{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T18:38:02Z","timestamp":1765823882709,"version":"3.48.0"},"reference-count":70,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T00:00:00Z","timestamp":1765756800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Institut Pasteur","award":["ACIP-2019-281"],"award-info":[{"award-number":["ACIP-2019-281"]}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-19-CE35-0001-01-DENWOLUTION"],"award-info":[{"award-number":["ANR-19-CE35-0001-01-DENWOLUTION"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fondation Ledoux - Jeunesse Internationale","award":["eDynaMIcS"],"award-info":[{"award-number":["eDynaMIcS"]}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["Investissements d\u2019Avenir grant ANR-16-CONV-0005"],"award-info":[{"award-number":["Investissements d\u2019Avenir grant ANR-16-CONV-0005"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ixcore doundation for research"},{"name":"French Government","award":["Investissement d'Avenir"],"award-info":[{"award-number":["Investissement d'Avenir"]}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"HERA project DURABLE","award":["101102733"],"award-info":[{"award-number":["101102733"]}]},{"name":"National Institute of Health","award":["U01AI151758"],"award-info":[{"award-number":["U01AI151758"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Comparing the\n                      <jats:italic>in vitro<\/jats:italic>\n                      fitness of dengue virus (DENV) isolates is a pivotal approach to assess the contribution of DENV strains\u2019 replicative fitness to epidemiological contexts, including serotype replacements. Competition assays are the gold standard to compare the\n                      <jats:italic>in vitro<\/jats:italic>\n                      replicative fitness of viral strains. Implementing competition assays between DENV serotypes requires an experimental setup and an appropriate read-out to quantify the viral progeny of strains belonging to different serotypes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      In the current study, we optimized an existing serotyping qRT-PCR by adapting primer\/probe design and multiplexing the serotype-specific qRT-PCR reactions, allowing to accurately detect and quantify all four DENV serotypes. We next developed an\n                      <jats:italic>in vitro<\/jats:italic>\n                      competition assay to compare the replicative fitness of two DENV serotypes in the human hepatic cell line HuH7.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>The qRT-PCR was specific, and had a limit of detection below 7.52, 1.19, 3.48 and 1.36 genome copies\/\u00b5L, an efficiency of 1.993, 1.975, 1.902, 1.898 and a linearity (R\u00b2) of 0.99975, 0.99975, 0.99850, 0.99965 for DENV-1, \u22122, \u22123 and \u22124, respectively. Challenge of this multiplex serotype-specific qRT-PCR on mixes of viral supernatants containing known concentrations of strains from two serotypes evidenced an accurate quantification of the amount of genome copies of each serotype. Quantification of the viral progeny of each serotype in the inoculum and the supernatant of competition assays using the serotype-specific multiplex qRT-PCR unveiled an enrichment of the supernatant in DENV-1 genome copies, uncovering the enhanced replicative fitness of this DENV-1 isolate.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This optimized qRT-PCR combined with a relevant cellular model allowed to accurately quantify the viral progeny of two DENV strains belonging to two different serotypes in a competition assay, allowing to determine which strain had a replicative advantage. This reliable experimental setup is adaptable to the comparative study of the replicative fitness of any DENV serotypes.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0339033","type":"journal-article","created":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T18:33:17Z","timestamp":1765823597000},"page":"e0339033","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of a competition assay to assess the in vitro fitness of dengue virus serotypes using an optimized serotype-specific qRT-PCR"],"prefix":"10.1371","volume":"20","author":[{"given":"Anne-Fleur","family":"Griffon","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Loe\u00efza","family":"Rault","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8765-6517","authenticated-orcid":true,"given":"Cl\u00e9ment","family":"Tanvet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Etienne","family":"Simon-Lori\u00e8re","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Myrielle","family":"Dupont-Rouzeyrol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1933-1515","authenticated-orcid":true,"given":"Catherine","family":"Inizan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,12,15]]},"reference":[{"issue":"5","key":"pone.0339033.ref001","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1097\/01.qco.0000244047.31135.fa","article-title":"Immunopathological mechanisms in dengue and dengue hemorrhagic fever","volume":"19","author":"S Green","year":"2006","journal-title":"Curr Opin Infect Dis"},{"key":"pone.0339033.ref002","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1186\/s12864-019-6311-z","article-title":"Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design","volume":"20","author":"LC Chong","year":"2019","journal-title":"BMC Genomics"},{"issue":"5","key":"pone.0339033.ref003","article-title":"Meta-Analysis of Dengue Severity during Infection by Different Dengue Virus Serotypes in Primary and Secondary Infections","volume":"11","author":"K-M Soo","year":"2016","journal-title":"PLoS One"},{"key":"pone.0339033.ref004","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1146\/annurev.micro.51.1.151","article-title":"RNA virus mutations and fitness for survival","volume":"51","author":"E Domingo","year":"1997","journal-title":"Annu Rev Microbiol"},{"issue":"5","key":"pone.0339033.ref005","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1016\/j.coviro.2012.07.007","article-title":"Viral fitness: definitions, measurement, and current insights","volume":"2","author":"AR Wargo","year":"2012","journal-title":"Curr Opin Virol"},{"issue":"11","key":"pone.0339033.ref006","doi-asserted-by":"crossref","first-page":"110899","DOI":"10.1016\/j.isci.2024.110899","article-title":"Emergence and increased epidemic potential of dengue variants with the NS5V357E mutation after consecutive years of transmission","volume":"27","author":"H-Y Ko","year":"2024","journal-title":"iScience"},{"issue":"1","key":"pone.0339033.ref007","article-title":"Fitness peaks of dengue virus populations","volume":"13","author":"WJ Liu","year":"2018","journal-title":"PLoS One"},{"issue":"1","key":"pone.0339033.ref008","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.bjid.2019.11.003","article-title":"Differential replicative fitness of the four dengue virus serotypes circulating in Colombia in human liver Huh7 cells","volume":"24","author":"H Guti\u00e9rrez-Barbosa","year":"2020","journal-title":"Braz J Infect Dis"},{"issue":"2","key":"pone.0339033.ref009","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.virol.2006.08.005","article-title":"Cell-specific adaptation of two flaviviruses following serial passage in mosquito cell culture","volume":"357","author":"AT Ciota","year":"2007","journal-title":"Virology"},{"key":"pone.0339033.ref010","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.virol.2019.07.029","article-title":"In vitro method to evaluate virus competition between BVDV-1 and BVDV-2 strains using the PrimeFlow RNA assay","volume":"536","author":"S Silveira","year":"2019","journal-title":"Virology"},{"issue":"4","key":"pone.0339033.ref011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1010491","article-title":"The E2 glycoprotein holds key residues for Mayaro virus adaptation to the urban Aedes aegypti mosquito","volume":"19","author":"C Cereghino","year":"2023","journal-title":"PLoS Pathog"},{"issue":"2","key":"pone.0339033.ref012","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1089\/vbz.2015.1804","article-title":"Infection of Mosquito Cells (C6\/36) by Dengue-2 Virus Interferes with Subsequent Infection by Yellow Fever Virus","volume":"16","author":"EP Abrao","year":"2016","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"6","key":"pone.0339033.ref013","first-page":"1388","article-title":"Competitive suppression between chikungunya and dengue virus in Aedes albopictus c6\/36 cell line","volume":"42","author":"R Potiwat","year":"2011","journal-title":"Southeast Asian J Trop Med Public Health"},{"key":"pone.0339033.ref014","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s13071-015-0667-y","article-title":"Sindbis virus interferes with dengue 4 virus replication and its potential transmission by Aedes albopictus","volume":"8","author":"EJ Muturi","year":"2015","journal-title":"Parasit Vectors"},{"issue":"1","key":"pone.0339033.ref015","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1186\/s13071-023-05778-1","article-title":"Co-infection of dengue and Zika viruses mutually enhances viral replication in the mosquito Aedes aegypti","volume":"16","author":"DC-D Lin","year":"2023","journal-title":"Parasit Vectors"},{"key":"pone.0339033.ref016","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1471-2180-10-14","article-title":"Persistent, triple-virus co-infections in mosquito cells","volume":"10","author":"N Kanthong","year":"2010","journal-title":"BMC Microbiol"},{"key":"pone.0339033.ref017","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/1471-2180-8-28","article-title":"Asymmetric competitive suppression between strains of dengue virus","volume":"8","author":"KM Pepin","year":"2008","journal-title":"BMC Microbiol"},{"issue":"6","key":"pone.0339033.ref018","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1089\/vbz.2008.0016","article-title":"Density-dependent competitive suppression of sylvatic dengue virus by endemic dengue virus in cultured mosquito cells","volume":"8","author":"KM Pepin","year":"2008","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"7","key":"pone.0339033.ref019","doi-asserted-by":"crossref","first-page":"876","DOI":"10.3855\/jidc.3978","article-title":"Differential replication of dengue virus serotypes 2 and 3 in coinfections of C6\/36 cells and Aedes aegypti mosquitoes","volume":"8","author":"DC Quintero-Gil","year":"2014","journal-title":"J Infect Dev Ctries"},{"issue":"8","key":"pone.0339033.ref020","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1099\/jgv.0.001092","article-title":"A single amino acid substitution in the NS4B protein of Dengue virus confers enhanced virus growth and fitness in human cells in vitro through IFN-dependent host response","volume":"99","author":"TT Bui","year":"2018","journal-title":"J Gen Virol"},{"issue":"12","key":"pone.0339033.ref021","doi-asserted-by":"crossref","first-page":"5935","DOI":"10.1128\/JCM.42.12.5935-5937.2004","article-title":"Development and evaluation of fluorogenic TaqMan reverse transcriptase PCR assays for detection of dengue virus types 1 to 4","volume":"42","author":"M Ito","year":"2004","journal-title":"J Clin Microbiol"},{"issue":"10","key":"pone.0339033.ref022","doi-asserted-by":"crossref","first-page":"4977","DOI":"10.1128\/JCM.43.10.4977-4983.2005","article-title":"Serotype-specific detection of dengue viruses in a fourplex real-time reverse transcriptase PCR assay","volume":"43","author":"BW Johnson","year":"2005","journal-title":"J Clin Microbiol"},{"issue":"1","key":"pone.0339033.ref023","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/S1567-1348(03)00004-2","article-title":"The origin, emergence and evolutionary genetics of dengue virus","volume":"3","author":"EC Holmes","year":"2003","journal-title":"Infect Genet Evol"},{"issue":"10","key":"pone.0339033.ref024","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1128\/JCM.00163-08","article-title":"Detection and serotyping of dengue virus in serum samples by multiplex reverse transcriptase PCR-ligase detection reaction assay","volume":"46","author":"S Das","year":"2008","journal-title":"J Clin Microbiol"},{"issue":"3","key":"pone.0339033.ref025","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/j.cell.2015.07.005","article-title":"Molecular Insight into Dengue Virus Pathogenesis and Its Implications for Disease Control","volume":"162","author":"MS Diamond","year":"2015","journal-title":"Cell"},{"issue":"7563","key":"pone.0339033.ref026","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature14612","article-title":"Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic","volume":"524","author":"E Simon-Loriere","year":"2015","journal-title":"Nature"},{"issue":"15","key":"pone.0339033.ref027","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0339033.ref028","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: a new versatile metagenomic assembler","volume":"27","author":"S Nurk","year":"2017","journal-title":"Genome Res"},{"key":"pone.0339033.ref029","article-title":"National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), N.C.f.","year":"1988","journal-title":"B.I"},{"issue":"1","key":"pone.0339033.ref030","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"B Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"pone.0339033.ref031","unstructured":"Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010."},{"issue":"14","key":"pone.0339033.ref032","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":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"2","key":"pone.0339033.ref033","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"P Danecek","year":"2021","journal-title":"GigaScience"},{"issue":"4","key":"pone.0339033.ref034","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":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pone.0339033.ref035","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":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pone.0339033.ref036","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"I Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0339033.ref037","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1080\/22221751.2021.1899057","article-title":"Viral evolution sustains a dengue outbreak of enhanced severity","volume":"10","author":"C Inizan","year":"2021","journal-title":"Emerg Microbes Infect"},{"issue":"4","key":"pone.0339033.ref038","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1002\/jmv.2176","article-title":"Single rapid TaqMan fluorogenic probe based PCR assay that detects all four dengue serotypes","volume":"66","author":"D Warrilow","year":"2002","journal-title":"J Med Virol"},{"issue":"8","key":"pone.0339033.ref039","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.52768\/jjgastro\/1040","article-title":"Origin and properties of hepatocellular carcinoma cell lines","volume":"1","author":"L Puttahanumantharayappa","year":"2021","journal-title":"Japanese J Gastroenterol Res"},{"key":"pone.0339033.ref040","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/B978-0-12-814515-9.00053-9","article-title":"Validating real-time polymerase chain reaction (PCR) assays","volume-title":"Encyclopedia of Virology","author":"M Smith","year":"2021"},{"key":"pone.0339033.ref041","doi-asserted-by":"crossref","first-page":"100789","DOI":"10.1016\/j.ijmmb.2025.100789","article-title":"Identification of Dengue virus serotype and genotype: A comprehensive study from AIIMS Patna, Bihar","volume":"53","author":"Apurva","year":"2025","journal-title":"Indian J Med Microbiol"},{"issue":"1","key":"pone.0339033.ref042","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1186\/s12879-021-06580-z","article-title":"Multifoci and multiserotypes circulation of dengue virus in Senegal between 2017 and 2018","volume":"21","author":"I Dieng","year":"2021","journal-title":"BMC Infect Dis"},{"key":"pone.0339033.ref043","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/1743-422X-11-61","article-title":"Epidemiological and molecular features of dengue virus type-1 in New Caledonia, South Pacific, 2001-2013","volume":"11","author":"M Dupont-Rouzeyrol","year":"2014","journal-title":"Virol J"},{"key":"pone.0339033.ref044","doi-asserted-by":"crossref","DOI":"10.21203\/rs.3.rs-1502293\/v1","article-title":"Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe","author":"E Simon-Loriere","year":"2022"},{"issue":"3","key":"pone.0339033.ref045","doi-asserted-by":"crossref","first-page":"107281","DOI":"10.1016\/j.ijantimicag.2024.107281","article-title":"Zanamivir and baloxavir combination to cure persistent influenza and coronavirus infections after hematopoietic stem cell transplant","volume":"64","author":"V Euzen","year":"2024","journal-title":"Int J Antimicrob Agents"},{"issue":"2","key":"pone.0339033.ref046","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/S0166-0934(02)00104-0","article-title":"Comparison of four reverse transcription-polymerase chain reaction procedures for the detection of dengue virus in clinical specimens","volume":"105","author":"B Raengsakulrach","year":"2002","journal-title":"J Virol Methods"},{"key":"pone.0339033.ref047","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.jviromet.2006.08.003","article-title":"Rapid detection, serotyping and quantitation of dengue viruses by TaqMan real-time one-step RT-PCR","volume":"138","author":"YY Kong","year":"2006","journal-title":"J Virol Methods"},{"key":"pone.0339033.ref048","doi-asserted-by":"crossref","first-page":"113862","DOI":"10.1016\/j.jviromet.2020.113862","article-title":"Improved detection of dengue and Zika viruses using multiplex RT-qPCR assays","volume":"282","author":"TP Ou","year":"2020","journal-title":"J Virol Methods"},{"issue":"1","key":"pone.0339033.ref049","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1007\/s11033-024-09847-1","article-title":"Utilization of novel molecular multiplex methods for the detection and, epidemiological surveillance of dengue virus serotypes and chikungunya virus in Burkina Faso, West Africa","volume":"51","author":"MK Gomgnimbou","year":"2024","journal-title":"Mol Biol Rep"},{"issue":"1","key":"pone.0339033.ref050","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1086\/315215","article-title":"Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity","volume":"181","author":"DW Vaughn","year":"2000","journal-title":"J Infect Dis"},{"issue":"1","key":"pone.0339033.ref051","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/s13071-018-2830-8","article-title":"History, epidemiology and diagnostics of dengue in the American and Brazilian contexts: a review","volume":"11","author":"TS Salles","year":"2018","journal-title":"Parasit Vectors"},{"issue":"9","key":"pone.0339033.ref052","doi-asserted-by":"crossref","first-page":"4320","DOI":"10.1128\/JVI.02647-15","article-title":"Increasing Clinical Severity during a Dengue Virus Type 3 Cuban Epidemic: Deep Sequencing of Evolving Viral Populations","volume":"90","author":"R Rodriguez-Roche","year":"2016","journal-title":"J Virol"},{"issue":"7","key":"pone.0339033.ref053","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgph.0003150","article-title":"Identifying the strains of dengue circulating in the western province of Sri Lanka during 2019-2022","volume":"4","author":"H Abeygoonawardena","year":"2024","journal-title":"PLOS Glob Public Health"},{"issue":"7","key":"pone.0339033.ref054","article-title":"Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia","volume":"4","author":"TTH Vu","year":"2010","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pone.0339033.ref055","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1080\/22221751.2021.1944789","article-title":"Potential role of vector-mediated natural selection in dengue virus genotype\/lineage replacements in two epidemiologically contrasted settings","volume":"10","author":"O O\u2019Connor","year":"2021","journal-title":"Emerg Microbes Infect"},{"key":"pone.0339033.ref056","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.92606","article-title":"Dengue viremia kinetics and effects on platelet count and clinical outcomes: An analysis of 2340 patients from Vietnam","volume":"13","author":"NL Vuong","year":"2024","journal-title":"Elife"},{"issue":"9","key":"pone.0339033.ref057","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1093\/infdis\/jir014","article-title":"Kinetics of plasma viremia and soluble nonstructural protein 1 concentrations in dengue: differential effects according to serotype and immune status","volume":"203","author":"HTL Duyen","year":"2011","journal-title":"J Infect Dis"},{"issue":"9","key":"pone.0339033.ref058","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0001309","article-title":"Kinetics of viremia and NS1 antigenemia are shaped by immune status and virus serotype in adults with dengue","volume":"5","author":"V Tricou","year":"2011","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pone.0339033.ref059","doi-asserted-by":"crossref","first-page":"8667","DOI":"10.1038\/s41467-024-52819-z","article-title":"Genomic surveillance reveals a dengue 2 virus epidemic lineage with a marked decrease in sensitivity to Mosnodenvir","volume":"15","author":"HS Bouzidi","year":"2024","journal-title":"Nat Commun"},{"key":"pone.0339033.ref060","article-title":"Dengue research needs related to surveillance and emergency response","author":"EE Ooi","year":"2006"},{"issue":"147","key":"pone.0339033.ref061","article-title":"Digital PCR-based Competitive Index for High-throughput Analysis of Fitness in Salmonella","author":"JA Shaw","year":"2019","journal-title":"J Vis Exp"},{"key":"pone.0339033.ref062","doi-asserted-by":"crossref","first-page":"198424","DOI":"10.1016\/j.virusres.2021.198424","article-title":"Variations in Env at amino acids 328 and 330 affect HIV-1 replicative fitness and entry inhibitor sensitivity","volume":"299","author":"H Wang","year":"2021","journal-title":"Virus Res"},{"issue":"1","key":"pone.0339033.ref063","article-title":"Human adenovirus type 7 infection causes a more severe disease than type 3","volume":"19","author":"Y Fu","year":"2019","journal-title":"BMC Infect Dis"},{"issue":"2","key":"pone.0339033.ref064","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0007135","article-title":"Comparative fitness of West Nile virus isolated during California epidemics","volume":"13","author":"G Worwa","year":"2019","journal-title":"PLoS Negl Trop Dis"},{"issue":"12","key":"pone.0339033.ref065","doi-asserted-by":"crossref","DOI":"10.1002\/jmv.29278","article-title":"Competitive fitness and homologous recombination of SARS-CoV-2 variants of concern","volume":"95","author":"Q Chen","year":"2023","journal-title":"J Med Virol"},{"key":"pone.0339033.ref066","doi-asserted-by":"crossref","first-page":"104901","DOI":"10.1016\/j.antiviral.2020.104901","article-title":"Viral fitness of MHV-68 viruses harboring drug resistance mutations in the protein kinase or thymidine kinase","volume":"182","author":"E Trompet","year":"2020","journal-title":"Antiviral Res"},{"key":"pone.0339033.ref067","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/j.jtbi.2015.07.003","article-title":"Quantifying relative within-host replication fitness in influenza virus competition experiments","volume":"382","author":"SM Petrie","year":"2015","journal-title":"J Theor Biol"},{"issue":"1","key":"pone.0339033.ref068","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1093\/infdis\/jiz418","article-title":"Impact of the Baloxavir-Resistant Polymerase Acid I38T Substitution on the Fitness of Contemporary Influenza A(H1N1)pdm09 and A(H3N2) Strains","volume":"221","author":"L Checkmahomed","year":"2020","journal-title":"J Infect Dis"},{"issue":"21","key":"pone.0339033.ref069","doi-asserted-by":"crossref","first-page":"12019","DOI":"10.1128\/JVI.00300-07","article-title":"Characterization of the early events in dengue virus cell entry by biochemical assays and single-virus tracking","volume":"81","author":"HM van der Schaar","year":"2007","journal-title":"J Virol"},{"issue":"7","key":"pone.0339033.ref070","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0007592","article-title":"The evolutionary dynamics of DENV 4 genotype I over a 60-year period","volume":"13","author":"S Sang","year":"2019","journal-title":"PLoS Negl Trop Dis"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0339033","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T18:33:31Z","timestamp":1765823611000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0339033"}},"subtitle":[],"editor":[{"given":"Julian","family":"Ruiz-Saenz","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,12,15]]},"references-count":70,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0339033","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,15]]}}}