{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T13:04:35Z","timestamp":1777899875776,"version":"3.51.4"},"reference-count":32,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T00:00:00Z","timestamp":1768953600000},"content-version":"vor","delay-in-days":20,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["101102366"],"award-info":[{"award-number":["101102366"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    The epidemiology of SARS\u2010CoV\u20102 is marked by the continuous emergence of new lineages. Early detection and assessment of their transmissibility can be challenging for surveillance systems that rely solely on case time series data. Genomic surveillance, focusing on identifying and characterizing circulating variants, can provide early insights into their epidemiological impact. Phylogenetic and phylodynamic methods were applied to sequence data collected between October 2023 and January 2024 to study the transmission of the JN.1 variant in Italy. The genomic surveillance encompassed two data flows: flash surveys estimating variant prevalence and continuous sampling to identify emerging variants. We estimated the effective reproduction number (R\n                    <jats:sub>e<\/jats:sub>\n                    ) of JN.1 using a phylodynamic birth\u2010death model. Results were compared with the daily net reproduction number (R\n                    <jats:sub>t<\/jats:sub>\n                    ) of SARS\u2010CoV\u20102 estimated from time series of hospital admissions recorded through epidemiological surveillance. We traced back the appearance of JN.1 in Italy to October 2023, with subvariants emerging and co\u2010circulating shortly thereafter. JN.1 became dominant nationwide by the end of 2023. According to phylodynamic analysis, the R\n                    <jats:sub>e<\/jats:sub>\n                    of JN.1 was 1.73 (95% CI: 1.36\u20132.28) in mid\u2010November, and its transmissibility declined over the following months. This trend aligned with R\n                    <jats:sub>t<\/jats:sub>\n                    estimates from epidemiological surveillance, encompassing all co\u2010circulating lineages. The high transmissibility of JN.1 anticipated the rise in its prevalence in the population and showed a temporal correlation with a transient increase in COVID\u201019 hospitalizations. Integrating genomic and epidemiological surveillance enhances pathogen monitoring and the assessment of new lineages\u2019 transmissibility, providing complementary evidence to patterns observed through standard surveillance.\n                  <\/jats:p>","DOI":"10.1002\/jmv.70775","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T13:23:35Z","timestamp":1769001815000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Genomic and Epidemiological Surveillance to Monitor SARS\u2010CoV\u20102 Variants in Italy: Insights From the JN.1 Case Study (2023\u20132024)"],"prefix":"10.1002","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3709-1199","authenticated-orcid":false,"given":"Mattia","family":"Manica","sequence":"first","affiliation":[{"name":"Center for Health Emergencies, Fondazione Bruno Kessler Trento Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuela","family":"Giombini","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martina","family":"Del Manso","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4071-7159","authenticated-orcid":false,"given":"Carla","family":"Molina Gran\u00e9","sequence":"additional","affiliation":[{"name":"Center for Health Emergencies, Fondazione Bruno Kessler Trento Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9063-3973","authenticated-orcid":false,"given":"Luigina","family":"Ambrosio","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonino","family":"Bella","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angela","family":"di Martino","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniele","family":"Petrone","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Flavia","family":"Riccardo","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piero","family":"Poletti","sequence":"additional","affiliation":[{"name":"Center for Health Emergencies, Fondazione Bruno Kessler Trento Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrizio","family":"Pezzotti","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna Teresa","family":"Palamara","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefano","family":"Merler","sequence":"additional","affiliation":[{"name":"Center for Health Emergencies, Fondazione Bruno Kessler Trento Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Stefanelli","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases Istituto Superiore di Sanit\u00e0 Rome Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2026,1,21]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfimm\/iqac003"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2023.104534"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-023-00878-2"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmgm.2022.108194"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-022-00841-7"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/aje\/kwt133"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pdig.0000052"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-022-00483-8"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veae020"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(23)00744-2"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.adg6605"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2023.104939"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1002\/mco2.675"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(23)00813-7"},{"key":"e_1_2_11_16_1","unstructured":"World Health Organization. COVID\u201019 Epidemiological Update\u201417 March 2025. Epidemic and Pandemic Preparedness and Prevention. March 17 2025.accessed November 11 2025 https:\/\/www.who.int\/publications\/m\/item\/covid-19-epidemiological-update-edition-177."},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2020.25.49.2000790"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.46234\/ccdcw2021.255"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw108"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad359"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1207965110"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-025-10685-0"},{"key":"e_1_2_11_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12916-023-03070-8"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.5582\/ddt.2024.01008"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-53033-7"},{"key":"e_1_2_11_27_1","unstructured":"Italian Ministry of Health. Indicazioni e raccomandazioni per la campagna di vaccinazione autunnale\/invernale 2023\/2024 anti COVID\u201019. Rome; 2023 https:\/\/www.trovanorme.salute.gov.it\/norme\/renderNormsanPdf?anno=2023&codLeg=96278&parte=1%20&serie=null."},{"key":"e_1_2_11_28_1","volume-title":"COVID\u201019 Vaccination Coverage in the EU\/EEA During the 2023\u201324 Season Campaigns","author":"European Centre for Disease Prevention and Control","year":"2024"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2021.24315"},{"key":"e_1_2_11_30_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2104241118"},{"key":"e_1_2_11_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2021.06.049"},{"key":"e_1_2_11_32_1","doi-asserted-by":"publisher","DOI":"10.1111\/irv.13181"},{"key":"e_1_2_11_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiae364"}],"container-title":["Journal of Medical Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jmv.70775","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jmv.70775","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jmv.70775","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T10:16:41Z","timestamp":1777630601000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jmv.70775"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1002\/jmv.70775"],"URL":"https:\/\/doi.org\/10.1002\/jmv.70775","archive":["Portico"],"relation":{},"ISSN":["0146-6615","1096-9071"],"issn-type":[{"value":"0146-6615","type":"print"},{"value":"1096-9071","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"2025-06-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-12-14","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-21","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70775"}}