{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T12:10:39Z","timestamp":1753877439604,"version":"3.41.2"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T00:00:00Z","timestamp":1746662400000},"content-version":"vor","delay-in-days":127,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"US National Institute of Allergy and Infectious Diseases","doi-asserted-by":"crossref","award":["75N93021C00016"],"award-info":[{"award-number":["75N93021C00016"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Institutes of Health, Department of Health and Human Services"},{"name":"Singapore Ministry of Health\u2019s National Medical Research Council","award":["OF-LCG\/MOH-000505-05"],"award-info":[{"award-number":["OF-LCG\/MOH-000505-05"]}]},{"name":"Singapore Duke-NUS Signature Research Programme"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The 2009 H1N1 pandemic (pdm09) lineage is a major component of the H1 influenza A virus (IAV) that causes seasonal outbreaks annually. Since its introduction in the 2009\u201310 season, this lineage has evolved into distinct, successive clades in humans. Predicting the fitness of influenza clades is essential to forecasting future prevalence, providing a critical opportunity to develop a response to mitigate infection. The relative fitness of pdm09 lineages was retrospectively inferred via relative reproduction rate (RRe) through RelRe, a programme that implements a renewal equation to estimate the relative difference in reproduction number between cocirculating clades. For this analysis, pdm09 lineage sequences from the USA, collected from 2017 to 2023 in both human and swine hosts, were downloaded from public databases. Clade designations were assigned using Nextclade. Human case count data were divided by each influenza season, and the RRe was estimated at 3-month intervals. The RRe was then used to forecast clade frequency 90\u00a0days into the future, and the predictions were compared to the historical data. The highest predicted frequency at 90\u00a0days corresponded to the most frequently detected lineage in 9 out of 13 predictions (69%). The pdm09 lineage plays an important role at the human\u2013swine influenza interface. Bayesian inference using both human and swine data indicated unequal transmission rates of the pdm09 lineage, with 53\u201379 noted transmissions from human to swine and 0\u20132 in reverse using the available genetic data. Metadata analysis revealed that new clades of pdm09 in humans were typically detected in swine as early as ~8\u201320\u00a0months after clade emergence in humans. Understanding RRe and the fitness of contemporary IAV strains enables the identification of high-risk reverse-zoonotic strains and provides critical time for responding to emergent human clades.<\/jats:p>","DOI":"10.1093\/ve\/veaf032","type":"journal-article","created":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T00:03:21Z","timestamp":1746662601000},"source":"Crossref","is-referenced-by-count":0,"title":["Forecasting influenza A pandemic lineage dominance in the United States using relative reproduction rates"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5505-6931","authenticated-orcid":false,"given":"Michael A","family":"Zeller","sequence":"first","affiliation":[{"name":"Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University , 1575 Vet Med, 1850 Christensen Dr, Ames, IA 50011-1134 ,","place":["United States"]},{"name":"Programme in Emerging Infectious Diseases, Duke-NUS Medical School , 8 College Road, Singapore 169857 ,","place":["Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Programme in Emerging Infectious Diseases, Duke-NUS Medical School , 8 College Road, Singapore 169857 ,","place":["Singapore"]},{"name":"Shanghai Institute of Infectious Disease and Biosecurity, Fudan University , 130 Dongan Road, Xuhui District, Shanghai 200032 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4349-9211","authenticated-orcid":false,"given":"Yvonne C F","family":"Su","sequence":"additional","affiliation":[{"name":"Programme in Emerging Infectious Diseases, Duke-NUS Medical School , 8 College Road, Singapore 169857 ,","place":["Singapore"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4986-1795","authenticated-orcid":false,"given":"Kimihitio","family":"Ito","sequence":"additional","affiliation":[{"name":"International Institute for Zoonosis Control, Hokkaido University , Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020 ,","place":["Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,5,8]]},"reference":[{"key":"2025071112132581200_ref1","doi-asserted-by":"publisher","first-page":"4193","DOI":"10.21105\/joss.04193","article-title":"smot: a python package and CLI tool for contextual phylogenetic subsampling","volume":"7","author":"Arendsee","year":"2022","journal-title":"J Open Source Softw"},{"key":"2025071112132581200_ref2","doi-asserted-by":"publisher","first-page":"e1003537","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for Bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2025071112132581200_ref3","doi-asserted-by":"publisher","first-page":"e1008628","DOI":"10.1371\/journal.ppat.1008628","article-title":"Timelines of infection and transmission dynamics of H1N1pdm09 in swine","volume":"16","author":"Canini","year":"2020","journal-title":"PLoS Pathog"},{"key":"2025071112132581200_ref4","article-title":"2022\u20132023 Influenza Season Week 27 ending July 8, 2023","author":"CDC","year":"2023","journal-title":"FluView"},{"key":"2025071112132581200_ref5","article-title":"FluView Summary ending on July 6, 2024","author":"CDC","year":"2024","journal-title":"FluView"},{"key":"2025071112132581200_ref6","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data","volume":"161","author":"Drummond","year":"2002","journal-title":"Genetics"},{"key":"2025071112132581200_ref7","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"Drummond","year":"2006","journal-title":"PLoS Biol"},{"key":"2025071112132581200_ref8","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1006\/tpbi.1994.1023","article-title":"Simulating probability distributions in the coalescent","volume":"46","author":"Griffiths","year":"1994","journal-title":"Theor Popul Biol"},{"key":"2025071112132581200_ref9","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"2025071112132581200_ref10","doi-asserted-by":"publisher","first-page":"19267","DOI":"10.2807\/ese.14.27.19267-en","article-title":"Epidemiology and control of influenza A(H1N1)v in the Netherlands: the first 115 cases","volume":"14","author":"Hahn\u00e9","year":"2009","journal-title":"Euro Surveill"},{"key":"2025071112132581200_ref11","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the human-ape splitting by a molecular clock of mitochondrial DNA","volume":"22","author":"Hasegawa","year":"1985","journal-title":"J Mol Evol"},{"key":"2025071112132581200_ref12","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2025071112132581200_ref13","doi-asserted-by":"publisher","first-page":"e1000520","DOI":"10.1371\/journal.pcbi.1000520","article-title":"Bayesian phylogeography finds its roots","volume":"5","author":"Lemey","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2025071112132581200_ref14","doi-asserted-by":"publisher","first-page":"2628","DOI":"10.1056\/NEJMoa0906089","article-title":"Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school","volume":"361","author":"Lessler","year":"2009","journal-title":"N Engl J Med"},{"key":"2025071112132581200_ref15","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.2147\/IJGM.S343940","article-title":"Decreased incidence of influenza during the COVID-19 pandemic","volume":"15","author":"Lu","year":"2022","journal-title":"Int J Gen Med"},{"key":"2025071112132581200_ref16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011476","article-title":"Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential","volume":"19","author":"Markin","year":"2023","journal-title":"PLoS Pathog"},{"key":"2025071112132581200_ref17","doi-asserted-by":"publisher","first-page":"e16777","DOI":"10.7554\/eLife.16777","article-title":"Origins of the 2009 H1N1 influenza pandemic in swine in Mexico","volume":"5","author":"Mena","year":"2016","journal-title":"Elife"},{"key":"2025071112132581200_ref18","doi-asserted-by":"publisher","first-page":"3681","DOI":"10.1111\/ajt.16381","article-title":"Decreased influenza activity during the COVID-19 pandemic\u2014United States, Australia, Chile, and South Africa, 2020","volume":"20","author":"Olsen","year":"2020","journal-title":"Am J Transplant"},{"key":"2025071112132581200_ref19","doi-asserted-by":"publisher","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025071112132581200_ref20","doi-asserted-by":"publisher","first-page":"2556","DOI":"10.3390\/v14112556","article-title":"Predicting the trajectory of replacements of SARS-CoV-2 variants using relative reproduction numbers","volume":"14","author":"Piantham","year":"2022","journal-title":"Viruses"},{"key":"2025071112132581200_ref21","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 \u2013 approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"article-title":"Tracer v1.6","year":"2007","author":"Rambaut","key":"2025071112132581200_ref22"},{"key":"2025071112132581200_ref23","doi-asserted-by":"publisher","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol"},{"key":"2025071112132581200_ref24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2334-11-92","article-title":"Onset of a pandemic: characterizing the initial phase of the swine flu (H1N1) epidemic in Israel","volume":"11","author":"Roll","year":"2011","journal-title":"BMC Infect Dis"},{"key":"2025071112132581200_ref25","doi-asserted-by":"publisher","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: global initiative on sharing all influenza data \u2013 from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Euro Surveill"},{"key":"2025071112132581200_ref26","doi-asserted-by":"publisher","first-page":"11709","DOI":"10.1073\/pnas.0904991106","article-title":"Dating the emergence of pandemic influenza viruses","volume":"106","author":"Smith","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"2025071112132581200_ref27","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1073\/pnas.1207965110","article-title":"Birth\u2013death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)","volume":"110","author":"Stadler","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"2025071112132581200_ref28","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/s00430-021-00720-7","article-title":"Influenza and RSV incidence during COVID-19 pandemic\u2014an observational study from in-hospital point-of-care testing","volume":"210","author":"Stamm","year":"2021","journal-title":"Med Microbiol Immunol"},{"key":"2025071112132581200_ref29","doi-asserted-by":"publisher","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol"},{"key":"2025071112132581200_ref30","doi-asserted-by":"publisher","first-page":"e1008259","DOI":"10.1371\/journal.ppat.1008259","article-title":"When pigs fly: pandemic influenza enters the 21st century","volume":"16","author":"Trov\u00e3o","year":"2020","journal-title":"PLoS Pathog"},{"key":"2025071112132581200_ref31","doi-asserted-by":"publisher","first-page":"19307","DOI":"10.1073\/pnas.1311790110","article-title":"Searching for efficient Markov chain Monte Carlo proposal kernels","volume":"110","author":"Yang","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"2025071112132581200_ref32","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1186\/s12859-018-2408-7","article-title":"ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of influenza A virus in swine","volume":"19","author":"Zeller","year":"2018","journal-title":"BMC Bioinf"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veaf032\/63104871\/veaf032.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf032\/63104871\/veaf032.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf032\/63104871\/veaf032.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T16:13:36Z","timestamp":1752250416000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veaf032\/8126749"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,9]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veaf032","relation":{},"ISSN":["2057-1577"],"issn-type":[{"type":"electronic","value":"2057-1577"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"veaf032"}}