ABSTRACT
An outbreak of a novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had emerged in 2019 and rapidly posed a global epidemic. Here, we report the breadth of concomitant virological features of a family cluster with COVID-19. The period of virus shedding is significantly different between upper respiratory and feces samples. Even the SARS-CoV-2 virus titers were undetectable in feces, it could be positive again soon and likely related to fluctuated inflammation levels (interleukin-6, etc.) and lowered immune responses (CD4 + T lymphocyte, etc.). Our findings expand the novel understanding of the breadth of concomitant virological features during a non-severe family cluster of COVID-19.
Subject(s)
COVID-19/physiopathology , Feces/virology , SARS-CoV-2 , Virus Shedding , Adolescent , Adult , COVID-19/virology , China , Disease Outbreaks , Family , Female , Humans , Male , Middle AgedABSTRACT
SARS-CoV-2 is the cause of the current global pandemic of COVID-19; this virus infects multiple organs, such as the lungs and gastrointestinal tract. The microbiome in these organs, including the bacteriome and virome, responds to infection and might also influence disease progression and treatment outcome. In a cohort of 13 COVID-19 patients in Beijing, China, we observed that the gut virome and bacteriome in the COVID-19 patients were notably different from those of five healthy controls. We identified a bacterial dysbiosis signature by observing reduced diversity and viral shifts in patients, and among the patients, the bacterial/viral compositions were different between patients of different severities, although these differences are not entirely distinguishable from the effect of antibiotics. Severe cases of COVID-19 exhibited a greater abundance of opportunistic pathogens but were depleted for butyrate-producing groups of bacteria compared with mild to moderate cases. We replicated our findings in a mouse COVID-19 model, confirmed virome differences and bacteriome dysbiosis due to SARS-CoV-2 infection, and observed that immune/infection-related genes were differentially expressed in gut epithelial cells during infection, possibly explaining the virome and bacteriome dynamics. Our results suggest that the components of the microbiome, including the bacteriome and virome, are affected by SARS-CoV-2 infections, while their compositional signatures could reflect or even contribute to disease severity and recovery processes.
Subject(s)
COVID-19/microbiology , COVID-19/virology , Dysbiosis/diagnosis , Gastrointestinal Microbiome , Virome , Adolescent , Adult , Aged , Aged, 80 and over , Animals , Anti-Bacterial Agents/therapeutic use , COVID-19/therapy , Case-Control Studies , China , Disease Models, Animal , Female , Genome, Viral , Humans , Male , Mice , Mice, Inbred C57BL , MicroRNAs , Middle Aged , TranscriptomeSubject(s)
COVID-19/immunology , COVID-19/metabolism , Cell-Free Nucleic Acids/blood , Cytokine Release Syndrome/immunology , Interleukin-6/metabolism , MicroRNAs/blood , Receptors, Interleukin-6/metabolism , COVID-19/blood , COVID-19/genetics , Cytokine Release Syndrome/blood , Down-Regulation , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , RNA/blood , Receptors, Interleukin-6/genetics , SARS-CoV-2ABSTRACT
The coronavirus disease 2019 (COVID-19) pandemic poses a current world-wide public health threat. However, little is known about its hallmarks compared to other infectious diseases. Here, we report the single-cell transcriptional landscape of longitudinally collected peripheral blood mononuclear cells (PBMCs) in both COVID-19- and influenza A virus (IAV)-infected patients. We observed increase of plasma cells in both COVID-19 and IAV patients and XIAP associated factor 1 (XAF1)-, tumor necrosis factor (TNF)-, and FAS-induced T cell apoptosis in COVID-19 patients. Further analyses revealed distinct signaling pathways activated in COVID-19 (STAT1 and IRF3) versus IAV (STAT3 and NFκB) patients and substantial differences in the expression of key factors. These factors include relatively increase of interleukin (IL)6R and IL6ST expression in COVID-19 patients but similarly increased IL-6 concentrations compared to IAV patients, supporting the clinical observations of increased proinflammatory cytokines in COVID-19 patients. Thus, we provide the landscape of PBMCs and unveil distinct immune response pathways in COVID-19 and IAV patients.