Mapping interindividual dynamics of innate immune response at single-cell resolution.

Common genetic variants across individuals modulate the cellular response to pathogens and are implicated in diverse immune pathologies, yet how they dynamically alter the response upon infection is not well understood. Here, we triggered antiviral responses in human fibroblasts from 68 healthy donors, and profiled tens of thousands of cells using single-cell RNA-sequencing. We developed GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity), a statistical approach designed to identify nonlinear dynamic genetic effects across transcriptional trajectories of cells. This approach identified 1,275 expression quantitative trait loci (local false discovery rate 10%) that manifested during the responses, many of which were colocalized with susceptibility loci identified by genome-wide association studies of infectious and autoimmune diseases, including the OAS1 splicing quantitative trait locus in a COVID-19 susceptibility locus. In summary, our analytical approach provides a unique framework for delineation of the genetic variants that shape a wide spectrum of transcriptional responses at single-cell resolution.

Obesity Is Associated with Attenuated Tissue Immunity in COVID-19.

RATIONALE: Obesity affects 40% of US adults, is associated with a pro-inflammatory state, and presents a significant risk factor for the development of severe COVID-19. To date, there is limited information on how obesity might affect immune cell responses in SARS-CoV-2 infection. OBJECTIVES: To determine the impact of obesity on respiratory tract immunity in COVID-19 across human lifespan. METHODS: We analysed single cell transcriptomes from bronchiolar lavage in three ventilated adult cohorts with (n=24) or without COVID-19 (n=9), from nasal immune cells in children with (n=14) or without COVID-19 (n=19), and from peripheral blood mononuclear cells in an independent adult COVID-19 cohort (n=42), comparing obese (Ob) and non-obese subjects (N-Ob). MEASUREMENTS AND MAIN RESULTS: Surprisingly, we found that adult Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN)α, IFNγ and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFNγ response genes, as well as decreased serum IFNα in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFNα and IFNγ response genes. CONCLUSIONS: These findings show blunted tissue immune responses in Ob COVID-19 patients, with implications for treatment stratification, supporting the specific application of inhaled recombinant type I IFNs in this vulnerable subset. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Roles of radiological technologists at Tsukuba Medical Examiner's Office equipped with a computed tomography system dedicated for the examination of corpses

The present study report introduces the roles of radiological technologists (RTs) at Tsukuba Medical Examiner's Office in Japan where a computed tomography system dedicated for examining corpses has been equipped. Several projects and enacted laws regarding postmortem imaging (PMI) have accelerated its use in many Japanese hospitals for detecting causes of death. The lack of sufficient forensic radiologists has led increasing need of RTs to assist forensic pathologists in a timely manner. Optimizing parameters and image processing of postmortem computed tomography (PMCT) and assistance in interpretation of PMCT using checklists by RTs help forensic pathologist to diagnose death causes and select needs for the following autopsy.

A Convenient Risk Prediction Score for COVID-19 for Determining Whether or Not Hospitalization Is Recommended: Kanagawa Admission Priority Assessment Score.

Objective Coronavirus disease 2019 (COVID-19) has caused a collapse of the medical care system, with effective triage proving vital. The Kanagawa admission priority assessment score, version-1 (KAPAS-1) and version-2 (KAPAS-2), was developed to determine the need for hospitalization. Patients with a high KAPAS (≥5) are recommended for hospitalization. We retrospectively investigated the correlation between the KAPAS and oxygen requirement during hospitalization. Methods We collected the clinical data of COVID-19 patients admitted between February 5 and December 6, 2020. Patients were divided into two groups: those who required oxygen therapy during hospitalization (OXY) and those who did not (NOXY). We assessed the correlations between the groups and KAPAS-1 and KAPAS-2. Results Overall, 117 COVID-19 patients were analyzed, including 20 OXY and 97 NOXY and 54 high KAPAS-1 and 63 high KAPAS-2. The median KAPAS-1 and KAPAS-2 were significantly higher in OXY than in NOXY (6.5 vs. 3, and 9 vs. 4, respectively). The areas under the receiver operating characteristic curves of KAPAS-1 and KAPAS-2 for oxygen requirement were 0.777 and 0.825, respectively, and the maximum values of Youden's index were 4 and 6, respectively. The proportions of high KAPAS-1 and high KAPAS-2 were significantly higher in OXY than in NOXY (90.0% vs. 37.1%, and 90.0% vs. 46.4%, respectively). Conclusion The KAPAS was significantly correlated with oxygen requirement. Furthermore, the KAPAS may be useful for deciding which patients are most likely to require hospitalization and for selecting non-hospitalized patients who should be carefully monitored.

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.

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.