{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T06:25:29Z","timestamp":1792736729826,"version":"4.5.0"},"reference-count":280,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:00:00Z","timestamp":1759968000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Viral metagenomic next-generation sequencing (vmNGS) has transformed our capacity for the untargeted detection and characterisation of (re)emerging zoonotic viruses, surpassing the limitations of traditional targeted diagnostics. In this review, we critically evaluate the current landscape of vmNGS, highlighting its integration within the One Health paradigm and its application to the surveillance and discovery of (re)emerging viruses at the human\u2013animal\u2013environment interface. We provide a detailed overview of vmNGS workflows including sample selection, nucleic acid extraction, host depletion, virus enrichment, sequencing platforms, and bioinformatic pipelines, all tailored to maximise sensitivity and specificity for diverse sample types. Through selected case studies, including SARS-CoV-2, mpox, Zika virus, and a novel henipavirus, we illustrate the impact of vmNGS in outbreak detection, genomic surveillance, molecular epidemiology, and the development of diagnostics and vaccines. The review further examines the relative strengths and limitations of vmNGS in both passive and active surveillance, addressing barriers such as cost, infrastructure requirements, and the need for interdisciplinary collaboration. By integrating molecular, ecological, and public health perspectives, vmNGS stands as a central tool for early warning, comprehensive monitoring, and informed intervention against (re)emerging viral threats, underscoring its critical role in global pandemic preparedness and zoonotic disease control.<\/jats:p>","DOI":"10.3390\/ijms26199831","type":"journal-article","created":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:50:16Z","timestamp":1760107816000},"page":"9831","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1962-0651","authenticated-orcid":false,"given":"Tristan","family":"Russell","sequence":"first","affiliation":[{"name":"UCD Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, D04 E1W1 Dublin, Ireland"},{"name":"UCD School of Medicine, University College Dublin, D04 C7X2 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisa","family":"Formiconi","sequence":"additional","affiliation":[{"name":"UCD Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, D04 E1W1 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00edche\u00e1l","family":"Casey","sequence":"additional","affiliation":[{"name":"Regional Veterinary Laboratories (RVL) Division, Department of Agriculture, Food and the Marine, Agriculture House, Backweston, T12 XD51 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ma\u00edre","family":"McElroy","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food, and the Marine Laboratories, Backweston, Celbridge, W23 VW2C Kildare, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick W. G.","family":"Mallon","sequence":"additional","affiliation":[{"name":"UCD Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, D04 E1W1 Dublin, Ireland"},{"name":"UCD School of Medicine, University College Dublin, D04 C7X2 Dublin, Ireland"},{"name":"Department of Infectious Diseases, St Vincent\u2019s University Hospital, D04 T6F4 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1862-2644","authenticated-orcid":false,"given":"Virginie W.","family":"Gautier","sequence":"additional","affiliation":[{"name":"UCD Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, D04 E1W1 Dublin, Ireland"},{"name":"UCD School of Medicine, University College Dublin, D04 C7X2 Dublin, Ireland"},{"name":"UCD Conway Institute, University College Dublin, D04 E1W1 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"ref_1","first-page":"2034","article-title":"A Brief Overview on the Threat of Zoonotic Viruses","volume":"6","author":"Shanmugaraj","year":"2024","journal-title":"Microbes Infect. 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