{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T01:52:45Z","timestamp":1791856365676,"version":"4.3.4"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UL1 TR001863"],"award-info":[{"award-number":["UL1 TR001863"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32AI055403"],"award-info":[{"award-number":["T32AI055403"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100023581","name":"National Science Foundation Graduate Research Fellowship Program","doi-asserted-by":"publisher","award":["DGE-2139841"],"award-info":[{"award-number":["DGE-2139841"]}],"id":[{"id":"10.13039\/100023581","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R21GM142011"],"award-info":[{"award-number":["R21GM142011"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["DP2AI176740"],"award-info":[{"award-number":["DP2AI176740"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (&gt;95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies\/\u03bcL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-024-10350-x","type":"journal-article","created":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T11:09:55Z","timestamp":1714561795000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus"],"prefix":"10.1186","volume":"25","author":[{"given":"Chantal B. F.","family":"Vogels","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verity","family":"Hill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mallery I.","family":"Breban","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chrispin","family":"Chaguza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren M.","family":"Paul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afeez","family":"Sodeinde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Taylor-Salmon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel M.","family":"Ott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary E.","family":"Petrone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Dijk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcel","family":"Jonges","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthijs R. A.","family":"Welkers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Locksmith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibo","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namratha","family":"Tarigopula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omer","family":"Tekin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Schmedes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvia","family":"Bunch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Cano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rayah","family":"Jaber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Panzera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Stryker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julieta","family":"Vergara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Zimler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edgar","family":"Kopp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lea","family":"Heberlein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaylee S.","family":"Herzog","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph R.","family":"Fauver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea M.","family":"Morrison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott F.","family":"Michael","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan D.","family":"Grubaugh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,1]]},"reference":[{"key":"10350_CR1","doi-asserted-by":"publisher","first-page":"e1760","DOI":"10.1371\/journal.pntd.0001760","volume":"6","author":"OJ Brady","year":"2012","unstructured":"Brady OJ, Gething PW, Bhatt S, Messina JP, Brownstein JS, Hoen AG, et al. Refining the global spatial limits of dengue virus transmission by evidence-based consensus. PLoS Negl Trop Dis. 2012;6:e1760.","journal-title":"PLoS Negl Trop Dis."},{"key":"10350_CR2","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2020.100712","volume":"32","author":"Z Zeng","year":"2021","unstructured":"Zeng Z, Zhan J, Chen L, Chen H, Cheng S. Global, regional, and national dengue burden from 1990 to 2017: A systematic analysis based on the global burden of disease study 2017. EClinicalMedicine. 2021;32:100712.","journal-title":"EClinicalMedicine."},{"key":"10350_CR3","unstructured":"Dengue \u2013 the Region of the Americas [Internet]. [cited 2023 Jul 26]. Available from: https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2023-DON475"},{"key":"10350_CR4","doi-asserted-by":"publisher","first-page":"e1501","DOI":"10.1016\/S2214-109X(23)00325-X","volume":"11","author":"GL Wallau","year":"2023","unstructured":"Wallau GL, Global Arbovirus Researchers United. Arbovirus researchers unite: expanding genomic surveillance for an urgent global need. Lancet Glob Health. 2023;11:e1501\u20132.","journal-title":"Lancet Glob Health"},{"key":"10350_CR5","doi-asserted-by":"publisher","first-page":"1562","DOI":"10.3390\/v3091562","volume":"3","author":"R Chen","year":"2011","unstructured":"Chen R, Vasilakis N. Dengue\u2013quo tu et quo vadis? Viruses. 2011;3:1562\u2013608.","journal-title":"Viruses."},{"key":"10350_CR6","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1126\/science.abk0058","volume":"374","author":"LC Katzelnick","year":"2021","unstructured":"Katzelnick LC, Coello Escoto A, Huang AT, Garcia-Carreras B, Chowdhury N, Maljkovic Berry I, et al. Antigenic evolution of dengue viruses over 20 years. Science. 2021;374:999\u20131004.","journal-title":"Science."},{"key":"10350_CR7","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/nature10355","volume":"476","author":"T Walker","year":"2011","unstructured":"Walker T, Johnson PH, Moreira LA, Iturbe-Ormaetxe I, Frentiu FD, McMeniman CJ, et al. The wMel Wolbachia strain blocks dengue and invades caged Aedes aegypti populations. Nature. 2011;476:450\u20133.","journal-title":"Nature."},{"key":"10350_CR8","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.3389\/fimmu.2020.01252","volume":"11","author":"JR Pinheiro-Michelsen","year":"2020","unstructured":"Pinheiro-Michelsen JR, Souza R da SO, Santana IVR, da Silva P de S, Mendez EC, Luiz WB, et al. Anti-dengue Vaccines: From Development to Clinical Trials. Front Immunol. 2020;11:1252.","journal-title":"Front Immunol"},{"key":"10350_CR9","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1038\/nprot.2017.066","volume":"12","author":"J Quick","year":"2017","unstructured":"Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, 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":"10350_CR10","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","volume":"20","author":"ND Grubaugh","year":"2019","unstructured":"Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol. 2019;20:8.","journal-title":"Genome Biol."},{"key":"10350_CR11","unstructured":"Artic Network [Internet]. [cited 2022 Jul 25]. Available from: https:\/\/artic.network\/ncov-2019"},{"key":"10350_CR12","doi-asserted-by":"publisher","first-page":"D571","DOI":"10.1093\/nar\/gku1207","volume":"43","author":"JR Brister","year":"2015","unstructured":"Brister JR, Ako-Adjei D, Bao Y, Blinkova O. NCBI viral genomes resource. Nucleic Acids Res. 2015;43:D571\u20137.","journal-title":"Nucleic Acids Res."},{"key":"10350_CR13","unstructured":"NCBI Virus [Internet]. [cited 2023 Aug 1]. Available from: https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/virus?SeqType_s=Nucleotide&VirusLineage_ss=Dengue%20virus,%20taxid:12637"},{"key":"10350_CR14","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/s12862-019-1567-0","volume":"19","author":"G Dudas","year":"2019","unstructured":"Dudas G, Bedford T. The ability of single genes vs full genomes to resolve time and space in outbreak analysis. BMC Evol Biol. 2019;19:232.","journal-title":"BMC Evol Biol."},{"issue":"6","key":"10350_CR15","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1016\/j.chom.2023.03.003","volume":"31","author":"V Hill","year":"2023","unstructured":"Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, et al. Toward a global virus genomic surveillance network. Cell Host Microbe. 2023;31(6):861\u201373.","journal-title":"Cell Host Microbe"},{"key":"10350_CR16","doi-asserted-by":"publisher","first-page":"e2311","DOI":"10.1371\/journal.pntd.0002311","volume":"7","author":"GA Santiago","year":"2013","unstructured":"Santiago GA, Vergne E, Quiles Y, Cosme J, Vazquez J, Medina JF, et al. Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus. PLoS Negl Trop Dis. 2013;7:e2311.","journal-title":"PLoS Negl Trop Dis."},{"key":"10350_CR17","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1093\/bioinformatics\/bty695","volume":"35","author":"M Vilsker","year":"2019","unstructured":"Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, et al. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics. 2019;35:871\u20133.","journal-title":"Bioinformatics."},{"key":"10350_CR18","doi-asserted-by":"publisher","first-page":"S89","DOI":"10.1093\/infdis\/jiw649","volume":"215","author":"DA Muller","year":"2017","unstructured":"Muller DA, Depelsenaire ACI, Young PR. Clinical and Laboratory Diagnosis of Dengue Virus Infection. J Infect Dis. 2017;215:S89\u201395.","journal-title":"J Infect Dis."},{"key":"10350_CR19","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1128\/CDLI.11.4.642-650.2004","volume":"11","author":"Shu Pei-Yun","year":"2004","unstructured":"Pei-Yun Shu, Jyh-Hsiung Huang. Current Advances in Dengue Diagnosis. Clin Vaccine Immunol. 2004;11:642\u201350.","journal-title":"Clin Vaccine Immunol."},{"key":"10350_CR20","doi-asserted-by":"publisher","first-page":"1080","DOI":"10.4269\/ajtmh.15-0892","volume":"94","author":"EHP Andrade","year":"2016","unstructured":"Andrade EHP, Figueiredo LB, Vilela APP, Rosa JCC, Oliveira JG, Zibaoui HM, et al. Spatial-Temporal Co-Circulation of Dengue Virus 1, 2, 3, and 4 Associated with Coinfection Cases in a Hyperendemic Area of Brazil: A 4-Week Survey. Am J Trop Med Hyg. 2016;94:1080\u20134.","journal-title":"Am J Trop Med Hyg."},{"key":"10350_CR21","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1017\/S0950268816001990","volume":"145","author":"A Tazeen","year":"2017","unstructured":"Tazeen A, Afreen N, Abdullah M, Deeba F, Haider SH, Kazim SN, et al. Occurrence of co-infection with dengue viruses during 2014 in New Delhi. India Epidemiol Infect. 2017;145:67\u201377.","journal-title":"India. Epidemiol Infect."},{"key":"10350_CR22","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1186\/s12879-016-1731-8","volume":"16","author":"A Dhanoa","year":"2016","unstructured":"Dhanoa A, Hassan SS, Ngim CF, Lau CF, Chan TS, Adnan NAA, et al. Impact of dengue virus (DENV) co-infection on clinical manifestations, disease severity and laboratory parameters. BMC Infect Dis. 2016;16:406.","journal-title":"BMC Infect Dis."},{"key":"10350_CR23","doi-asserted-by":"publisher","first-page":"e3002151","DOI":"10.1371\/journal.pbio.3002151","volume":"21","author":"NFG Chen","year":"2023","unstructured":"Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, et al. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLoS Biol. 2023;21:e3002151.","journal-title":"PLoS Biol."},{"key":"10350_CR24","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s12985-020-1294-6","volume":"17","author":"SCB Stubbs","year":"2020","unstructured":"Stubbs SCB, Blacklaws BA, Yohan B, Yudhaputri FA, Hayati RF, Schwem B, et al. Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia. Virol J. 2020;17:24.","journal-title":"Virol J."},{"key":"10350_CR25","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01210-22","volume":"10","author":"W Su","year":"2022","unstructured":"Su W, Jiang L, Lu W, Xie H, Cao Y, Di B, et al. A Serotype-Specific and Multiplex PCR Method for Whole-Genome Sequencing of Dengue Virus Directly from Clinical Samples. Microbiol Spectr. 2022;10: e0121022.","journal-title":"Microbiol Spectr."},{"key":"10350_CR26","doi-asserted-by":"publisher","first-page":"2296","DOI":"10.1038\/s41467-021-22607-0","volume":"12","author":"T\u00c9R Adelino","year":"2021","unstructured":"Adelino T\u00c9R, Giovanetti M, Fonseca V, Xavier J, de Abreu \u00c1S, do Nascimento VA, et al. Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil. Nat Commun. 2021;12:2296.","journal-title":"Nat Commun"},{"key":"10350_CR27","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/j.jviromet.2016.06.001","volume":"235","author":"CD Cruz","year":"2016","unstructured":"Cruz CD, Torre A, Troncos G, Lambrechts L, Leguia M. Targeted full-genome amplification and sequencing of dengue virus types 1\u20134 from South America. J Virol Methods. 2016;235:158\u201367.","journal-title":"J Virol Methods."},{"key":"10350_CR28","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/978-1-4939-0348-1_12","volume-title":"Dengue: Methods and Protocols","author":"PPK Aw","year":"2014","unstructured":"Aw PPK, de Sessions PF, Wilm A, Hoang LT, Nagarajan N, Sessions OM, et al. Next-Generation Whole Genome Sequencing of Dengue Virus. In: Padmanabhan R, Vasudevan SG, editors., et al., Dengue: Methods and Protocols. Springer, New York: New York, NY; 2014;175\u201395."},{"key":"10350_CR29","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/j.jviromet.2010.06.013","volume":"169","author":"JG Christenbury","year":"2010","unstructured":"Christenbury JG, Aw PPK, Ong SH, Schreiber MJ, Chow A, Gubler DJ, et al. A method for full genome sequencing of all four serotypes of the dengue virus. J Virol Methods. 2010;169:202\u20136.","journal-title":"J Virol Methods."},{"key":"10350_CR30","doi-asserted-by":"publisher","first-page":"vead012","DOI":"10.1093\/ve\/vead012","volume":"9","author":"J Ashall","year":"2023","unstructured":"Ashall J, Shah S, Biggs JR, Chang JNR, Jafari Y, Brady OJ, et al. A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains. Virus Evol. 2023;9:vead012.","journal-title":"Virus Evol"},{"key":"10350_CR31","doi-asserted-by":"crossref","unstructured":"Vogels C, Chaguza C, Breban MI, Sodeinde A, Porzucek AJ, Grubaugh ND, et al. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus. 2023 [cited 2023 Jul 28]; Available from: https:\/\/www.protocols.io\/view\/dengueseq-a-pan-serotype-whole-genome-amplicon-seq-kqdg39xxeg25\/v2","DOI":"10.17504\/protocols.io.kqdg39xxeg25\/v3"},{"key":"10350_CR32","doi-asserted-by":"crossref","unstructured":"Freed N, Murphy L, Schwessinger B, Silander O. \u201cMidnight\u201d SARS-CoV2 genome sequencing protocol using 1200bp amplicon primer set v2 and the Nanopo. 2023 [cited 2023 Aug 28]; Available from: https:\/\/www.protocols.io\/view\/34-midnight-34-sars-cov2-genome-sequencing-protoc-14egn2q2yg5d\/v1","DOI":"10.17504\/protocols.io.14egn2q2yg5d\/v1"},{"key":"10350_CR33","unstructured":"Rambaut NLWR. ARTIC Network nCoV-2019 novel coronavirus bioinformatics protocol. 2020 [cited 2022 Jan 17]. Available from: https:\/\/artic.network\/ncov-2019\/ncov2019-bioinformatics-sop.html"},{"key":"10350_CR34","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN]. 2013. Available from: http:\/\/arxiv.org\/abs\/1303.3997"},{"key":"10350_CR35","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics. 2009;25:2078\u20139.","journal-title":"Bioinformatics."},{"key":"10350_CR36","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":"10350_CR37","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772\u201380.","journal-title":"Mol Biol Evol."},{"key":"10350_CR38","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJA Cock","year":"2009","unstructured":"Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422\u20133.","journal-title":"Bioinformatics."},{"key":"10350_CR39","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841\u20132.","journal-title":"Bioinformatics."},{"key":"10350_CR40","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1038\/nature16996","volume":"530","author":"J Quick","year":"2016","unstructured":"Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530:228\u201332.","journal-title":"Nature."},{"key":"10350_CR41","unstructured":"fieldbioinformatics: The ARTIC field bioinformatics pipeline. Github; [cited 2024 Jan 11]. Available from: https:\/\/github.com\/artic-network\/fieldbioinformatics"},{"key":"10350_CR42","unstructured":"R Core Team. The R Project for Statistical Computing [Internet]. R: A language and environment for statistical computing. 2022 [cited 2022 Sep 12]. Available from: https:\/\/www.r-project.org\/"},{"key":"10350_CR43","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2","author":"H Wickham","year":"2009","unstructured":"Wickham H. ggplot2. New York: Springer; 2009."},{"key":"10350_CR44","unstructured":"Wickham H, Fran\u00e7ois R, Henry L, M\u00fcller K. dplyr: A Grammar of Data Manipulation [Internet]. Comprehensive R Archive Network (CRAN); 2022 [cited 2022 Sep 12]. Available from: https:\/\/cran.r-project.org\/web\/packages\/dplyr\/index.html"},{"key":"10350_CR45","unstructured":"Wickham H, Girlich M. tidyr: Tidy Messy Data [Internet]. Comprehensive R Archive Network (CRAN); 2022 [cited 2022 Sep 12]. Available from: https:\/\/cran.r-project.org\/web\/packages\/tidyr\/index.html"},{"key":"10350_CR46","unstructured":"Wilke CO. cowplot: Streamlined Plot Theme and Plot Annotations for \u201cggplot2\u201d [Internet]. 2020 [cited 2022 Sep 12]. Available from: https:\/\/CRAN.R-project.org\/package=cowplot"},{"key":"10350_CR47","unstructured":"Scale Functions for Visualization [R package scales version 1.2.1]. 2022 [cited 2023 Jul 28]; Available from: https:\/\/cran.r-project.org\/web\/packages\/scales\/index.html"},{"key":"10350_CR48","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268\u201374.","journal-title":"Mol Biol Evol."},{"key":"10350_CR49","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1007\/BF02101694","volume":"22","author":"M Hasegawa","year":"1985","unstructured":"Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22:160\u201374.","journal-title":"J Mol Evol."},{"key":"10350_CR50","unstructured":"Dudas G. baltic: baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis\/baltic branch (i.e. here) [Internet]. Github; [cited 2023 Jul 28]. Available from: https:\/\/github.com\/evogytis\/baltic"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10350-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-024-10350-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-024-10350-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T11:10:03Z","timestamp":1714561803000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-024-10350-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,1]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["10350"],"URL":"https:\/\/doi.org\/10.1186\/s12864-024-10350-x","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.10.13.23296997","asserted-by":"object"}]},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,1]]},"assertion":[{"value":"16 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 April 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The Florida Department of Health shared de-identified remnant clinical specimens that tested positive for dengue virus for sequencing at the Yale School of Public Health. The Institutional Review Boards (IRB) from the Yale University Human Research Protection Program, Florida Gulf Coast University, and Florida Department of Health determined that pathogen genomic sequencing of de-identified remnant diagnostic samples as conducted in this study is not research involving human subjects (Yale IRB Protocol ID: 2000033281 and 2000028599).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","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":"433"}}