteins: Potential Impacts on Viral Pathogenesis and Host Immune Evasion","volume":"170","author":"Hossain","year":"2022","journal-title":"Microb. Pathog."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5760","DOI":"10.1038\/s41467-022-33498-0","article-title":"Household Transmission of SARS-CoV-2 Omicron Variant of Concern Subvariants BA.1 and BA.2 in Denmark","volume":"13","author":"Lyngse","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1038\/s41591-022-01911-2","article-title":"Emergence of SARS-CoV-2 Omicron Lineages BA.4 and BA.5 in South Africa","volume":"28","author":"Tegally","year":"2022","journal-title":"Nat. Med."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.ijid.2023.01.024","article-title":"Emergence and Geographic Dominance of Omicron Subvariants XBB\/XBB.1.5 and BF.7\u2014the Public Health Challenges","volume":"128","author":"Velavan","year":"2023","journal-title":"Int. J. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.chom.2024.01.001","article-title":"Virological Characteristics of the SARS-CoV-2 BA.2.86 Variant","volume":"32","author":"Tamura","year":"2024","journal-title":"Cell Host Microbe"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"938","DOI":"10.15585\/mmwr.mm7342a1","article-title":"Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron XBB and JN.1 Lineages\u2014United States, May 2023\u2013September 2024","volume":"73","author":"Ma","year":"2024","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41586-022-05049-6","article-title":"Wastewater Sequencing Reveals Early Cryptic SARS-CoV-2 Variant Transmission","volume":"609","author":"Karthikeyan","year":"2022","journal-title":"Nature"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"148002","DOI":"10.1016\/j.scitotenv.2021.148002","article-title":"Detection of SARS-CoV-2 Variants by Genomic Analysis of Wastewater Samples in Israel","volume":"789","author":"Weil","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"6325","DOI":"10.1038\/s41467-023-41369-5","article-title":"SARS-CoV-2 Genomic Surveillance in Wastewater as a Model for Monitoring Evolution of Endemic Viruses","volume":"14","author":"Yousif","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Gupta, P., Liao, S., Ezekiel, M., Novak, N., Rossi, A., LaCross, N., Oakeson, K., and Rohrwasser, A. (2023). Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.00391-23"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"156741","DOI":"10.1016\/j.scitotenv.2022.156741","article-title":"Rapid Transition between SARS-CoV-2 Variants of Concern Delta and Omicron Detected by Monitoring Municipal Wastewater from Three Canadian Cities","volume":"841","author":"Oloye","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"155767","DOI":"10.1016\/j.scitotenv.2022.155767","article-title":"The Rapid Spread of SARS-CoV-2 Omicron Variant in Italy Reflected Early through Wastewater Surveillance","volume":"837","author":"Iaconelli","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"162339","DOI":"10.1016\/j.scitotenv.2023.162339","article-title":"Wastewater Surveillance of SARS-CoV-2 Variants in October\u2013November 2022 in Italy: Detection of XBB.1, BA.2.75 and Rapid Spread of the BQ.1 Lineage","volume":"873","author":"Brandtner","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1007\/s12560-024-09607-1","article-title":"Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis","volume":"16","author":"Veneri","year":"2024","journal-title":"Food Environ. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"170355","DOI":"10.1016\/j.scitotenv.2024.170355","article-title":"BA.2.86 Variant Emergence and Spread Dynamics through Wastewater Monitoring in Paris, France","volume":"917","author":"Wurtzer","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"173164","DOI":"10.1016\/j.scitotenv.2024.173164","article-title":"Incursion of SARS-CoV-2 BA.2.86.1 Variant into Israel: National-Scale Wastewater Surveillance Using a Novel Quantitative Real-Time PCR Assay","volume":"933","author":"Erster","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"taae040","DOI":"10.1093\/jtm\/taae040","article-title":"Wastewater-Based Epidemiological Surveillance of SARS-CoV-2 New Variants BA.2.86 and Offspring JN.1 in South and Southeast Asia","volume":"31","author":"Wannigama","year":"2024","journal-title":"J. Travel Med."},{"key":"ref_38","first-page":"2300595","article-title":"Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage through Integrated Genomic Surveillance of Wastewater and COVID-19 Cases in Sweden, Weeks 31 to 38 2023","volume":"28","author":"Berg","year":"2023","journal-title":"Eurosurveillance"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"332","DOI":"10.46234\/ccdcw2024.063","article-title":"Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay-Shenzhen City, Guangdong Province, China, 2023","volume":"6","author":"Du","year":"2024","journal-title":"China CDC Wkly."},{"key":"ref_40","unstructured":"(2025, April 28). SARS-CoV-2 Variants of Concern as of 25 April 2025. Available online: https:\/\/www.ecdc.europa.eu\/en\/covid-19\/variants-concern."},{"key":"ref_41","unstructured":"La Rosa, G., Bonadonna, L., and Suffredini, E. (2025, January 02). Protocollo Della Sorveglianza Di SARS-CoV-2 in Reflui Urbani (SARI)-Rev. 3. Available online: https:\/\/zenodo.org\/record\/5758725."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map Format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Grubaugh, N.D., Gangavarapu, K., Quick, J., Matteson, N.L., De Jesus, J.G., Main, B.J., Tan, A.L., Paul, L.M., Brackney, D.E., and Grewal, S. (2019). An Amplicon-Based Sequencing Framework for Accurately Measuring Intrahost Virus Diversity Using PrimalSeq and IVar. Genome Biol., 20.","DOI":"10.1186\/s13059-018-1618-7"},{"key":"ref_46","unstructured":"Freyja (2024, July 17). UShER Global Phylogenetic Tree. Available online: https:\/\/github.com\/andersen-lab\/Freyja."},{"key":"ref_47","unstructured":"(2024, July 22). Pango Lineages. Available online: https:\/\/cov-lineages.org."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Rueca, M., Giombini, E., Messina, F., Bartolini, B., Di Caro, A., Capobianchi, M.R., and Gruber, C.E.M. (2022). The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study. JMIR Bioinform. Biotechnol., 3.","DOI":"10.2196\/31536"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.46234\/ccdcw2021.255","article-title":"GISAID\u2019s Role in Pandemic Response","volume":"3","author":"Khare","year":"2021","journal-title":"China CDC Wkly."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: Clade Assignment, Mutation Calling and Quality Control for Viral Genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Bicchieraro, G., Ciurnelli, R., Graziani, A., Wong, A.Y.W., Camilloni, B., Mencacci, A., and Spaccapelo, R. (2024). SARS-CoV-2 Molecular Evolution: A Focus on Omicron Variants in Umbria, Italy. Microorganisms, 12.","DOI":"10.3390\/microorganisms12071330"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"100617","DOI":"10.1016\/j.onehlt.2023.100617","article-title":"Developing One Health Surveillance Systems","volume":"17","author":"Hayman","year":"2023","journal-title":"One Health"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"5324","DOI":"10.1038\/s41467-024-49417-4","article-title":"Realising a Global One Health Disease Surveillance Approach: Insights from Wastewater and Beyond","volume":"15","author":"Hill","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"171877","DOI":"10.1016\/j.scitotenv.2024.171877","article-title":"Application of Wastewater-Based Epidemiology for Monitoring COVID-19 in Hospital and Housing Wastewaters","volume":"931","author":"Tandukar","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1080\/23744235.2024.2369177","article-title":"Leveraging Wastewater-Based Epidemiology to Monitor the Spread of Neglected Tropical Diseases in African Communities","volume":"56","author":"Ofori","year":"2024","journal-title":"Infect. Dis."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"124045","DOI":"10.1016\/j.envpol.2024.124045","article-title":"Wastewater-Based Epidemiology as a Public Health Resource in Low- and Middle-Income Settings","volume":"351","author":"Hamilton","year":"2024","journal-title":"Environ. Pollut."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2300460","DOI":"10.2807\/1560-7917.ES.2023.28.36.2300460","article-title":"First Cases of SARS-CoV-2 BA.2.86 in Denmark, 2023","volume":"28","author":"Rasmussen","year":"2023","journal-title":"Eurosurveillance"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"e42534","DOI":"10.1016\/j.heliyon.2025.e42534","article-title":"Wastewater Surveillance of Open Drains for Mapping the Trajectory and Succession of SARS-CoV-2 Lineages in 23 Cities of Maharashtra State (India) during June 2022 to May 2023","volume":"11","author":"Matra","year":"2025","journal-title":"Heliyon"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Bartel, A., Grau, J.H., Bitzegeio, J., Werber, D., Linzner, N., Schumacher, V., Garske, S., Liere, K., Hackenbeck, T., and Rupp, S.I. (2024). Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany. Viruses, 16.","DOI":"10.3390\/v16010102"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e464","DOI":"10.1016\/S1473-3099(23)00620-5","article-title":"Tracing the New SARS-CoV-2 Variant BA.2.86 in the Community through Wastewater Surveillance in Bangkok, Thailand","volume":"23","author":"Wannigama","year":"2023","journal-title":"Lancet Infect. Dis."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e29462","DOI":"10.1016\/j.heliyon.2024.e29462","article-title":"Temporal Assessment of SARS-CoV-2 Detection in Wastewater and Its Epidemiological Implications in COVID-19 Case Dynamics","volume":"10","author":"Li","year":"2024","journal-title":"Heliyon"}],"container-title":["Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-1729\/15\/6\/850\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:39:44Z","timestamp":1760031584000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-1729\/15\/6\/850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,24]]},"references-count":64,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["life15060850"],"URL":"https:\/\/doi.org\/10.3390\/life15060850","relation":{},"ISSN":["2075-1729"],"issn-type":[{"value":"2075-1729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,24]]}}}