Single-cell temporal analysis of natural dengue infection reveals skin-homing lymphocyte expansion one day before defervescence.

Effective clinical management of acute dengue virus (DENV) infection relies on the timing of suitable treatments during the disease progression. We analyzed single-cell transcriptomic profiles of the peripheral blood mononuclear cell samples from two DENV patients, collected daily during acute phase and also at convalescence. Key immune cell types demonstrated different dynamic responses over the course of the infection. On the day before defervescence (Day -1), we observed the peak expression of several prominent genes in the adaptive immunological pathways. We also characterized unique effector T cell clusters that expressed skin-homing signature genes at Day -1, whereas upregulation of skin and gut homing genes was also observed in plasma cells and plasmablasts during the febrile period. This work provides an overview of unique molecular dynamics that signify the entry of the critical phase, and the findings could improve the patient management of DENV infection

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.

We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells' potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.This work was supported by the Wellcome Sanger Institute core funding (WT206194) and the Wellcome Strategic Scientific Support award “Pilot projects for the Human Cell Atlas” (WT211276/Z/18/Z), a Seed Network grant from the Chan Zuckerberg Initiative to P.B., T.D., T.E.D., O.E., P.H., N.H., N.K., M.K., K.B.M., A.M., M.C.N., M.N., D.P., J.R., P.R.T., S.Q., A.R., O.R., M.S., J.S., J.G.S., C.E.S., H.B.S., D.S., A.T., J.W. and K.Z. and by the European Union’s H2020 research and innovation program under grant agreement No 874656 (discovAIR) to P.B., A.B., M.K., S.L., J.L., K.B.M., M.C.N., K.S.P., C.S., H.B.S., J.S., F.J.T. and M.vd.B. W.S. acknowledges funding from the Newton Fund, Medical Research Council (MRC), The Thailand Research Fund (TRF), and Thailand’s National Science and Technology Development Agency (NSTDA). M.C.N acknowledges funding from GSK Ltd, Netherlands Lung Foundation project no. 5.1.14.020 and 4.1.18.226. T.D. acknowledges funding from HubMap consortium and Stanford Child Health Research Institute- Woods Family Faculty Scholarship. T.E.D. acknowledges funding from HubMap. P.H. acknowledges funding from LENDULET-BIOMAG Grant (2018-342) and the European Regional Development Funds (GINOP-2.3.2-15-2016-00006, GINOP-2.3.2-15-2016-00026, GINOP-2.3.2-15-2016-00037). J.L.B. acknowledges funding from Medical Research Council (MRC), and the UK Regenerative Medicine Platform (MR/ 5005579/1). P.B. acknowledges funding from Fondation pour la Recherche Médicale (DEQ20180339158), Agence Nationale de la Recherche (UCAJEDI, ANR-15-IDEX-01; SAHARRA, ANR-19-CE14-0027; France Génomique, ANR-10-INBS-09-03), and Conseil Départemental des Alpes Maritimes (2016-294DGADSH-CV; 2019-390DGADSH-CV). N.E.B. and J.K. acknowledge funding from NIH grant R01HL145372 and DOD grant W81XWH1910416. I.G. acknowledges funding from NIH (5R24HD000836) and the Eunice Kennedy Shriver National Institute of Child Health and Human. N.H., J.G.S. and C.E.S. acknowledge funding by the Leducq foundation. N.H. is recipient of an ERC Advanced Grant. J.K. acknowledges funding from NIH grant K08HL130595 and the Doris Duke Charitable Foundation. N.K. acknowledges funding from NIH grants R01HL127349, U01HL145567 and an unrestricted grant from Three Lakes Foundation. M.K. acknowledges HHMI and Wall Center for Pulmonary Vascular Disease. H.L. acknowledges funding from National Research Foundation of Korea. K.M. acknowledges funding from Wellcome Trust. A.M. acknowledges funding from NIH grants HL135124, AG049665 and AI135964. M.Z.N. acknowledges funding from Rutherford Fund Fellowship allocated by the Medical Research Council and the UK Regenerative Medicine Platform (MR/ 5005579/1 to M.Z.N.). M.Z.N. and M.Y. have been funded by the Rosetrees Grant (Grant number M899). M.N. acknowledges funding from a BHF/DZHK grant and British Heart Foundation (PG/16/47/32156). J.O.-M. acknowledges funding from Richard and Susan Smith Family Foundation. D.P. acknowledges funding from Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center. J.P. acknowledges funding from National Health and Medical Research Council. P.R.T. acknowledges funding from R01HL146557 from NHLBI/NIH. E.L.R. acknowledges funding from MRC MR/P009581/1 and MR/SO35907/1. A.R. and O. R. acknowledge HHMI, the Klarman Cell Observatory, and the Manton Foundation. K.S.-P. acknowledges NIHR Cambridge Biomedical Research Centre. C.S. acknowledges Swedish research Council, Swedish Cancer Society, and CPI. H.B.S. acknowledges German Center for Lung Research and Helmholtz Association. J.S. acknowledges Boehringer Ingelheim, by the German Research Foundation (DFG; EXC2151/1, ImmunoSensation2 - the immune sensory system, project number 390873048), project numbers 329123747, 347286815) and by the HGF grant sparse2big. A.K.S. acknowledges the Beckman Young Investigator Program, a Sloan Fellowship in Chemistry, the NIH (5U24AI118672), and the Bill and Melinda Gates Foundation. F.J.T. acknowledges the German Center for Lung Research. M.vd.B. acknowledges from Ministry of Economic Affairs and Climate Policy by means of the PPP. K.B.W. is funded by the University College London-Birkbeck MRC Doctoral Training Programme. J.W. and Y.Y. acknowledge NIH, U01 HL148856 LungMap Phase II. R.X. acknowledges the NIH (DK043351). H.Z. is supported by the National Key R&D Program (no. 2019YFA0801703) and National Natural Science Foundation of China (no. 31871370

The local and systemic response to SARS-CoV-2 infection in children and adults

While a substantial proportion of adults infected with SARS-CoV-2 progress to develop severe disease, children rarely manifest respiratory complications. Therefore, understanding differences in the local and systemic response to SARS-CoV-2 infection between children and adults may provide important clues about the pathogenesis of SARS-CoV-2 infection. To address this, we first generated a healthy reference multi-omics single cell data set from children (n=30) in whom we have profiled triple matched samples: nasal and tracheal brushings and PBMCs, where we track the developmental changes for 42 airway and 31 blood cell populations from infancy, through childhood to adolescence. This has revealed the presence of naive B and T lymphocytes in neonates and infants with a unique gene expression signature bearing hallmarks of innate immunity. We then contrast the healthy reference with equivalent data from severe paediatric and adult COVID-19 patients (total n=27), from the same three types of samples: upper and lower airways and blood. We found striking differences: children with COVID-19 as opposed to adults had a higher proportion of innate lymphoid and non-clonally expanded naive T cells in peripheral blood, and a limited interferon-response signature. In the airway epithelium, we found the highest viral load in goblet and ciliated cells and describe a novel inflammatory epithelial cell population. These cells represent a transitional regenerative state between secretory and ciliated cells; they were found in healthy children and were enriched in paediatric and adult COVID-19 patients. Epithelial cells display an antiviral and neutrophil-recruiting gene signature that is weaker in severe paediatric versus adult COVID-19. Our matched blood and airway samples allowed us to study the spatial dynamics of infection. Lastly, we provide a user-friendly interface for this data1 as a highly granular reference for the study of immune responses in airways and blood in children

Local and systemic responses to SARS-CoV-2 infection in children and adults

It is not fully understood why COVID-19 is typically milder in children1–3. To examine differences in response to SARS-CoV-2 infection in children and adults, we analysed paediatric and adult COVID-19 patients and healthy controls (total n=93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In healthy paediatric airways, we observed cells already in an interferon-activated state, that upon SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon-responses restrict viral replication and disease progression. The systemic response in children was characterised by increases in naive lymphocytes and a depletion of natural killer cells, while in adults cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signaling in early infection, and identify novel epithelial cell states that associate with COVID-19 and age. Our matching nasal and blood data showed a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were massively reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children

Single-cell multi-omics analysis of the immune response in COVID-19

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy

Single-cell multi-omics analysis of the immune response in COVID-19

Peer reviewedPublisher PD

Local and systemic responses to SARS-CoV-2 infection in children and adults.

It is not fully understood why COVID-19 is typically milder in children1-3. Here, to examine the differences between children and adults in their response to SARS-CoV-2 infection, we analysed paediatric and adult patients with COVID-19 as well as healthy control individuals (total n = 93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In the airways of healthy paediatric individuals, we observed cells that were already in an interferon-activated state, which after SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon responses restrict viral replication and disease progression. The systemic response in children was characterized by increases in naive lymphocytes and a depletion of natural killer cells, whereas, in adults, cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signalling in early infection, and identify epithelial cell states associated with COVID-19 and age. Our matching nasal and blood data show a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were substantially reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children

Single-cell multi-omics analysis of the immune response in COVID-19

Funder: Lister Institute of Preventive Medicine; doi: https://doi.org/10.13039/501100001255Funder: University College London, Birkbeck MRC Doctoral Training ProgrammeFunder: The Jikei University School of MedicineFunder: Action Medical Research (GN2779)Funder: NIHR Clinical Lectureship (CL-2017-01-004)Funder: NIHR (ACF-2018-01-004) and the BMA FoundationFunder: Chan Zuckerberg Initiative (grant 2017-174169) and from Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194)Funder: UKRI Innovation/Rutherford Fund Fellowship allocated by the MRC and the UK Regenerative Medicine Platform (MR/5005579/1 to M.Z.N.). M.Z.N. and K.B.M. have been funded by the Rosetrees Trust (M944)Funder: Barbour FoundationFunder: ERC Consolidator and EU MRG-Grammar awardsFunder: Versus Arthritis Cure Challenge Research Grant (21777), and an NIHR Research Professorship (RP-2017-08-ST2-002)Funder: European Molecular Biology Laboratory (EMBL)Abstract: Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells' potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.Peer reviewe