Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

Lu, Bo; Yan, Yi; Dong, Liting; Han, Lingling; Liu, Yawei; Yu, Junping; Chen, Jianjun; Yi, Danyang; Zhang, Meiling; Deng, Xin; Wang, Chao; Wang, Runkun; Wang, Dengpeng; Wei, Hongping; Liu, Di; Yi, Chengqi

doi:10.1038/s41421-021-00248-3

Cited by 14 publications

(10 citation statements)

References 49 publications

(38 reference statements)

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“…These 40 genes were not found to be DE between pH1N1 vs control samples, suggesting these as ( Figure 4F ) distinctly regulated for COVID-19 patients. Of these COVID-19 specific genes, the inflammatory response-related gene NFAM1 and TNF receptor gene TNFRSF10A are found to be up-regulated in concordance with previous reports suggesting up-regulation in the throat swab samples 55 and in T cells 56 of COVID-19 patients, respectively. Of the downregulated genes, of particular interest is IL1RL1 (which encodes the ST2 protein and is involved in the IL-33/ST2 signalling pathway with its receptor cytokine IL-33.…”

Section: Resultssupporting

confidence: 91%

Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage

Kulasinghe

Liu

Tan

et al. 2022

Preprint

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to present with pulmonary and extra-pulmonary organ complications. In comparison with the 2009 pandemic (pH1N1), SARS-CoV-2 infection is likely to lead to more severe disease, with multi-organ effects, including cardiovascular disease. SARS-CoV-2 has been associated with acute and long-term cardiovascular disease, but the molecular changes govern this remain unknown. In this study, we investigated the landscape of cardiac tissues collected at rapid autopsy from SARS-CoV-2, pH1N1, and control patients using targeted spatial transcriptomics approaches. Although SARS-CoV-2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1-like macrophage infiltration in the cardiac tissues of COVID-19 patients. The DNA damage present in the SARS-CoV-2 patient samples, were further confirmed by gamma-H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of Interferon-stimulated genes (ISGs), in particular interferon and complement pathways, when compared with COVID-19 patients. These data demonstrate the emergence of distinct transcriptomic profiles in cardiac tissues of SARS-CoV-2 and pH1N1 influenza infection supporting the need for a greater understanding of the effects on extra-pulmonary organs, including the cardiovascular system of COVID-19 patients, to delineate the immunopathobiology of SARS-CoV-2 infection, and long term impact on health.

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Section: Resultssupporting

confidence: 91%

Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage

Kulasinghe

Liu

Tan

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…These 40 genes were not found to be DE between pH1N1 versus control samples, suggesting these as (Figure 4f ) distinctly regulated for COVID‐19 patients. Of these COVID‐19 specific genes, the inflammatory response‐related gene NFAM1 and TNF receptor gene TNFRSF10A are found to be upregulated in concordance with previous reports suggesting higher expression in the throat swab samples [ 55 ] and in T cells [ 56 ] of COVID‐19 patients, respectively. Of the downregulated genes, of particular interest is IL1RL1 (which encodes the ST2 protein and is involved in the IL‐33/ST2 signalling pathway with its receptor cytokine IL‐33).…”

Section: Resultssupporting

confidence: 90%

Transcriptomic profiling of cardiac tissues from SARS‐CoV‐2 patients identifies DNA damage

et al. 2022

View full text Add to dashboard Cite

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is known to present with pulmonary and extra‐pulmonary organ complications. In comparison with the 2009 pandemic (pH1N1), SARS‐CoV‐2 infection is likely to lead to more severe disease, with multi‐organ effects, including cardiovascular disease. SARS‐CoV‐2 has been associated with acute and long‐term cardiovascular disease, but the molecular changes that govern this remain unknown. In this study, we investigated the host transcriptome landscape of cardiac tissues collected at rapid autopsy from seven SARS‐CoV‐2, two pH1N1, and six control patients using targeted spatial transcriptomics approaches. Although SARS‐CoV‐2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1‐like macrophage infiltration in the cardiac tissues of COVID‐19 patients. The DNA damage present in the SARS‐CoV‐2 patient samples, were further confirmed by γ‐H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of interferon‐stimulated genes, in particular interferon and complement pathways, when compared with COVID‐19 patients. These data demonstrate the emergence of distinct transcriptomic profiles in cardiac tissues of SARS‐CoV‐2 and pH1N1 influenza infection supporting the need for a greater understanding of the effects on extra‐pulmonary organs, including the cardiovascular system of COVID‐19 patients, to delineate the immunopathobiology of SARS‐CoV‐2 infection, and long term impact on health.

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“…However, metagenomics based on next‐generation sequencing (mNGS) was rarely applied to the clinical samples of SARS‐CoV‐2. 5 , 16 , 17 This technology could be used to uncover all microbiomes interacting in the same pathological niche, which might lead to ultimate pathophysiological conditions. The present study aims to perform metagenomic in‐depth bioanalysis to characterize SARS‐CoV‐2 diabetic and nondiabetic patients compared with controls to identify the microbial interaction associated with the fatal consequences.…”

Section: Introductionmentioning

confidence: 99%

Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID‐19 patients comorbidly affected by Type 2 diabetes

Al‐Emran¹,

Rahman²,

Hasan³

et al. 2022

Journal of Medical Virology

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The mortality of coronavirus disease 2019 (COVID‐19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2)‐infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS‐CoV‐2‐infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next‐generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan‐package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6–1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS‐CoV‐2 diabetic group exhibited a significant increase in pathogens and secondary infection‐causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID‐19‐infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.

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Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

Cited by 14 publications

References 49 publications

Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage

Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage

Transcriptomic profiling of cardiac tissues from SARS‐CoV‐2 patients identifies DNA damage

Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID‐19 patients comorbidly affected by Type 2 diabetes

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