{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T19:20:38Z","timestamp":1790968838287,"version":"4.1.0"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,6,3]],"date-time":"2020-06-03T00:00:00Z","timestamp":1591142400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,6,3]],"date-time":"2020-06-03T00:00:00Z","timestamp":1591142400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Dengue is one of the most widespread vector-borne viral diseases in the world. However, the size, heterogeneity, and temporal dynamics of the cell-associated viral reservoir during acute dengue virus (DENV) infection remains unclear. In this study, we analyzed cells infected\n                    <jats:italic>in vitro<\/jats:italic>\n                    with DENV and PBMC from an individual experiencing a natural DENV infection utilizing 5\u2019 capture single cell RNA sequencing (scRNAseq). Both positive- and negative-sense DENV RNA was detected in reactions containing either an oligo(dT) primer alone, or in reactions supplemented with a DENV-specific primer. The addition of a DENV-specific primer did not increase the total amount of DENV RNA captured or the fraction of cells identified as containing DENV RNA. However, inclusion of a DENV-specific cDNA primer did increase the viral genome coverage immediately 5\u2019 to the primer binding site. Furthermore, while the majority of intracellular DENV sequence captured in this analysis mapped to the 5\u2019 end of the viral genome, distinct patterns of enhanced coverage within the DENV polyprotein coding region were observed. The 5\u2019 capture scRNAseq analysis of PBMC not only recapitulated previously published reports by detecting virally infected memory and na\u00efve B cells, but also identified cell-associated genomic variants not observed in contemporaneous serum samples. These results demonstrate that oligo(dT) primed 5\u2019 capture scRNAseq can detect DENV RNA and quantify virus-infected cells in physiologically relevant conditions, and provides insight into viral sequence variability within infected cells.\n                  <\/jats:p>","DOI":"10.1038\/s41598-020-65939-5","type":"journal-article","created":{"date-parts":[[2020,6,3]],"date-time":"2020-06-03T11:01:45Z","timestamp":1591182105000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Analysis of cell-associated DENV RNA by oligo(dT) primed 5\u2019 capture scRNAseq"],"prefix":"10.1038","volume":"10","author":[{"given":"Mark A.","family":"Sanborn","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaitlin","family":"Victor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hayden","family":"Siegfried","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Fung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan L.","family":"Rothman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anon","family":"Srikiatkhachorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Fernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damon","family":"Ellison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard G.","family":"Jarman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather","family":"Friberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irina","family":"Maljkovic Berry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey R.","family":"Currier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam T.","family":"Waickman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,3]]},"reference":[{"key":"65939_CR1","doi-asserted-by":"publisher","first-page":"571","DOI":"10.4269\/ajtmh.1989.40.571","volume":"40","author":"DJ Gubler","year":"1989","unstructured":"Gubler, D. J. Aedes aegypti and Aedes aegypti-borne disease control in the 1990s: top down or bottom up. Charles Franklin Craig Lecture. Am J Trop Med Hyg 40, 571\u2013578, https:\/\/doi.org\/10.4269\/ajtmh.1989.40.571 (1989).","journal-title":"Am J Trop Med Hyg"},{"key":"65939_CR2","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1038\/nature12060","volume":"496","author":"S Bhatt","year":"2013","unstructured":"Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504\u2013507, https:\/\/doi.org\/10.1038\/nature12060 (2013).","journal-title":"Nature"},{"key":"65939_CR3","doi-asserted-by":"publisher","first-page":"200","DOI":"10.4269\/ajtmh.2011.10-0503","volume":"84","author":"DS Shepard","year":"2011","unstructured":"Shepard, D. S., Coudeville, L., Halasa, Y. A., Zambrano, B. & Dayan, G. H. Economic impact of dengue illness in the Americas. Am J Trop Med Hyg 84, 200\u2013207, https:\/\/doi.org\/10.4269\/ajtmh.2011.10-0503 (2011).","journal-title":"Am J Trop Med Hyg"},{"key":"65939_CR4","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1016\/S0140-6736(14)60572-9","volume":"385","author":"MG Guzman","year":"2015","unstructured":"Guzman, M. G. & Harris, E. Dengue. Lancet 385, 453\u2013465, https:\/\/doi.org\/10.1016\/S0140-6736(14)60572-9 (2015).","journal-title":"Lancet"},{"key":"65939_CR5","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1093\/oxfordjournals.aje.a113932","volume":"120","author":"N Sangkawibha","year":"1984","unstructured":"Sangkawibha, N. et al. Risk factors in dengue shock syndrome: a prospective epidemiologic study in Rayong, Thailand. I. The 1980 outbreak. Am J Epidemiol 120, 653\u2013669, https:\/\/doi.org\/10.1093\/oxfordjournals.aje.a113932 (1984).","journal-title":"Am J Epidemiol"},{"key":"65939_CR6","doi-asserted-by":"publisher","first-page":"566","DOI":"10.4269\/ajtmh.1997.56.566","volume":"56","author":"S Thein","year":"1997","unstructured":"Thein, S. et al. Risk factors in dengue shock syndrome. Am J Trop Med Hyg 56, 566\u2013572, https:\/\/doi.org\/10.4269\/ajtmh.1997.56.566 (1997).","journal-title":"Am J Trop Med Hyg"},{"key":"65939_CR7","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.4269\/ajtmh.13-0424","volume":"89","author":"IK Yoon","year":"2013","unstructured":"Yoon, I. K. et al. Characteristics of mild dengue virus infection in Thai children. Am J Trop Med Hyg 89, 1081\u20131087, https:\/\/doi.org\/10.4269\/ajtmh.13-0424 (2013).","journal-title":"Am J Trop Med Hyg"},{"key":"65939_CR8","doi-asserted-by":"publisher","first-page":"2773","DOI":"10.1007\/s00018-010-0357-z","volume":"67","author":"IA Rodenhuis-Zybert","year":"2010","unstructured":"Rodenhuis-Zybert, I. A., Wilschut, J. & Smit, J. M. Dengue virus life cycle: viral and host factors modulating infectivity. Cell Mol Life Sci 67, 2773\u20132786, https:\/\/doi.org\/10.1007\/s00018-010-0357-z (2010).","journal-title":"Cell Mol Life Sci"},{"key":"65939_CR9","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1086\/518007","volume":"195","author":"JL Kyle","year":"2007","unstructured":"Kyle, J. L., Beatty, P. R. & Harris, E. Dengue virus infects macrophages and dendritic cells in a mouse model of infection. J Infect Dis 195, 1808\u20131817, https:\/\/doi.org\/10.1086\/518007 (2007).","journal-title":"J Infect Dis"},{"key":"65939_CR10","doi-asserted-by":"publisher","first-page":"e17","DOI":"10.1371\/journal.ppat.0040017","volume":"4","author":"JL Miller","year":"2008","unstructured":"Miller, J. L. et al. The mannose receptor mediates dengue virus infection of macrophages. PLoS Pathog 4, e17, https:\/\/doi.org\/10.1371\/journal.ppat.0040017 (2008).","journal-title":"PLoS Pathog"},{"key":"65939_CR11","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1038\/77553","volume":"6","author":"SJ Wu","year":"2000","unstructured":"Wu, S. J. et al. Human skin Langerhans cells are targets of dengue virus infection. Nat Med 6, 816\u2013820, https:\/\/doi.org\/10.1038\/77553 (2000).","journal-title":"Nat Med"},{"key":"65939_CR12","doi-asserted-by":"publisher","first-page":"e1004541","DOI":"10.1371\/journal.ppat.1004541","volume":"10","author":"MA Schmid","year":"2014","unstructured":"Schmid, M. A. & Harris, E. Monocyte recruitment to the dermis and differentiation to dendritic cells increases the targets for dengue virus replication. PLoS Pathog 10, e1004541, https:\/\/doi.org\/10.1371\/journal.ppat.1004541 (2014).","journal-title":"PLoS Pathog"},{"key":"65939_CR13","doi-asserted-by":"publisher","first-page":"e51335","DOI":"10.1371\/journal.pone.0051335","volume":"7","author":"A Srikiatkhachorn","year":"2012","unstructured":"Srikiatkhachorn, A. et al. Dengue viral RNA levels in peripheral blood mononuclear cells are associated with disease severity and preexisting dengue immune status. PLoS One 7, e51335, https:\/\/doi.org\/10.1371\/journal.pone.0051335 (2012).","journal-title":"PLoS One"},{"key":"65939_CR14","first-page":"1352","volume":"41","author":"MO Baclig","year":"2010","unstructured":"Baclig, M. O. et al. Flow cytometric analysis of dengue virus-infected cells in peripheral blood. Southeast Asian J Trop Med Public Health 41, 1352\u20131358 (2010).","journal-title":"Southeast Asian J Trop Med Public Health"},{"key":"65939_CR15","first-page":"718","volume":"30","author":"AD King","year":"1999","unstructured":"King, A. D. et al. B cells are the principal circulating mononuclear cells infected by dengue virus. Southeast Asian J Trop Med Public Health 30, 718\u2013728 (1999).","journal-title":"Southeast Asian J Trop Med Public Health"},{"key":"65939_CR16","doi-asserted-by":"publisher","DOI":"10.1038\/s12276-018-0071-8","volume":"50","author":"B Hwang","year":"2018","unstructured":"Hwang, B., Lee, J. H., Bang, D. & Single-cell, R. N. A. sequencing technologies and bioinformatics pipelines. Exp Mol Med 50, 96, https:\/\/doi.org\/10.1038\/s12276-018-0071-8 (2018).","journal-title":"Exp Mol Med"},{"key":"65939_CR17","doi-asserted-by":"publisher","unstructured":"Russell, A. B., Elshina, E., Kowalsky, J. R., Te Velthuis, A. J. W. & Bloom, J. D. Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity. J Virol 93, https:\/\/doi.org\/10.1128\/JVI.00500-19 (2019).","DOI":"10.1128\/JVI.00500-19"},{"key":"65939_CR18","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1016\/j.cels.2018.05.008","volume":"6","author":"Y Steuerman","year":"2018","unstructured":"Steuerman, Y. et al. Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing. Cell Syst 6, 679\u2013691 e674, https:\/\/doi.org\/10.1016\/j.cels.2018.05.008 (2018).","journal-title":"Cell Syst"},{"key":"65939_CR19","doi-asserted-by":"publisher","unstructured":"O\u2019Neal, J. T. et al. West Nile Virus-Inclusive Single-Cell RNA Sequencing Reveals Heterogeneity in the Type I Interferon Response within Single Cells. J Virol 93, https:\/\/doi.org\/10.1128\/JVI.01778-18 (2019).","DOI":"10.1128\/JVI.01778-18"},{"key":"65939_CR20","doi-asserted-by":"publisher","unstructured":"Zanini, F., Pu, S. Y., Bekerman, E., Einav, S. & Quake, S. R. Single-cell transcriptional dynamics of flavivirus infection. Elife 7 https:\/\/doi.org\/10.7554\/eLife.32942 (2018).","DOI":"10.7554\/eLife.32942"},{"key":"65939_CR21","doi-asserted-by":"publisher","first-page":"E12363","DOI":"10.1073\/pnas.1813819115","volume":"115","author":"F Zanini","year":"2018","unstructured":"Zanini, F. et al. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proc Natl Acad Sci USA 115, E12363\u2013E12369, https:\/\/doi.org\/10.1073\/pnas.1813819115 (2018).","journal-title":"Proc Natl Acad Sci USA"},{"key":"65939_CR22","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/nprot.2014.006","volume":"9","author":"S Picelli","year":"2014","unstructured":"Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq. 2. Nat Protoc 9, 171\u2013181, https:\/\/doi.org\/10.1038\/nprot.2014.006 (2014).","journal-title":"Nat Protoc"},{"key":"65939_CR23","doi-asserted-by":"publisher","first-page":"317","DOI":"10.3389\/fgene.2019.00317","volume":"10","author":"G Chen","year":"2019","unstructured":"Chen, G. & Ning, B. & Shi, T. Single-Cell RNA-Seq Technologies and Related Computational Data Analysis. Front Genet 10, 317, https:\/\/doi.org\/10.3389\/fgene.2019.00317 (2019).","journal-title":"Front Genet"},{"key":"65939_CR24","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/0042-6822(81)90654-1","volume":"111","author":"GR Cleaves","year":"1981","unstructured":"Cleaves, G. R., Ryan, T. E. & Schlesinger, R. W. Identification and characterization of type 2 dengue virus replicative intermediate and replicative form RNAs. Virology 111, 73\u201383, https:\/\/doi.org\/10.1016\/0042-6822(81)90654-1 (1981).","journal-title":"Virology"},{"key":"65939_CR25","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1146\/annurev.mi.44.100190.003245","volume":"44","author":"TJ Chambers","year":"1990","unstructured":"Chambers, T. J., Hahn, C. S., Galler, R. & Rice, C. M. Flavivirus genome organization, expression, and replication. Annu Rev Microbiol 44, 649\u2013688, https:\/\/doi.org\/10.1146\/annurev.mi.44.100190.003245 (1990).","journal-title":"Annu Rev Microbiol"},{"key":"65939_CR26","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/j.chom.2017.08.003","volume":"22","author":"P Parameswaran","year":"2017","unstructured":"Parameswaran, P. et al. Intrahost Selection Pressures Drive Rapid Dengue Virus Microevolution in Acute Human Infections. Cell Host Microbe 22, 400\u2013410 e405, https:\/\/doi.org\/10.1016\/j.chom.2017.08.003 (2017).","journal-title":"Cell Host Microbe"},{"key":"65939_CR27","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1007\/s11904-015-0265-9","volume":"12","author":"MM Bednar","year":"2015","unstructured":"Bednar, M. M. et al. Compartmentalization, Viral. Evolution, and Viral Latency of HIV in the CNS. Curr HIV\/AIDS Rep 12, 262\u2013271, https:\/\/doi.org\/10.1007\/s11904-015-0265-9 (2015).","journal-title":"Evolution, and Viral Latency of HIV in the CNS. Curr HIV\/AIDS Rep"},{"issue":"Pt 12","key":"65939_CR28","doi-asserted-by":"publisher","first-page":"2173","DOI":"10.1099\/0022-1317-65-12-2173","volume":"65","author":"J Blok","year":"1984","unstructured":"Blok, J., Henchal, E. A. & Gorman, B. M. Comparison of dengue viruses and some other flaviviruses by cDNA-RNA hybridization analysis and detection of a close relationship between dengue virus serotype 2 and Edge Hill virus. J Gen Virol 65(Pt 12), 2173\u20132181, https:\/\/doi.org\/10.1099\/0022-1317-65-12-2173 (1984).","journal-title":"J Gen Virol"},{"key":"65939_CR29","doi-asserted-by":"publisher","first-page":"6152","DOI":"10.1073\/pnas.092140899","volume":"99","author":"DK Nam","year":"2002","unstructured":"Nam, D. K. et al. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci USA 99, 6152\u20136156, https:\/\/doi.org\/10.1073\/pnas.092140899 (2002).","journal-title":"Proc Natl Acad Sci USA"},{"key":"65939_CR30","doi-asserted-by":"publisher","first-page":"888","DOI":"10.1093\/nar\/27.3.888","volume":"27","author":"JH Graber","year":"1999","unstructured":"Graber, J. H., Cantor, C. R., Mohr, S. C. & Smith, T. F. Genomic detection of new yeast pre-mRNA 3\u2019-end-processing signals. Nucleic Acids Res 27, 888\u2013894, https:\/\/doi.org\/10.1093\/nar\/27.3.888 (1999).","journal-title":"Nucleic Acids Res"},{"key":"65939_CR31","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1101\/gr.10.7.1001","volume":"10","author":"E Beaudoing","year":"2000","unstructured":"Beaudoing, E., Freier, S., Wyatt, J. R., Claverie, J. M. & Gautheret, D. Patterns of variant polyadenylation signal usage in human genes. Genome Res 10, 1001\u20131010, https:\/\/doi.org\/10.1101\/gr.10.7.1001 (2000).","journal-title":"Genome Res"},{"key":"65939_CR32","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1101\/gr.190501","volume":"11","author":"E Beaudoing","year":"2001","unstructured":"Beaudoing, E. & Gautheret, D. Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res 11, 1520\u20131526, https:\/\/doi.org\/10.1101\/gr.190501 (2001).","journal-title":"Genome Res"},{"key":"65939_CR33","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.ymeth.2019.05.016","volume":"176","author":"Kevin R. Roy","year":"2020","unstructured":"Roy, K. R. & Chanfreau, G. F. Robust mapping of polyadenylated and non-polyadenylated RNA 3\u2019 ends at nucleotide resolution by 3\u2019-end sequencing. Methods, https:\/\/doi.org\/10.1016\/j.ymeth.2019.05.016 (2019).","journal-title":"Methods"},{"key":"65939_CR34","doi-asserted-by":"publisher","first-page":"3433","DOI":"10.1093\/nar\/26.14.3433","volume":"26","author":"GP Harrison","year":"1998","unstructured":"Harrison, G. P., Mayo, M. S., Hunter, E. & Lever, A. M. Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5\u2019 and 3\u2019 of the catalytic site. Nucleic Acids Res 26, 3433\u20133442, https:\/\/doi.org\/10.1093\/nar\/26.14.3433 (1998).","journal-title":"Nucleic Acids Res"},{"key":"65939_CR35","doi-asserted-by":"crossref","first-page":"7423","DOI":"10.1016\/S0021-9258(20)89464-2","volume":"266","author":"JJ DeStefano","year":"1991","unstructured":"DeStefano, J. J. et al. Polymerization and RNase H activities of the reverse transcriptases from avian myeloblastosis, human immunodeficiency, and Moloney murine leukemia viruses are functionally uncoupled. J Biol Chem 266, 7423\u20137431 (1991).","journal-title":"J Biol Chem"},{"key":"65939_CR36","doi-asserted-by":"publisher","first-page":"3930","DOI":"10.1128\/JVI.70.6.3930-3937.1996","volume":"70","author":"R Men","year":"1996","unstructured":"Men, R., Bray, M., Clark, D., Chanock, R. M. & Lai, C. J. Dengue type 4 virus mutants containing deletions in the 3\u2019 noncoding region of the RNA genome: analysis of growth restriction in cell culture and altered viremia pattern and immunogenicity in rhesus monkeys. J Virol 70, 3930\u20133937 (1996).","journal-title":"J Virol"},{"key":"65939_CR37","doi-asserted-by":"publisher","first-page":"3291","DOI":"10.1099\/vir.0.82182-0","volume":"87","author":"TA Romero","year":"2006","unstructured":"Romero, T. A., Tumban, E., Jun, J., Lott, W. B. & Hanley, K. A. Secondary structure of dengue virus type 4 3\u2019 untranslated region: impact of deletion and substitution mutations. J Gen Virol 87, 3291\u20133296, https:\/\/doi.org\/10.1099\/vir.0.82182-0 (2006).","journal-title":"J Gen Virol"},{"key":"65939_CR38","doi-asserted-by":"publisher","first-page":"1748","DOI":"10.1099\/vir.0.82455-0","volume":"88","author":"W Sirigulpanit","year":"2007","unstructured":"Sirigulpanit, W., Kinney, R. M. & Leardkamolkarn, V. Substitution or deletion mutations between nt 54 and 70 in the 5\u2019 non-coding region of dengue type 2 virus produce variable effects on virus viability. J Gen Virol 88, 1748\u20131752, https:\/\/doi.org\/10.1099\/vir.0.82455-0 (2007).","journal-title":"J Gen Virol"},{"key":"65939_CR39","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1099\/vir.0.19462-0","volume":"85","author":"C Thurner","year":"2004","unstructured":"Thurner, C., Witwer, C., Hofacker, I. L. & Stadler, P. F. Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol 85, 1113\u20131124, https:\/\/doi.org\/10.1099\/vir.0.19462-0 (2004).","journal-title":"J Gen Virol"},{"key":"65939_CR40","doi-asserted-by":"publisher","first-page":"11513","DOI":"10.1073\/pnas.1716689115","volume":"115","author":"EA Dethoff","year":"2018","unstructured":"Dethoff, E. A. et al. Pervasive tertiary structure in the dengue virus RNA genome. Proc Natl Acad Sci USA 115, 11513\u201311518, https:\/\/doi.org\/10.1073\/pnas.1716689115 (2018).","journal-title":"Proc Natl Acad Sci USA"},{"key":"65939_CR41","doi-asserted-by":"publisher","first-page":"2170","DOI":"10.1128\/JVI.80.5.2170-2182.2006","volume":"80","author":"K Clyde","year":"2006","unstructured":"Clyde, K. & Harris, E. RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication. J Virol 80, 2170\u20132182, https:\/\/doi.org\/10.1128\/JVI.80.5.2170-2182.2006 (2006).","journal-title":"J Virol"},{"key":"65939_CR42","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.virol.2008.06.034","volume":"379","author":"K Clyde","year":"2008","unstructured":"Clyde, K., Barrera, J. & Harris, E. The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis. Virology 379, 314\u2013323, https:\/\/doi.org\/10.1016\/j.virol.2008.06.034 (2008).","journal-title":"Virology"},{"key":"65939_CR43","doi-asserted-by":"publisher","first-page":"6804","DOI":"10.1128\/JVI.00243-13","volume":"87","author":"ZY Liu","year":"2013","unstructured":"Liu, Z. Y. et al. Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization. J Virol 87, 6804\u20136818, https:\/\/doi.org\/10.1128\/JVI.00243-13 (2013).","journal-title":"J Virol"},{"key":"65939_CR44","doi-asserted-by":"crossref","first-page":"971","DOI":"10.4049\/jimmunol.134.2.971","volume":"134","author":"DN Howell","year":"1985","unstructured":"Howell, D. N., Andreotti, P. E., Dawson, J. R. & Cresswell, P. Natural killing target antigens as inducers of interferon: studies with an immunoselected, natural killing-resistant human T lymphoblastoid cell line. J Immunol 134, 971\u2013976 (1985).","journal-title":"J Immunol"},{"key":"65939_CR45","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1086\/514048","volume":"176","author":"DW Vaughn","year":"1997","unstructured":"Vaughn, D. W. et al. Dengue in the early febrile phase: viremia and antibody responses. J Infect Dis 176, 322\u2013330, https:\/\/doi.org\/10.1086\/514048 (1997).","journal-title":"J Infect Dis"},{"key":"65939_CR46","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1086\/514047","volume":"176","author":"S Kalayanarooj","year":"1997","unstructured":"Kalayanarooj, S. et al. Early clinical and laboratory indicators of acute dengue illness. J Infect Dis 176, 313\u2013321, https:\/\/doi.org\/10.1086\/514047 (1997).","journal-title":"J Infect Dis"},{"key":"65939_CR47","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1086\/340365","volume":"185","author":"DH Libraty","year":"2002","unstructured":"Libraty, D. H. et al. Differing influences of virus burden and immune activation on disease severity in secondary dengue-3 virus infections. J Infect Dis 185, 1213\u20131221, https:\/\/doi.org\/10.1086\/340365 (2002).","journal-title":"J Infect Dis"},{"key":"65939_CR48","doi-asserted-by":"publisher","first-page":"418","DOI":"10.4269\/ajtmh.1989.40.418","volume":"40","author":"BL Innis","year":"1989","unstructured":"Innis, B. L. et al. An enzyme-linked immunosorbent assay to characterize dengue infections where dengue and Japanese encephalitis co-circulate. Am J Trop Med Hyg 40, 418\u2013427, https:\/\/doi.org\/10.4269\/ajtmh.1989.40.418 (1989).","journal-title":"Am J Trop Med Hyg"},{"key":"65939_CR49","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049","volume":"8","author":"GX Zheng","year":"2017","unstructured":"Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun 8, 14049, https:\/\/doi.org\/10.1038\/ncomms14049 (2017).","journal-title":"Nat Commun"},{"key":"65939_CR50","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive Integration of Single-Cell Data. Cell 177, 1888\u20131902 e1821, https:\/\/doi.org\/10.1016\/j.cell.2019.05.031 (2019).","journal-title":"Cell"},{"key":"65939_CR51","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","volume":"36","author":"A Butler","year":"2018","unstructured":"Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36, 411\u2013420, https:\/\/doi.org\/10.1038\/nbt.4096 (2018).","journal-title":"Nat Biotechnol"},{"key":"65939_CR52","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1101\/gr.209601.116","volume":"27","author":"T Smith","year":"2017","unstructured":"Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res 27, 491\u2013499, https:\/\/doi.org\/10.1101\/gr.209601.116 (2017).","journal-title":"Genome Res"},{"key":"65939_CR53","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842, https:\/\/doi.org\/10.1093\/bioinformatics\/btq033 (2010).","journal-title":"Bioinformatics"},{"key":"65939_CR54","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352 (2009).","journal-title":"Bioinformatics"},{"key":"65939_CR55","doi-asserted-by":"publisher","first-page":"1302","DOI":"10.1126\/science.aaj9384","volume":"355","author":"H Salje","year":"2017","unstructured":"Salje, H. et al. Dengue diversity across spatial and temporal scales: Local structure and the effect of host population size. Science 355, 1302\u20131306, https:\/\/doi.org\/10.1126\/science.aaj9384 (2017).","journal-title":"Science"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-65939-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-65939-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-65939-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,1]],"date-time":"2023-10-01T18:14:23Z","timestamp":1696184063000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-65939-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,3]]},"references-count":55,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["65939"],"URL":"https:\/\/doi.org\/10.1038\/s41598-020-65939-5","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.01.23.917757","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,3]]},"assertion":[{"value":"20 February 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 June 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A.T.W. reports grants from Military Infectious Disease Research Program, during the conduct of the study. A.L.R. reports grants from National Institute of Allergy and Infectious Diseases, during the conduct of the study. All other authors declare no competing interests","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"9047"}}