{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:16:18Z","timestamp":1792790178793,"version":"4.5.0"},"reference-count":60,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T00:00:00Z","timestamp":1614038400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000193","name":"International Development Research Centre","doi-asserted-by":"publisher","award":["108411-001"],"award-info":[{"award-number":["108411-001"]}],"id":[{"id":"10.13039\/501100000193","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Laboratoire d'Excellence &quot;Integrative Biology of Emerging Infectious Diseases&quot;, French Government's Investissement d'Avenir program.","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}]},{"DOI":"10.13039\/501100004586","name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","doi-asserted-by":"publisher","award":["E-26\/2002.930\/2016"],"award-info":[{"award-number":["E-26\/2002.930\/2016"]}],"id":[{"id":"10.13039\/501100004586","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union's Horizon 2020 under grant agreements ZIKACTION","award":["734857"],"award-info":[{"award-number":["734857"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Intrahost genetic diversity is thought to facilitate arbovirus adaptation to changing environments and hosts, and it might also be linked to viral pathogenesis. Dengue virus serotype 2 (DENV-2) has circulated in Brazil since 1990 and is associated with severe disease and explosive outbreaks. Intending to shed light on the viral determinants for severe dengue pathogenesis, we sought to analyze the DENV-2 intrahost genetic diversity in 68 patient cases clinically classified as dengue fever (n = 31), dengue with warning signs (n = 19), and severe dengue (n = 18). Unlike previous DENV intrahost diversity studies whose approaches employed PCR, here we performed viral whole-genome deep sequencing from clinical samples with an amplicon-free approach, representing the real intrahost diversity scenario. Striking differences were detected in the viral population structure between the three clinical categories, which appear to be driven mainly by different infection times and selection pressures, rather than being linked with the clinical outcome itself. Diversity in the NS2B gene, however, showed to be constrained, irrespective of clinical outcome and infection time. Finally, 385 non-synonymous intrahost single-nucleotide variants located along the viral polyprotein, plus variants located in the untranslated regions, were consistently identified among the samples. Of them, 124 were exclusively or highly detected among cases with warning signs and among severe cases. However, there was no variant that by itself appeared to characterize the cases of greater severity, either due to its low intrahost frequency or the conservative effect on amino acid substitution. Although further studies are necessary to determine their real effect on viral proteins, this heightens the possibility of epistatic interactions. The present analysis represents an initial effort to correlate DENV-2 genetic diversity to its pathogenic potential and thus contribute to understanding the virus\u2019s dynamics within its human host.<\/jats:p>","DOI":"10.3390\/v13020349","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T20:19:36Z","timestamp":1614111576000},"page":"349","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8955-8972","authenticated-orcid":false,"given":"Maria","family":"Torres","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio de Flaviv\u00edrus, Instituto Oswaldo Cruz, Fiocruz, 21040-360 Rio de Janeiro, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcos","family":"Lima de 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Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil"},{"name":"Coordena\u00e7\u00e3o Geral dos Laborat\u00f3rios de Sa\u00fade P\u00fablica\/Secretaria de Vigil\u00e2ncia em Sa\u00fade, Minist\u00e9rio da Sa\u00fade, (CGLAB\/SVS-MS) Bras\u00edlia, 70719-040 Distrito Federal, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"Superintend\u00eancia Secretaria de Vigil\u00e2ncia em Sa\u00fade do Estado do Rio de Janeiro, 20031-142 Rio de Janeiro, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Brand\u00e3o","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central Noel Nutels\/LACEN, 20231-092 Rio de Janeiro, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6622-7043","authenticated-orcid":false,"given":"Rivaldo","family":"Ven\u00e2ncio da 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Dengue Guidelines for Diagnosis, Treatment, Prevention and Control. Available online: https:\/\/apps.who.int\/iris\/handle\/10665\/44188."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1126\/science.aan6836","article-title":"Antibody-dependent enhancement of severe dengue disease in humans","volume":"358","author":"Katzelnick","year":"2017","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1038\/nri3014","article-title":"Immunity to dengue virus: A tale of original antigenic sin and tropical cytokine storms","volume":"11","author":"Rothman","year":"2011","journal-title":"Nat. Rev. Immunol."},{"key":"ref_5","unstructured":"Knipe, D.M., and Howley, P.M. (2007). Flaviviridae: Their Viruses and Their Replication. Fields Virology, Lippincott-Raven Publishers. [5th ed.]."},{"key":"ref_6","unstructured":"Harvey, P.H., and May, R.M. (2009). The RNA Virus Quasispecies. The Evolution and Emergence of RNA Viruses, Oxford University Press."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Tsetsarkin, K.A., Vanlandingham, D.L., McGee, C.E., and Higgs, S. (2007). A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog., 3.","DOI":"10.1371\/journal.ppat.0030201"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"7289","DOI":"10.1073\/pnas.1232294100","article-title":"A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity","volume":"100","author":"Pfeiffer","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Fitzsimmons, W.J., Woods, R.J., McCrone, J.T., Woodman, A., Arnold, J.J., Yennawar, M., Evans, R., Cameron, C.E., and Lauring, A.S. (2018). A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. PLoS Biol., 16.","DOI":"10.1101\/309880"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Lee, H.Y., Perelson, A.S., Park, S.C., and Leitner, T. (2008). Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput. Biol., 4.","DOI":"10.1371\/journal.pcbi.1000240"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1086\/518895","article-title":"Hepatitis C virus dynamics during natural infection are associated with long-term histological outcome of chronic hepatitis C disease","volume":"196","author":"Sullivan","year":"2007","journal-title":"J. Infect. Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/s41564-019-0465-y","article-title":"Defective viral genomes are key drivers of the virus-host interaction","volume":"4","author":"Vignuzzi","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Cuypers, L., Libin, P.J.K., Simmonds, P., Now\u00e9, A., Mu\u00f1oz-Jord\u00e1n, J., Alcantara, L.C.J., Vandamme, A.M., Santiago, G.A., and Theys, K. (2018). Time to Harmonise Dengue Nomenclature and Classification. Viruses, 10.","DOI":"10.3390\/v10100569"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1590\/S0074-02761990000200022","article-title":"Isolation of dengue virus type 2 in Rio de Janeiro","volume":"85","author":"Nogueira","year":"1990","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_15","unstructured":"Sistema de Vigil\u00e2ncia em Sa\u00fade (SVS) (2019, June 14). Dengue Epidemiological Bulletin: Weeks 1 to 52 of 2009. Minist\u00e9rio da Sa\u00fade, Secretaria de Vigil\u00e2ncia em Sa\u00fade. Bras\u00edlia\/DF, Available online: http:\/\/portal.saude.gov.br\/portal\/arquivos\/pdf\/informe_epidemiologico_semana_1a52_09_revisado.pdf."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1002\/jmv.24464","article-title":"Dengue severity associated with age and a new lineage of dengue virus-type 2 during an outbreak in Rio De Janeiro, Brazil","volume":"88","author":"Nunes","year":"2016","journal-title":"J. Med. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Descloux, E., Cao-Lormeau, V.M., Roche, C., and De, L.X. (2009). Dengue 1 diversity and microevolution, French Polynesia 2001\u20132006: Connection with epidemiology and clinics. PLoS Negl. Trop. Dis., 3.","DOI":"10.1371\/journal.pntd.0000493"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1128\/JVI.05985-11","article-title":"High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections","volume":"86","author":"Thai","year":"2012","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"8546","DOI":"10.1128\/JVI.00736-12","article-title":"Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity","volume":"86","author":"Parameswaran","year":"2012","journal-title":"J. Virol."},{"key":"ref_20","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":"Blanc","year":"2016","journal-title":"J. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S1386-6532(99)00059-1","article-title":"Evaluation of an IgG enzyme linked immunosorbent assay for dengue diagnosis","volume":"14","author":"Miagostovich","year":"1999","journal-title":"J. Clin. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Santiago, G.A., Vergne, E., Quiles, Y., Cosme, J., Vazquez, J., Medina, J.F., Medina, F., Col\u00f3n, C., Margolis, H., and Mu\u00f1oz-Jord\u00e1n, J.L. (2013). Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus. PLoS Negl. Trop. Dis., 7.","DOI":"10.1371\/annotation\/ae27d48b-025f-47ce-8427-4af59f821ad7"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1590\/S0074-02762007005000011","article-title":"Wild dengue virus types 1, 2 and 3 viremia in rhesus monkeys","volume":"102","author":"Freire","year":"2007","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_24","first-page":"e54117","article-title":"Unbiased Deep Sequencing of RNA Viruses from Clinical Samples","volume":"113","author":"Matranga","year":"2016","journal-title":"J. Vis. Exp."},{"key":"ref_25","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":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","article-title":"Adaptive seeds tame genomic sequence comparison","volume":"21","author":"Wan","year":"2011","journal-title":"Genome Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1016\/j.cell.2015.06.007","article-title":"Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone","volume":"161","author":"Park","year":"2015","journal-title":"Cell"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"11189","DOI":"10.1093\/nar\/gks918","article-title":"LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets","volume":"40","author":"Wilm","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: Phylogenetic Model Averaging","volume":"25","author":"Posada","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/j.celrep.2017.03.076","article-title":"Mosquitoes Transmit Unique West Nile Virus Populations during Each Feeding Episode","volume":"19","author":"Grubaugh","year":"2017","journal-title":"Cell Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3299","DOI":"10.1093\/molbev\/msx248","article-title":"DnaSP 6: DNA sequence polymorphism analysis of large data sets","volume":"1","author":"Rozas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1590\/S0103-40142008000300004","article-title":"Dengue","volume":"22","year":"2008","journal-title":"Estudos Avan\u00e7ados"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Drumond, B.P., Mondini, A., Schmidt, D.J., de Morais Bronzoni, R.V., Bosch, I., and Nogueira, M.L. (2013). Circulation of different lineages of Dengue virus 2, genotype American\/Asian in Brazil: Dynamics and molecular and phylogenetic characterisation. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059422"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e190423","DOI":"10.1590\/0074-02760190423","article-title":"Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019","volume":"115","author":"Dutra","year":"2020","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1126\/science.1247749","article-title":"Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system","volume":"343","author":"Akey","year":"2014","journal-title":"Science"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Sotcheff, S., and Routh, A. (2020). Understanding Flavivirus Capsid Protein Functions: The Tip of the Iceberg. Pathogens, 9.","DOI":"10.3390\/pathogens9010042"},{"key":"ref_45","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":"Diamond","year":"2015","journal-title":"Cell"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Ng, W.C., Soto-Acosta, R., Bradrick, S.S., Garcia-Blanco, M.A., and Ooi, E.E. (2017). The 5\u2032 and 3\u2032 Untranslated Regions of the Flaviviral Genome. Viruses, 9.","DOI":"10.3390\/v9060137"},{"key":"ref_47","first-page":"46","article-title":"Viral quasispecies","volume":"479","author":"Andino","year":"2016","journal-title":"Virology"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Sim, S., Aw, P.P., Wilm, A., Teoh, G., Hue, K.D., Nguyen, N.M., Nagarajan, N., Simmons, C.P., and Hibberd, M.L. (2015). Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission. PLoS Negl. Trop. Dis., 9.","DOI":"10.1371\/journal.pntd.0004052"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.chom.2016.03.002","article-title":"Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching","volume":"19","author":"Grubaugh","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.chom.2017.08.003","article-title":"Intrahost Selection Pressures Drive Rapid Dengue Virus Microevolution in Acute Human Infections","volume":"22","author":"Parameswaran","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.3389\/fmicb.2020.01371","article-title":"Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology","volume":"11","author":"Ko","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.virol.2016.03.017","article-title":"Viral quasispecies complexity measures","volume":"493","author":"Gregori","year":"2016","journal-title":"Virology"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12985-015-0456-4","article-title":"Recombinant Dengue virus protein NS2B alters membrane permeability in different membrane models","volume":"13","author":"Shrivastava","year":"2016","journal-title":"Virol. J."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3543","DOI":"10.1128\/JVI.74.8.3543-3547.2000","article-title":"Memory in viral quasispecies","volume":"74","author":"Arias","year":"2000","journal-title":"J. Virol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.gene.2006.07.037","article-title":"Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo","volume":"384","author":"Briones","year":"2006","journal-title":"Gene"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1016\/j.virol.2015.08.009","article-title":"Flavivirus sfRNA suppresses antiviral RNA interference in cultured cells and mosquitoes and directly interacts with the RNAi machinery","volume":"485","author":"Moon","year":"2015","journal-title":"Virology"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"11038","DOI":"10.1073\/pnas.1919287117","article-title":"Positive epistasis between viral polymerase and the 3\u2032 untranslated region of its genome reveals the epidemiologic fitness of dengue virus","volume":"117","author":"Syenina","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"18404","DOI":"10.1038\/s41598-020-75042-4","article-title":"Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection","volume":"10","author":"Bellone","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1016\/j.jmb.2004.08.003","article-title":"Positive selection of synonymous mutations in vesicular stomatitis virus","volume":"342","author":"Novella","year":"2004","journal-title":"J. Mol. Biol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Nougairede, A., De Fabritus, L., Aubry, F., Gould, E.A., Holmes, E.C., and de Lamballerie, X. (2013). Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. PLoS Pathog., 9.","DOI":"10.1371\/journal.ppat.1003172"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/2\/349\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:27:01Z","timestamp":1760160421000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/2\/349"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,23]]},"references-count":60,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2]]}},"alternative-id":["v13020349"],"URL":"https:\/\/doi.org\/10.3390\/v13020349","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,23]]}}}