{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T18:20:39Z","timestamp":1791483639127,"version":"4.3.4"},"reference-count":60,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T00:00:00Z","timestamp":1679616000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Virologica Sinica"],"published-print":{"date-parts":[[2023,4]]},"DOI":"10.1016\/j.virs.2023.03.006","type":"journal-article","created":{"date-parts":[[2023,3,25]],"date-time":"2023-03-25T15:16:36Z","timestamp":1679757396000},"page":"327-333","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":17,"title":["Perspective on the application of genome sequencing for monkeypox virus surveillance"],"prefix":"10.1016","volume":"38","author":[{"given":"Yuda","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changcheng","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruhan","family":"A","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongxian","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5963-1136","authenticated-orcid":false,"given":"Wenjie","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.virs.2023.03.006_bib1","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J.\u00a0Open Source Softw."},{"key":"10.1016\/j.virs.2023.03.006_bib2","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.3390\/v12111257","article-title":"Monkeypox virus in Nigeria: infection biology, epidemiology, and evolution","volume":"12","author":"Alakunle","year":"2020","journal-title":"Viruses"},{"key":"10.1016\/j.virs.2023.03.006_bib3","series-title":"A\u00a0Draft of the First Genome Sequence of Monkeypox Virus Associated with the Multi-Country Outbreak in May 2022 from the Canary Islands, spain","author":"Alcoba-Florez","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib4","doi-asserted-by":"crossref","first-page":"e86","DOI":"10.1002\/cphg.86","article-title":"Best practices for illumina library preparation","volume":"102","author":"Bronner","year":"2019","journal-title":"Curr Protoc Hum Genet"},{"key":"10.1016\/j.virs.2023.03.006_bib5","series-title":"Second Draft Genome from spain of the Monkeypox Virus 2022 Outbreak","author":"Buenestado-Serrano","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib6","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.virol.2005.05.030","article-title":"Virulence differences between monkeypox virus isolates from west africa and the Congo basin","volume":"340","author":"Chen","year":"2005","journal-title":"Virology"},{"key":"10.1016\/j.virs.2023.03.006_bib7","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one fastq preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.virs.2023.03.006_bib8","article-title":"Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus","author":"Chen","year":"2023","journal-title":"medRxiv"},{"key":"10.1016\/j.virs.2023.03.006_bib9","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.virs.2023.03.006_bib10","series-title":"First Monkeypox Virus Genome Sequence from brazil","author":"Claro","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib11","series-title":"First French Draft Genome Sequence of Monkeypox Virus","author":"Croville","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib12","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1101\/gr.180501","article-title":"Rapid amplification of plasmid and phage DNA using phi 29 DNA polymerase and multiply-primed rolling circle amplification","volume":"11","author":"Dean","year":"2001","journal-title":"Genome Res."},{"key":"10.1016\/j.virs.2023.03.006_bib13","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/S1473-3099(03)00856-9","article-title":"Human monkeypox: an emerging zoonosis","volume":"4","author":"Di Giulio","year":"2004","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.virs.2023.03.006_bib15","doi-asserted-by":"crossref","first-page":"980","DOI":"10.3201\/eid2505.190076","article-title":"Diagnosis of imported monkeypox, Israel, 2018","volume":"25","author":"Erez","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.virs.2023.03.006_bib16","series-title":"Monkeypox Virus Genome Sequences from Multiple Lesions Indicates Co-infection of a uk Returning Traveller","author":"Filipe","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib17","series-title":"Travel-associated Monkeypox Virus Genomes from Two German Patients and of a Derived Virus Isolate All Closely Related to a Us Sequence","author":"Fuchs","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib18","series-title":"First Monkeypox Virus Sequence from Northern mexico","author":"Gal\u00e1n-Huerta","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib19","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1126\/science.add4153","article-title":"Multiple lineages of monkeypox virus detected in the United States, 2021-2022","volume":"378","author":"Gigante","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.virs.2023.03.006_bib20","series-title":"Minion-produced Illumina-Confirmed Genomes of the Two First Isolated Cases from france","author":"Gorg\u00e9","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib21","series-title":"Urgent Need for a Non-discriminatory and Non-stigmatizing Nomenclature for Monkeypox Virus","author":"Happi","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib22","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1016\/j.bsheal.2022.10.005","article-title":"Development of two multiplex real-time pcr assays for simultaneous detection and differentiation of monkeypox virus iia, iib, and i clades and the b.1 lineage","volume":"4","author":"Huo","year":"2022","journal-title":"Biosaf Health"},{"key":"10.1016\/j.virs.2023.03.006_bib23","series-title":"First Draft Genome Sequence of Monkeypox Virus Associated with the Suspected Multi-Country Outbreak, May 2022 (Confirmed Case in portugal)","author":"Isidro","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib24","series-title":"Multi-country Outbreak of Monkeypox Virus: Genetic Divergence and First Signs of Microevolution","author":"Isidro","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib25","series-title":"First Israeli Whole-Genome Sequence of Monkeypox Virus Associated with the May 2022 Multi Country Outbreak","author":"Israeli","year":"2022"},{"key":"10.1016\/j.virs.2023.03.006_bib26","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1002\/jmv.25348","article-title":"A\u00a0review of the monkeypox virus and a recent outbreak of skin rash disease in nigeria","volume":"91","author":"Kabuga","year":"2019","journal-title":"J.\u00a0Med. Virol."},{"key":"10.1016\/j.virs.2023.03.006_bib27","doi-asserted-by":"crossref","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":"10.1016\/j.virs.2023.03.006_bib28","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/labinvest.3700143","article-title":"Monkeypox virus detection in rodents using real-time 3'-minor groove binder taqman assays on the roche lightcycler","volume":"84","author":"Kulesh","year":"2004","journal-title":"Lab. Invest."},{"key":"10.1016\/j.virs.2023.03.006_bib29","first-page":"593","article-title":"A\u00a0human infection caused by monkeypox virus in basankusu territory, democratic republic of the Congo","volume":"46","author":"Ladnyj","year":"1972","journal-title":"Bull. World Health Organ."},{"key":"10.1016\/j.virs.2023.03.006_bib30","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.virusres.2006.01.016","article-title":"Poxviruses: past, present and future","volume":"117","author":"Lefkowitz","year":"2006","journal-title":"Virus Res."},{"key":"10.1016\/j.virs.2023.03.006_bib31","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A\u00a0statistical framework for snp calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.virs.2023.03.006_bib32","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with burrows-wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.virs.2023.03.006_bib33","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.jcv.2006.03.012","article-title":"Detection of monkeypox virus with real-time pcr assays","volume":"36","author":"Li","year":"2006","journal-title":"J.\u00a0Clin. Virol."},{"key":"10.1016\/j.virs.2023.03.006_bib34","first-page":"2078","article-title":"Genome project data processing S","volume":"25","author":"Li","year":"2009","journal-title":"The sequence alignment\/map format and samtools. Bioinformatics"},{"key":"10.1016\/j.virs.2023.03.006_bib35","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.jviromet.2010.07.012","article-title":"Real-time pcr assays for the specific detection of monkeypox virus west african and Congo basin strain DNA","volume":"169","author":"Li","year":"2010","journal-title":"J.\u00a0Virol Methods"},{"key":"10.1016\/j.virs.2023.03.006_bib36","doi-asserted-by":"crossref","first-page":"8329","DOI":"10.3390\/ijms21218329","article-title":"Tn5 transposase applied in genomics research","volume":"21","author":"Li","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.virs.2023.03.006_bib37","unstructured":"Hoz-S\u00e1nchez Bdl, L\u00f3pez-Ortiz M, Guti\u00e9rrez-Arroyo A, Roces-\u00c1lvarez P, L\u00e1zaro-Perona F, Dahdouh E, Bloise I, Garc\u00eda-Rodr\u00edguez J, Mingorance J. (2022). Whole Genome Sequences of Monkey Pox Virus from Two Cases in Madrid, Spain, May-June 2022. [https:\/\/virological.org\/t\/whole-genome-sequences-of-monkey-pox-virus-from-two-cases-in-madrid-spain-may-june-2022\/877.] (Accessed 23 June 2022)."},{"key":"10.1016\/j.virs.2023.03.006_bib38","author":"Mart\u00ednez-Puchol"},{"key":"10.1016\/j.virs.2023.03.006_bib39","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.virs.2023.03.006_bib40","doi-asserted-by":"crossref","first-page":"2168","DOI":"10.3390\/v7042168","article-title":"A\u00a0phylogeographic investigation of african monkeypox","volume":"7","author":"Nakazawa","year":"2015","journal-title":"Viruses"},{"key":"10.1016\/j.virs.2023.03.006_bib41","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1016\/S1473-3099(19)30537-7","article-title":"A\u00a0case of imported monkeypox in Singapore","volume":"19","author":"Ng","year":"2019","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.virs.2023.03.006_bib42","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"Iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.virs.2023.03.006_bib43","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1099\/vir.0.070219-0","article-title":"Orthopoxvirus infection among wildlife in Zambia","volume":"96","author":"Orba","year":"2015","journal-title":"J.\u00a0Gen. Virol."},{"key":"10.1016\/j.virs.2023.03.006_bib44","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S1473-3099(22)00586-2","article-title":"Viral loads in clinical samples of men with monkeypox virus infection: a French case series","volume":"23","author":"Palich","year":"2023","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.virs.2023.03.006_bib45","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1126\/science.ade6360","article-title":"Structure of monkeypox virus DNA polymerase holoenzyme","volume":"379","author":"Peng","year":"2023","journal-title":"Science"},{"key":"10.1016\/j.virs.2023.03.006_bib46","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.tig.2007.12.006","article-title":"Bioinformatics challenges of new sequencing technology","volume":"24","author":"Pop","year":"2008","journal-title":"Trends Genet."},{"key":"10.1016\/j.virs.2023.03.006_bib47","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-021-97158-x","article-title":"Nanopore sequencing and de novo assembly of a misidentified camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides","volume":"11","author":"Saud","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.virs.2023.03.006_bib48","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0014-5793(01)03144-1","article-title":"Human monkeypox and smallpox viruses: genomic comparison","volume":"509","author":"Shchelkunov","year":"2001","journal-title":"FEBS Lett."},{"key":"10.1016\/j.virs.2023.03.006_bib49","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.jviromet.2011.05.002","article-title":"Species-specific identification of variola, monkeypox, cowpox, and vaccinia viruses by multiplex real-time pcr assay","volume":"175","author":"Shchelkunov","year":"2011","journal-title":"J.\u00a0Virol Methods"},{"key":"10.1016\/j.virs.2023.03.006_bib50","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S1473-3099(22)00794-0","article-title":"Viral dynamics in patients with monkeypox infection: a prospective cohort study in Spain","volume":"23","author":"Suner","year":"2022","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.virs.2023.03.006_bib51","first-page":"847","article-title":"Neglected zoonotic monkeypox in africa but now back in the spotlight worldwide","volume":"4","author":"Tan","year":"2022","journal-title":"China CDC Weekly"},{"key":"10.1016\/j.virs.2023.03.006_bib52","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1016\/0888-7543(92)90147-K","article-title":"Degenerate oligonucleotide-primed pcr: general amplification of target DNA by a single degenerate primer","volume":"13","author":"Telenius","year":"1992","journal-title":"Genomics"},{"key":"10.1016\/j.virs.2023.03.006_bib53","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-022-15073-1","article-title":"Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic","volume":"12","author":"Vandenbogaert","year":"2022","journal-title":"Sci. Rep."},{"key":"10.1016\/j.virs.2023.03.006_bib54","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2018.23.38.1800509","article-title":"Two cases of monkeypox imported to the United Kingdom, september 2018","volume":"23","author":"Vaughan","year":"2018","journal-title":"Euro Surveill."},{"key":"10.1016\/j.virs.2023.03.006_bib55","unstructured":"WHO, 2022a. Who director-general's statement at the press conference following ihr emergency committee regarding the multi-country outbreak of monkeypox - 23 July 2022. [https:\/\/www.who.int\/news-room\/speeches\/item\/who-director-general-s-statement-on-the-press-conference-following-IHR-emergency-committee-regarding-the-multi--country-outbreak-of-monkeypox--23-july-2022.] (Accessed 23 July 2022)."},{"key":"10.1016\/j.virs.2023.03.006_bib57","article-title":"Mpox (monkeypox) outbreak","year":"2023","journal-title":"Global trends"},{"key":"10.1016\/j.virs.2023.03.006_bib58","doi-asserted-by":"crossref","first-page":"13139","DOI":"10.1128\/JVI.79.20.13139-13149.2005","article-title":"An orally bioavailable antipoxvirus compound (st-246) inhibits extracellular virus formation and protects mice from lethal orthopoxvirus challenge","volume":"79","author":"Yang","year":"2005","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.virs.2023.03.006_bib59","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.virs.2022.10.004","article-title":"Immunization of mice with vaccinia virus tiantan strain yields antibodies cross-reactive with protective antigens of monkeypox virus","volume":"38","author":"Yang","year":"2022","journal-title":"Virol. Sin."},{"key":"10.1016\/j.virs.2023.03.006_bib60","first-page":"853","article-title":"The first imported case of monkeypox in the mainland of China \u2014 chongqing municipality, China, september 16, 2022","volume":"4","author":"Zhao","year":"2022","journal-title":"CCDC Weekly"},{"key":"10.1016\/j.virs.2023.03.006_bib61","first-page":"703","article-title":"Rapid detection and differentiation of smallpox or monkeypox virus infection by real-time pcr assay","volume":"17","author":"Zhou","year":"2006","journal-title":"Letters in Biotechnology"},{"key":"10.1016\/j.virs.2023.03.006_bib62","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1126\/science.1229164","article-title":"Genome-wide detection of single-nucleotide and copy-number variations of a single human cell","volume":"338","author":"Zong","year":"2012","journal-title":"Science"}],"container-title":["Virologica Sinica"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1995820X23000275?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1995820X23000275?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T19:19:06Z","timestamp":1761851946000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1995820X23000275"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4]]},"references-count":60,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2023,4]]}},"alternative-id":["S1995820X23000275"],"URL":"https:\/\/doi.org\/10.1016\/j.virs.2023.03.006","relation":{},"ISSN":["1995-820X"],"issn-type":[{"value":"1995-820X","type":"print"}],"subject":[],"published":{"date-parts":[[2023,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Perspective on the application of genome sequencing for monkeypox virus surveillance","name":"articletitle","label":"Article Title"},{"value":"Virologica Sinica","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.virs.2023.03.006","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.","name":"copyright","label":"Copyright"}]}}