{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:53:51Z","timestamp":1789692831052,"version":"4.0.1"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,5,6]],"date-time":"2023-05-06T00:00:00Z","timestamp":1683331200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,5,6]],"date-time":"2023-05-06T00:00:00Z","timestamp":1683331200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Virol J"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Insufficient tracking of virus introduction, spread, and new lineage emergence for the human monkeypox (mpox) virus 1 (hMPXV1) outbreak of 2022 hindered epidemiological studies and public health response. hMPXV1 mutations accumulated unexpectedly faster than predicted. Thus, new variants with altered pathogenicity could emerge and spread without early detection. Whole genome sequencing addresses this gap when implemented but requires widely accessible and standardized methodologies to be effective both regionally and globally. Here we developed a rapid nanopore whole genome sequencing method complete with working protocols, from DNA extraction to phylogenetic analysis tools. Using this method, we sequenced 84 complete hMPXV1 genomes from Illinois, a Midwestern region of the United States, spanning the first few months of the outbreak. The resulting five-fold increase in hMPXV1 genomes from this region established two previously unnamed global lineages, several mutational profiles not seen elsewhere, multiple separate introductions of the virus into the region, and the likely emergence and spread of new lineages from within this region. These results demonstrate that a dearth of genomic sequencing of hMPXV1 slowed our understanding and response to the mpox outbreak. This accessible nanopore sequencing approach makes near real-time mpox tracking and rapid lineage discovery straightforward and creates a blueprint for how to deploy nanopore sequencing for genomic surveillance of diverse viruses and future outbreaks.<\/jats:p>","DOI":"10.1186\/s12985-023-02059-2","type":"journal-article","created":{"date-parts":[[2023,5,6]],"date-time":"2023-05-06T10:01:29Z","timestamp":1683367289000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing"],"prefix":"10.1186","volume":"20","author":[{"given":"Michael S.","family":"Bosmeny","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam A.","family":"White","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian A.","family":"Pater","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Crew","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Geltz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keith T.","family":"Gagnon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,5,6]]},"reference":[{"key":"2059_CR1","unstructured":"WHO (https:\/\/www.who.int\/news\/item\/28-11-2022-who-recommends-new-name-for-monkeypox-disease; 2022)."},{"key":"2059_CR2","doi-asserted-by":"publisher","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","volume":"50","author":"EW Sayers","year":"2022","unstructured":"Sayers EW, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2022;50:D20-d26.","journal-title":"Nucleic Acids Res"},{"key":"2059_CR3","unstructured":"Prevention, C.f.D.C.a. (2022)."},{"key":"2059_CR4","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1038\/s41591-022-01907-y","volume":"28","author":"J Isidro","year":"2022","unstructured":"Isidro J, et al. Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat Med. 2022;28:1569\u201372.","journal-title":"Nat Med"},{"key":"2059_CR5","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1093\/cid\/cit703","volume":"58","author":"AM McCollum","year":"2013","unstructured":"McCollum AM, Damon IK. Human Monkeypox. Clin Infect Dis. 2013;58:260\u20137.","journal-title":"Clin Infect Dis"},{"key":"2059_CR6","doi-asserted-by":"publisher","first-page":"e3001769","DOI":"10.1371\/journal.pbio.3001769","volume":"20","author":"C Happi","year":"2022","unstructured":"Happi C, et al. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. PLoS Biol. 2022;20:e3001769.","journal-title":"PLoS Biol"},{"key":"2059_CR7","doi-asserted-by":"crossref","unstructured":"Tyson, JR et al. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. bioRxiv (2020).","DOI":"10.1101\/2020.09.04.283077"},{"key":"2059_CR8","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.14440\/jbm.2021.360","volume":"8","author":"AA Pater","year":"2021","unstructured":"Pater AA, et al. High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples. J Biol Methods. 2021;8:e155.","journal-title":"J Biol Methods"},{"key":"2059_CR9","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1038\/nprot.2017.066","volume":"12","author":"J Quick","year":"2017","unstructured":"Quick J, et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12:1261\u201376.","journal-title":"Nat Protoc"},{"key":"2059_CR10","doi-asserted-by":"publisher","first-page":"3773","DOI":"10.21105\/joss.03773","volume":"6","author":"I Aksamentov","year":"2021","unstructured":"Aksamentov I, Roemer C, Hodcroft E, Neher R. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6:3773.","journal-title":"J Open Source Softw"},{"key":"2059_CR11","unstructured":"mpxv-lineages\/lineage-designation (https:\/\/github.com\/mpxv-lineages\/lineage-designation; 2022)."},{"key":"2059_CR12","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.3390\/microorganisms8121899","volume":"8","author":"WK Xu","year":"2020","unstructured":"Xu WK, Byun H, Dudley JP. The role of APOBECs in viral replication. Microorganisms. 2020;8:1899.","journal-title":"Microorganisms"},{"key":"2059_CR13","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.1016\/j.tig.2021.07.003","volume":"37","author":"K Cervantes-Gracia","year":"2021","unstructured":"Cervantes-Gracia K, Gramalla-Schmitz A, Weischedel J, Chahwan R. APOBECs orchestrate genomic and epigenomic editing across health and disease. Trends Genet TIG. 2021;37:1028\u201343.","journal-title":"Trends Genet TIG"},{"key":"2059_CR14","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.3390\/v7042126","volume":"7","author":"EL Hatcher","year":"2015","unstructured":"Hatcher EL, Wang C, Lefkowitz EJ. Genome variability and gene content in chordopoxviruses: dependence on microsatellites. Viruses. 2015;7:2126\u201346.","journal-title":"Viruses"},{"key":"2059_CR15","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/nbt.3935","volume":"35","author":"C Quince","year":"2017","unstructured":"Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 2017;35:833\u201344.","journal-title":"Nat Biotechnol"},{"key":"2059_CR16","doi-asserted-by":"publisher","first-page":"e0180321","DOI":"10.1128\/Spectrum.01803-21","volume":"9","author":"JJ Davis","year":"2021","unstructured":"Davis JJ, et al. Analysis of the ARTIC version 3 and version 4 SARS-CoV-2 primers and their impact on the detection of the G142D amino acid substitution in the spike protein. Microbiol Spectr. 2021;9:e0180321.","journal-title":"Microbiol Spectr"}],"container-title":["Virology Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12985-023-02059-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12985-023-02059-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12985-023-02059-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,19]],"date-time":"2024-10-19T18:48:41Z","timestamp":1729363721000},"score":1,"resource":{"primary":{"URL":"https:\/\/virologyj.biomedcentral.com\/articles\/10.1186\/s12985-023-02059-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,6]]},"references-count":16,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["2059"],"URL":"https:\/\/doi.org\/10.1186\/s12985-023-02059-2","relation":{},"ISSN":["1743-422X"],"issn-type":[{"value":"1743-422X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,5,6]]},"assertion":[{"value":"26 April 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 May 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 May 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Patient consent was waived for this study by the Southern Illinois University School of Medicine Institutional Review Board (IRB) since no significant patient-identifiable information was shared or generated in this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Publication consent was not required for this study.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"90"}}