{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T11:02:02Z","timestamp":1790420522981,"version":"4.1.0"},"posted":{"date-parts":[[2026,9,23]]},"group-title":"Epidemiology","reference-count":82,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Population-scale pathogen surveillance is limited worldwide, particularly in resource-constrained settings, where clinical systems only monitor select priority pathogens and reach only those who can access healthcare. Wastewater-based epidemiology addresses many of these gaps, offering cost-effective surveillance that is adaptable across diverse implementation contexts. In Lagos, Nigeria, a high enteric pathogen burden coincides with a complex sanitation landscape. However, circulating pathogen diversity in Lagos is largely uncharacterised outside of outbreak contexts. Here we characterize human-associated pathogen diversity in Lagos with virus-enriched metagenomic and metatranscriptomic sequencing of untreated wastewater sampled from open drainage canals from July-August 2024. We detected a diverse human-associated virome dominated by enteric adenoviruses, astroviruses and caliciviruses. We recovered numerous partial and near-complete genomes from pathogens of public health concern, including noroviruses, enteroviruses and sapoviruses. Although our enrichment targeted viruses, we detected diverse bacterial pathogens, including recurrent detection of\n                  <jats:italic>Vibrio cholerae<\/jats:italic>\n                  , other enteric bacteria, and zoonotic pathogens such as\n                  <jats:italic>Streptococcus suis.<\/jats:italic>\n                  We also detected antimicrobial resistance genes, including aminoglycoside, beta-lactam and fluoroquinolone resistance and clinically important genes such as\n                  <jats:italic>mcr<\/jats:italic>\n                  . Together, these results establish a regional baseline of pathogen diversity and demonstrate the utility of virus-enriched sequencing for integrated wastewater surveillance.\n                <\/jats:p>","DOI":"10.64898\/2026.09.22.26363641","type":"posted-content","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T18:45:12Z","timestamp":1790189112000},"source":"Crossref","is-referenced-by-count":0,"title":["Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8312-1446","authenticated-orcid":false,"given":"Edyth","family":"Parker","sequence":"first","affiliation":[{"name":"Institute of Genomics and Global Health (IGH), Redeemer\u2019s University, Ede, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faith","family":"Oladipo","sequence":"additional","affiliation":[{"name":"Institute of Genomics and Global Health (IGH), Redeemer\u2019s University, Ede, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua I.","family":"Levy","sequence":"additional","affiliation":[{"name":"Department of Translational Medicine, The Scripps Research Institute, La Jolla, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oludayo O.","family":"Ope-Ewe","sequence":"additional","affiliation":[{"name":"Institute of Genomics and Global Health (IGH), Redeemer\u2019s University, Ede, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harouna","family":"Soumare","sequence":"additional","affiliation":[{"name":"Institute of Genomics and Global Health (IGH), Redeemer\u2019s University, Ede, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristian","family":"Andersen","sequence":"additional","affiliation":[{"name":"Department of Translational Medicine, The Scripps Research Institute, La Jolla, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anise N","family":"Happi","sequence":"additional","affiliation":[{"name":"Institute of Genomics and Global Health (IGH), Redeemer\u2019s University, Ede, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3056-6705","authenticated-orcid":false,"given":"Christian T.","family":"Happi","sequence":"additional","affiliation":[{"name":"Institute of Genomics and Global Health (IGH), Redeemer\u2019s University, Ede, Nigeria"},{"name":"Department of Biological Sciences, Faculty of Natural Sciences, Redeemer\u2019s University, Ede, Nigeria"},{"name":"Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092603550984000_2026.09.22.26363641v1.1","doi-asserted-by":"publisher","DOI":"10.2471\/blt.22.288220"},{"key":"2026092603550984000_2026.09.22.26363641v1.2","first-page":"10","article-title":"Tracking virus outbreaks in the twenty-first century","volume":"4","year":"2019","journal-title":"Nat. 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