{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T06:12:34Z","timestamp":1792131154441,"version":"4.4.0"},"reference-count":44,"publisher":"National Academy of Sciences","issue":"52","license":[{"start":{"date-parts":[[2018,12,7]],"date-time":"2018-12-07T00:00:00Z","timestamp":1544140800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004410","name":"European Molecular Biology Organisation","doi-asserted-by":"crossref","award":["ALTF 269-2016"],"award-info":[{"award-number":["ALTF 269-2016"]}],"id":[{"id":"10.13039\/100004410","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["5U19AI057229-15"],"award-info":[{"award-number":["5U19AI057229-15"]}]},{"DOI":"10.13039\/100000900","name":"California Institute for Regenerative Medicine","doi-asserted-by":"publisher","award":["GC1R-06673"],"award-info":[{"award-number":["GC1R-06673"]}],"id":[{"id":"10.13039\/100000900","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Stanford Advanced Residency Training at Stanford","award":["N.A."],"award-info":[{"award-number":["N.A."]}]},{"name":"Stanford Bio-X Interdisciplinary Initiatives Seed Grants","award":["N.A."],"award-info":[{"award-number":["N.A."]}]},{"name":"Stanford Translational Research and Applied Medicine","award":["N.A."],"award-info":[{"award-number":["N.A."]}]},{"name":"Stanford SPARK","award":["N.A."],"award-info":[{"award-number":["N.A."]}]},{"name":"Stanford Child Health Research Institute","award":["N.A."],"award-info":[{"award-number":["N.A."]}]},{"name":"Stanford Institute for Immunity, Transplantation, and Infection","award":["N.A."],"award-info":[{"award-number":["N.A."]}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2018,12,26]]},"abstract":"<jats:p>\n                    Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here, we applied virus-inclusive single-cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls and to characterize distinct leukocyte subtypes that harbor viral RNA (vRNA). Multiple IFN response genes, particularly MX2 in naive B cells and CD163 in CD14\n                    <jats:sup>+<\/jats:sup>\n                    CD16\n                    <jats:sup>+<\/jats:sup>\n                    monocytes, were up-regulated in a cell-specific manner before progression to SD. The majority of vRNA-containing cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and various antiviral genes, followed by monocytes. Bystander, non-vRNA\u2013containing B cells also demonstrated immune activation, and IgG1 plasmablasts from two patients exhibited clonal expansions. Lastly, assembly of the DENV genome sequence revealed diversity at unexpected sites. This study presents a multifaceted molecular elucidation of natural dengue infection in humans with implications for any tissue and viral infection and proposes candidate biomarkers for prediction of SD.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1813819115","type":"journal-article","created":{"date-parts":[[2018,12,7]],"date-time":"2018-12-07T20:55:31Z","timestamp":1544216131000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":174,"title":["Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue"],"prefix":"10.1073","volume":"115","author":[{"given":"Fabio","family":"Zanini","sequence":"first","affiliation":[{"name":"Department of Bioengineering, Stanford University, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makeda L.","family":"Robinson","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;"},{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek","family":"Croote","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanford University, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malaya Kumar","family":"Sahoo","sequence":"additional","affiliation":[{"name":"Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Maria","family":"Sanz","sequence":"additional","affiliation":[{"name":"Clinical Research Center, Fundaci\u00f3n Valle del Lili, Cali 760026, Colombia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eliana","family":"Ortiz-Lasso","sequence":"additional","affiliation":[{"name":"Pathology and Laboratory Department, Fundaci\u00f3n Valle del Lili, Cali 760026, Colombia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludwig Luis","family":"Albornoz","sequence":"additional","affiliation":[{"name":"Pathology and Laboratory Department, Fundaci\u00f3n Valle del Lili, Cali 760026, Colombia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Rosso","sequence":"additional","affiliation":[{"name":"Clinical Research Center, Fundaci\u00f3n Valle del Lili, Cali 760026, Colombia;"},{"name":"Division of Infectious Diseases, Department of Internal Medicine, Fundaci\u00f3n Valle del Lili, Cali 760026, Colombia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose G.","family":"Montoya","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leslie","family":"Goo","sequence":"additional","affiliation":[{"name":"Chan Zuckerberg Biohub, San Francisco, CA 94158;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8751-4810","authenticated-orcid":false,"given":"Benjamin A.","family":"Pinsky","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305;"},{"name":"Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen R.","family":"Quake","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanford University, Stanford, CA 94305;"},{"name":"Chan Zuckerberg Biohub, San Francisco, CA 94158;"},{"name":"Department of Applied Physics, Stanford University, Stanford, CA 94305"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shirit","family":"Einav","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;"},{"name":"Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2018,12,7]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/nature12060","article-title":"The global distribution and burden of dengue","volume":"496","author":"Bhatt S","year":"2013","unstructured":"S Bhatt, , The global distribution and burden of dengue. 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J Pak Med Assoc 63, 670\u2013674 (2013).","journal-title":"J Pak Med Assoc"},{"key":"e_1_3_4_4_2","volume-title":"Dengue Guidelines for Diagnosis, Treatment, Prevention and Control: New Edition","author":"World Health Organization","year":"2009","unstructured":"; World Health Organization Dengue Guidelines for Diagnosis, Treatment, Prevention and Control: New Edition (World Health Organization Press, Geneva, 2009)."},{"key":"e_1_3_4_5_2","unstructured":"; World Health Organization Dengue and Severe Dengue . Available at www.who.int\/news-room\/fact-sheets\/detail\/dengue-and-severe-dengue. Accessed June 25 2018. 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