{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T06:01:20Z","timestamp":1781157680609,"version":"3.54.1"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Wastewater based epidemiology (WBE) has become a crucial epidemiological tool to supplement clinical surveillance to monitor the spread of SARS-CoV-2 and variant dynamics on the population level. As viral shedding occurs early and independently of healthcare seeking behavior, WBE provides advanced signals of infection trends and variant emergence.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and methods<\/jats:title>\n                    <jats:p>This longitudinal, multicenter, quantitative and genomic surveillance study of SARS CoV2 was done using wastewater samples from Ahmedabad, Gandhinagar and Vadodara between January 2023 to July 2024. Digital PCR (dPCR) was used to determine the amount of viral load in 2,130 wastewater samples followed by whole genome sequencing (WGS) of high-titer samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The concentration of wastewater viral genome has strong statistical correlation with reported cases of clinical COVID-19 (Pearson correlation coefficient r\u202f=\u202f0.898;\n                      <jats:italic>p<\/jats:italic>\n                      \u202f&amp;lt;\u202f0.001), which serves as a robust predictor. Wastewater showed strongest predictive value at 1-week lag in Gandhinagar and Vadodara, while Ahmedabad showed statistical significance for 2\u202fweeks lag. Notably, abundance-based dominance analysis showed that wastewater monitoring also predicted alterations in dominant variants. In Ahmedabad, JN.1 was detected one week earlier than in clinical samples, while KP.x had a lead time of three weeks in Ahmedabad. Temporal mapping at the mutation level also supported the initial occurrence and maintenance of mutations that define lineages in wastewater even before clinical identification, suggesting that there was a gradual formation of new variants on the population level.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>This study demonstrates that comprehensive quantitative and genomic wastewater monitoring aids to detect presence of SARS-CoV-2 in community early with proactive understanding of the changes in the most common variants within the community. These results highlight the importance of wastewater monitoring as a sensitive, scalable, and proactive tool of population health in terms of early warning and preparedness of pandemics.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1791178","type":"journal-article","created":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T05:47:41Z","timestamp":1781156861000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Wastewater genomic surveillance identifies the emergence of the SARS-CoV-2 JN.1 lineage in urban settings of Gujarat"],"prefix":"10.3389","volume":"17","author":[{"given":"Jill","family":"Gada","sequence":"first","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pranav C.","family":"Patel","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harshal","family":"Purohit","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaitanya","family":"Joshi","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madhvi","family":"Joshi","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priyank","family":"Chavda","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Snehal","family":"Bagatharia","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amrutlal","family":"Patel","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhumika","family":"Prajapati","sequence":"additional","affiliation":[{"name":"Gujarat Biotechnology Research Centre","place":["Gandhinagar, Gujarat, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,11]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"138764","DOI":"10.1016\/j.scitotenv.2020.138764","article-title":"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","volume":"728","author":"Ahmed","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1871","DOI":"10.1021\/acsestwater.1c00387","article-title":"Comparison of RT-qPCR and RT-dPCR platforms for the trace detection of SARS-CoV-2 RNA in wastewater","volume":"2","author":"Ahmed","year":"2022","journal-title":"ACS EST Water"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"152597","DOI":"10.1016\/j.scitotenv.2021.152597","article-title":"Association of SARS-CoV-2 presence in sewage with public adherence to precautionary measures and reported COVID-19 prevalence in Tehran","volume":"812","author":"Amereh","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"153290","DOI":"10.1016\/j.scitotenv.2022.153290","article-title":"Factors influencing SARS-CoV-2 RNA concentrations in wastewater up to the sampling stage: a systematic review","volume":"820","author":"Bertels","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"3643","DOI":"10.1038\/s41467-021-23733-5","article-title":"Insights into household transmission of SARS-CoV-2 from a population-based serological survey","volume":"12","author":"Bi","year":"2021","journal-title":"Nat. Commun."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1021\/acs.estlett.0c00730","article-title":"Persistence of SARS-CoV-2 in water and wastewater","volume":"7","author":"Bivins","year":"2020","journal-title":"Environ. Sci. Technol. Lett."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"106998","DOI":"10.1016\/j.envint.2021.106998","article-title":"A nationwide indicator to smooth and normalize heterogeneous SARS-CoV-2 RNA data in wastewater","volume":"158","author":"Cluzel","year":"2022","journal-title":"Environ. 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Total Environ."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"570","DOI":"10.25259\/ijmr_299_24","article-title":"Wastewater-based genomic surveillance of SARS-CoV-2 in vulnerable communities in Mumbai","volume":"160","author":"Kadam","year":"2024","journal-title":"Indian J. Med. Res."},{"key":"ref15","doi-asserted-by":"publisher","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":"ref16","article-title":"The potential of wastewater testing for public health and safety","author":"Keshaviah","year":"2017","journal-title":"Wash. Math. 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Sci.Total Environ","author":"Kumar","year":"2023"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"139652","DOI":"10.1016\/j.scitotenv.2020.139652","article-title":"First detection of SARS-CoV-2 in untreated wastewaters in Italy","volume":"736","author":"La Rosa","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1016\/j.lansea.2023.100151","article-title":"SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater\u2013a longitudinal study in Bengaluru, India","volume":"11","author":"Lamba","year":"2023","journal-title":"Lancet Reg. Health"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"BSR20181170","DOI":"10.1042\/BSR20181170","article-title":"Application of droplet digital PCR to detect the pathogens of infectious diseases","volume":"38","author":"Li","year":"2018","journal-title":"Biosci. Rep."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1002\/jmv.25786","article-title":"Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19","volume":"92","author":"Li","year":"2020","journal-title":"J. Med. Virol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1016\/S2468-1253(20)30087-X","article-title":"SARS-CoV-2 in wastewater: potential health risk, but also data source","volume":"5","author":"Lodder","year":"2020","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref9002","doi-asserted-by":"publisher","first-page":"141245","DOI":"10.1016\/j.scitotenv.2020.141245","article-title":"Primary concentration \u2013 The critical step in implementing the wastewater based epidemiology for the COVID-19 pandemic: A mini-review","volume":"747","author":"Lu","year":"2020","journal-title":"Sci. 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Total Environ."},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2022.e10547","article-title":"Predicting the dispersal of SARS-CoV-2 RNA from the wastewater treatment plant to the coast","volume":"8","author":"Robins","year":"2022","journal-title":"Heliyon"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"e0313927","DOI":"10.1371\/journal.pone.0313927","article-title":"SARS-CoV-2 surveillance in US wastewater: leading indicators and data variability analysis in 2023\u20132024","volume":"19","author":"Schenk","year":"2024","journal-title":"PLoS One"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1763","DOI":"10.1213\/ANE.0000000000002864","article-title":"Correlation coefficients: appropriate use and interpretation","volume":"126","author":"Schober","year":"2018","journal-title":"Anesth. Analg."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"100115","DOI":"10.1016\/j.cscee.2021.100115","article-title":"Reflections of COVID-19 cases in the wastewater loading of SARS-CoV-2 RNA: a case of three major cities of Gujarat, India","volume":"4","author":"Srivastava","year":"2021","journal-title":"Case Stud. Chem. Environ. Eng."},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"118220","DOI":"10.1016\/j.watres.2022.118220","article-title":"Detection and quantification of SARS-CoV-2 RNA in wastewater influent in relation to reported COVID-19 incidence in Finland","volume":"215","author":"Tiwari","year":"2022","journal-title":"Water Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"145790","DOI":"10.1016\/j.scitotenv.2021.145790","article-title":"Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds","volume":"775","author":"Weidhaas","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"2279","DOI":"10.3201\/eid3011.240771","article-title":"Wastewater surveillance for poliovirus in selected jurisdictions, United States, 2022\u20132023","volume":"30","author":"Whitehouse","year":"2024","journal-title":"Emerg. Infect. Dis."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1093\/cid\/ciaa199","article-title":"Clinical characteristics of imported cases of coronavirus disease 2019 (COVID-19) in Jiangsu Province: a multicenter descriptive study","volume":"71","author":"Wu","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"150121","DOI":"10.1016\/j.scitotenv.2021.150121","article-title":"SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases","volume":"805","author":"Wu","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1831","DOI":"10.1053\/j.gastro.2020.02.055","article-title":"Evidence for gastrointestinal infection of SARS-CoV-2","volume":"158","author":"Xiao","year":"2020","journal-title":"Gastroenterology"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"3547","DOI":"10.1038\/s41467-022-31276-6","article-title":"Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses","volume":"13","author":"Xu","year":"2022","journal-title":"Nat. Commun."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1186\/s12889-025-22306-1","article-title":"The use of wastewater surveillance to estimate SARS-CoV-2 fecal viral shedding pattern and identify time periods with intensified transmission","volume":"25","author":"Yang","year":"2025","journal-title":"BMC Public Health"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e00645","DOI":"10.1128\/msphere.00645-24","article-title":"Detection of Hepatovirus a (HAV) in wastewater indicates widespread national distribution and association with socioeconomic indicators of vulnerability","volume":"9","author":"Zulli","year":"2024","journal-title":"mSphere"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1791178\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T05:47:42Z","timestamp":1781156862000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1791178\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,11]]},"references-count":46,"alternative-id":["10.3389\/fmicb.2026.1791178"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1791178","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,11]]},"article-number":"1791178"}}