{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T21:39:10Z","timestamp":1792705150028,"version":"4.5.0"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T00:00:00Z","timestamp":1757635200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005915","name":"Tata Trusts","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005915","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosglobalpublichealth.org"],"crossmark-restriction":false},"short-container-title":["PLOS Glob Public Health"],"abstract":"<jats:p>Recent global pandemics have been caused by respiratory viruses in humans and animals with zoonotic spillover potential. Respiratory viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus (RSV), influenza A virus (IAV), and influenza B virus (IBV), share overlapping ecology and similar symptoms. However, respiratory disease surveillance is often passive, relying on clinical specimen testing. Wastewater surveillance has been used for early detection of SARS-CoV-2 variants and can differentiate between respiratory virus infections and SARS-CoV-2 peaks at the community level. In this retrospective longitudinal study covering four SARS-CoV-2 Omicron waves, we conducted monthly sampling for 28 months (812 samples) between August 2021 and December 2023 at 28 sewershed sites in Bengaluru (~11 million inhabitants), India. Using RT-qPCR kits, we quantified SARS-CoV-2 RNA concentrations, IAV, IBV, and RSV to understand community viral infections. We found 86% of samples positive for SARS-CoV-2, while positivity rates for influenza virus and RSV were lower (37% for IAV, 16% for IBV, and 15% for RSV) and this pattern was consistent across sites. We observed a seasonal increase in influenza viruses during the monsoon, peaking in October, with mean IAV viral loads of 755 copies\/person\/day in 2021, 2000 copies\/person\/day in 2022, and 1749 copies\/person\/day in 2023. IAV was present in January and February but absent the rest of 2022. However, IAV viral load was detected throughout 2023 (except in June). IBV showed a similar trend, peaking in October, with mean viral loads of 616.56 copies\/person\/day in 2021, 323.37 copies\/person\/day in November 2022, and 373.37 copies\/person\/day in September 2023. RSV displayed a shorter transmission window, peaking at around 2000 copies\/person\/day in October. Using genomic data, we provide evidence of changes in the relative abundance of influenza subtypes and SARS-CoV-2 variants, identifying all eight segments of influenza virus genomes and emerging SARS-CoV-2 variants in wastewater samples. Wastewater surveillance provides data on the diversity and relative abundance of respiratory viruses in urban Bengaluru that would not be reported otherwise. Under the One Health framework, wastewater surveillance can offer early warning signs and enhance traceability of infectious diseases in wildlife and humans.<\/jats:p>","DOI":"10.1371\/journal.pgph.0004640","type":"journal-article","created":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T17:36:05Z","timestamp":1757698565000},"page":"e0004640","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgph.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Respiratory virus infection dynamics and genomic surveillance to detect seasonal influenza subtypes in wastewater: A longitudinal study in Bengaluru, India"],"prefix":"10.1371","volume":"5","author":[{"given":"Namrta","family":"Daroch","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subash K.","family":"Kannan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vishwanath","family":"Srikantaiah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rakesh","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6762-7014","authenticated-orcid":true,"given":"Farah","family":"Ishtiaq","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,9,12]]},"reference":[{"key":"pgph.0004640.ref001","volume-title":"Management of childhood illness in developing countries-rationale for an integrated strategy","author":"World Health Organization (WHO)","year":"1998"},{"issue":"6","key":"pgph.0004640.ref002","article-title":"National, regional, and state-level all-cause and cause-specific under-5 mortality in India in 2000-15: a systematic analysis with implications for the Sustainable Development Goals","volume":"7","author":"L Liu","year":"2019","journal-title":"Lancet Glob Health"},{"key":"pgph.0004640.ref003","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1111\/irv.12824","article-title":"Influenza and COVID-19: what does coexistence mean?","volume":"15","author":"T Chotpitayasunondh","year":"2021","journal-title":"Influenza Other Respir Viruses"},{"issue":"10223","key":"pgph.0004640.ref004","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S0140-6736(20)30183-5","article-title":"Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China","volume":"395","author":"C Huang","year":"2020","journal-title":"Lancet"},{"issue":"5","key":"pgph.0004640.ref005","first-page":"100306","article-title":"Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges","volume":"3","author":"J Yang","year":"2022","journal-title":"Innovation (Camb)"},{"issue":"2","key":"pgph.0004640.ref006","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1111\/j.1750-2659.2009.00077.x","article-title":"Seasonal and pandemic influenza surveillance considerations for constructing multicomponent systems","volume":"3","author":"L Brammer","year":"2009","journal-title":"Influenza Other Respir Viruses"},{"key":"pgph.0004640.ref007","doi-asserted-by":"crossref","first-page":"980","DOI":"10.3390\/v15040980","article-title":"Zoonotic animal influenza virus and potential mixing vessel hosts","volume":"15","author":"EM Abdelwhab","year":"2023","journal-title":"Viruses"},{"key":"pgph.0004640.ref008","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41572-018-0002-y","article-title":"Influenza","volume":"4","author":"F Krammer","year":"2018","journal-title":"Nat Rev Dis Primers"},{"issue":"1775","key":"pgph.0004640.ref009","doi-asserted-by":"crossref","first-page":"20180257","DOI":"10.1098\/rstb.2018.0257","article-title":"A brief history of bird flu","volume":"374","author":"SJ Lycett","year":"2019","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"5468","key":"pgph.0004640.ref010","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1126\/science.288.5468.1051","article-title":"Influenza B virus in seals","volume":"288","author":"AD Osterhaus","year":"2000","journal-title":"Science"},{"key":"pgph.0004640.ref011","unstructured":"Centers for Disease Control and Prevention (CDC). Types of influenza viruses [Internet]. 2023. Available from: https:\/\/www.cdc.gov\/flu\/about\/viruses\/types.htm"},{"issue":"1","key":"pgph.0004640.ref012","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/0042-6822(90)90186-U","article-title":"Cocirculation of two distinct evolutionary lineages of influenza type B virus since 1983","volume":"175","author":"PA Rota","year":"1990","journal-title":"Virology"},{"issue":"6","key":"pgph.0004640.ref013","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1007\/s00239-008-9119-z","article-title":"The evolutionary dynamics of human influenza B virus","volume":"66","author":"R Chen","year":"2008","journal-title":"J Mol Evol"},{"key":"pgph.0004640.ref014","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.3201\/eid2408.180063","article-title":"Variation in influenza B virus epidemiology by lineage, China","volume":"24","author":"J Yang","year":"2018","journal-title":"Emerg Infect Dis"},{"issue":"4","key":"pgph.0004640.ref015","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1007\/s13337-018-0487-8","article-title":"Influenza B in a temperate region of northern India 2010-2016: co-circulation of the two lineages with northern hemispherical seasonality","volume":"29","author":"PA Koul","year":"2018","journal-title":"Virusdisease"},{"issue":"6","key":"pgph.0004640.ref016","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00951-13","article-title":"Whole-genome analysis of influenza B viruses of multiple genotypes cocirculating in India","volume":"1","author":"KN Patil","year":"2013","journal-title":"Genome Announc"},{"issue":"11","key":"pgph.0004640.ref017","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgph.0001001","article-title":"Multisite surveillance for influenza and other respiratory viruses in India: 2016\u20132018","volume":"2","author":"M Chadha","year":"2022","journal-title":"PLOS Glob Public Health"},{"key":"pgph.0004640.ref018","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/1743-422X-6-89","article-title":"Respiratory viral infections detected by multiplex PCR among pediatric patients with lower respiratory tract infections seen at an urban hospital in Delhi from 2005 to 2007","volume":"6","author":"P Bharaj","year":"2009","journal-title":"Virol J"},{"issue":"4","key":"pgph.0004640.ref019","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s12098-008-0035-4","article-title":"Respiratory viruses in acute respiratory tract infections in Western India","volume":"75","author":"LR Yeolekar","year":"2008","journal-title":"Indian J Pediatr"},{"key":"pgph.0004640.ref020","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.pt.2023.12.005","article-title":"Wastewater-based surveillance of vector-borne pathogens","volume":"40","author":"F Ishtiaq","year":"2023","journal-title":"Trends Parasitol"},{"key":"pgph.0004640.ref021","doi-asserted-by":"crossref","first-page":"100151","DOI":"10.1016\/j.lansea.2023.100151","article-title":"SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater - a longitudinal study in Bengaluru, India","volume":"11","author":"S Lamba","year":"2023","journal-title":"Lancet Reg Health Southeast Asia"},{"issue":"3","key":"pgph.0004640.ref022","doi-asserted-by":"crossref","first-page":"418","DOI":"10.2166\/wrd.2024.032","article-title":"Metagenomic analysis reveals differential effects of sewage treatment on the microbiome and antibiotic resistome in Bengaluru, India","volume":"14","author":"A Nataraj","year":"2024","journal-title":"Water Reuse"},{"issue":"3","key":"pgph.0004640.ref023","doi-asserted-by":"crossref","first-page":"39","DOI":"10.3390\/environments9030039","article-title":"Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden","volume":"9","author":"F Isaksson","year":"2022","journal-title":"Environments"},{"key":"pgph.0004640.ref024","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/biomet\/33.3.239","article-title":"The treatment of ties in ranking problems","volume":"33","author":"MG Kendall","year":"1945","journal-title":"Biometrika"},{"issue":"18","key":"pgph.0004640.ref025","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1056\/NEJMoa1804498","article-title":"Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018","volume":"379","author":"KJ Siddle","year":"2018","journal-title":"N Engl J Med"},{"issue":"15","key":"pgph.0004640.ref026","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":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"12","key":"pgph.0004640.ref027","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1038\/s41596-022-00738-y","article-title":"Metagenome analysis using the Kraken software suite","volume":"17","author":"J Lu","year":"2022","journal-title":"Nat Protoc"},{"issue":"3","key":"pgph.0004640.ref028","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"issue":"16","key":"pgph.0004640.ref029","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pgph.0004640.ref030","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1186\/1471-2164-12-382","article-title":"Addressing challenges in the production and analysis of illumina sequencing data","volume":"12","author":"M Kircher","year":"2011","journal-title":"BMC Genomics"},{"issue":"1","key":"pgph.0004640.ref031","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr771","article-title":"Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform","volume":"40","author":"M Kircher","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pgph.0004640.ref032","doi-asserted-by":"crossref","first-page":"113916","DOI":"10.1016\/j.jviromet.2020.113916","article-title":"Evaluation of a commercial exogenous internal process control for diagnostic RNA virus metagenomics from different animal clinical samples","volume":"283","author":"S Van Borm","year":"2020","journal-title":"J Virol Methods"},{"key":"pgph.0004640.ref033","author":"RStudio Team","year":"2023"},{"key":"pgph.0004640.ref034","article-title":"Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM [poster]","author":"H Li","year":"2014","journal-title":"figshare"},{"issue":"1","key":"pgph.0004640.ref035","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"ND Grubaugh","year":"2019","journal-title":"Genome Biol"},{"issue":"7925","key":"pgph.0004640.ref036","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":"S Karthikeyan","year":"2022","journal-title":"Nature"},{"key":"pgph.0004640.ref037","doi-asserted-by":"crossref","unstructured":"Tsueng G, Mullen JL, Alkuzweny M, et al. Outbreak Info Research Library: A Standardized, Searchable Platform To Discover and Explore COVID-19 Resources. 2021.","DOI":"10.1101\/2022.01.20.477133"},{"issue":"12","key":"pgph.0004640.ref038","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgph.0001377","article-title":"Cost of wastewater-based environmental surveillance for SARS-CoV-2: Evidence from pilot sites in Blantyre, Malawi and Kathmandu, Nepal","volume":"2","author":"LG Ngwira","year":"2022","journal-title":"PLOS Glob Public Health"},{"issue":"6","key":"pgph.0004640.ref039","doi-asserted-by":"crossref","DOI":"10.1016\/S2666-5247(23)00010-1","article-title":"Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (December, 2019-December, 2021)","volume":"4","author":"ET Rogawski McQuade","year":"2023","journal-title":"Lancet Microbe"},{"key":"pgph.0004640.ref040","doi-asserted-by":"crossref","first-page":"100299","DOI":"10.1016\/j.lansea.2023.100299","article-title":"Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater - a study in District East, Karachi, Pakistan","volume":"20","author":"N Ansari","year":"2023","journal-title":"Lancet Reg Health Southeast Asia"},{"issue":"5","key":"pgph.0004640.ref041","doi-asserted-by":"crossref","first-page":"2919","DOI":"10.1128\/AEM.69.5.2919-2927.2003","article-title":"Environmental surveillance system to track wild poliovirus transmission","volume":"69","author":"JM Deshpande","year":"2003","journal-title":"Appl Environ Microbiol"},{"key":"pgph.0004640.ref042","doi-asserted-by":"crossref","first-page":"151038","DOI":"10.1016\/j.scitotenv.2021.151038","article-title":"High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India","volume":"807","author":"T Dharmadhikari","year":"2022","journal-title":"Sci Total Environ"},{"key":"pgph.0004640.ref043","doi-asserted-by":"crossref","first-page":"119757","DOI":"10.1016\/j.envpol.2022.119757","article-title":"Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India)","volume":"310","author":"M Joshi","year":"2022","journal-title":"Environ Pollut"},{"key":"pgph.0004640.ref044","author":"National Academies of Sciences, Engineering, and Medicine","year":"2023","journal-title":"Wastewater-based Disease Surveillance for Public Health Action. Washington, DC: The National Academies Press"},{"key":"pgph.0004640.ref045","first-page":"104","article-title":"Guidelines for drinking-water quality","year":"2011","edition":"4"},{"issue":"3","key":"pgph.0004640.ref046","doi-asserted-by":"crossref","first-page":"434","DOI":"10.2166\/wh.2011.019","article-title":"Surveillance of influenza A and the pandemic influenza A (H1N1) 2009 in sewage and surface water in the Netherlands","volume":"9","author":"L Heijnen","year":"2011","journal-title":"J Water Health"},{"key":"pgph.0004640.ref047","article-title":"India must scale up wastewater analysis for health surveillance","author":"F Ishtiaq","year":"2022","journal-title":"Nature India"},{"issue":"4","key":"pgph.0004640.ref048","doi-asserted-by":"crossref","DOI":"10.1111\/1758-2229.13317","article-title":"Surveillance of influenza A and B viruses from community and hospital wastewater treatment plants","volume":"16","author":"S Panneerselvam","year":"2024","journal-title":"Environ Microbiol Rep"},{"issue":"4","key":"pgph.0004640.ref049","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1128\/JCM.03060-15","article-title":"Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel","volume":"54","author":"EH Graf","year":"2016","journal-title":"J Clin Microbiol"},{"issue":"10","key":"pgph.0004640.ref050","article-title":"Redefining the influenza equator","volume":"10","author":"PA Koul","year":"2022","journal-title":"Lancet Glob Health"},{"key":"pgph.0004640.ref051","doi-asserted-by":"crossref","first-page":"100619","DOI":"10.1016\/j.lansea.2025.100619","article-title":"Identifying bellwether sewershed sites for sustainable disease surveillance in low-resource settings","volume":"39","author":"RF Daniel","year":"2025","journal-title":"Lancet Reg Health Southeast Asia"},{"key":"pgph.0004640.ref052","doi-asserted-by":"crossref","first-page":"138875","DOI":"10.1016\/j.scitotenv.2020.138875","article-title":"Computational analysis of SARS-CoV-2\/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and challenges","volume":"730","author":"OE Hart","year":"2020","journal-title":"Sci Total Environ"},{"key":"pgph.0004640.ref053","volume-title":"Developing wastewater sampling plans to monitor public health","author":"K Ensor","year":"2022"},{"key":"pgph.0004640.ref054","doi-asserted-by":"crossref","first-page":"1218292","DOI":"10.3389\/fpubh.2023.1218292","article-title":"Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis","volume":"11","author":"V Potdar","year":"2023","journal-title":"Front Public Health"},{"issue":"3","key":"pgph.0004640.ref055","first-page":"195","article-title":"The effects of the COVID-19 pandemic on community respiratory virus activity","volume":"21","author":"EJ Chow","year":"2023","journal-title":"Nat Rev Microbiol"},{"issue":"6722","key":"pgph.0004640.ref056","doi-asserted-by":"crossref","DOI":"10.1126\/science.adq3003","article-title":"COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses","volume":"386","author":"Z Chen","year":"2024","journal-title":"Science"},{"issue":"1","key":"pgph.0004640.ref057","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.1038\/s41467-022-30485-3","article-title":"Off-season RSV epidemics in Australia after easing of COVID-19 restrictions","volume":"13","author":"J-S Eden","year":"2022","journal-title":"Nat Commun"},{"issue":"4","key":"pgph.0004640.ref058","doi-asserted-by":"crossref","first-page":"401","DOI":"10.4103\/lungindia.lungindia_320_21","article-title":"Negligible circulation of influenza in COVID times in Northern India","volume":"38","author":"H Mir","year":"2021","journal-title":"Lung India"},{"issue":"6","key":"pgph.0004640.ref059","doi-asserted-by":"crossref","first-page":"110","DOI":"10.3390\/tropicalmed7060110","article-title":"Trends in Influenza Infections in Three States of India from 2015-2021: Has There Been a Change during COVID-19 Pandemic?","volume":"7","author":"A Jayaram","year":"2022","journal-title":"Trop Med Infect Dis"}],"container-title":["PLOS Global Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgph.0004640","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T17:36:13Z","timestamp":1757698573000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgph.0004640"}},"subtitle":[],"editor":[{"given":"Mohan","family":"Amarasiri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,9,12]]},"references-count":59,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgph.0004640","relation":{},"ISSN":["2767-3375"],"issn-type":[{"value":"2767-3375","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,12]]}}}