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1.
PLoS One ; 15(8): e0238490, 2020.
Article in English | MEDLINE | ID: covidwho-732989

ABSTRACT

SARS-CoV-2 is still rampaging throughout the world while the many evolutionary studies on it are simultaneously springing up. Researchers have simply utilized the public RNA-seq data to find out the so-called SNPs in the virus genome. The evolutionary analyses were largely based on these mutations. Here, we claim that we reliably detected A-to-G RNA modifications in the RNA-seq data of SARS-CoV-2 with high signal to noise ratios, presumably caused by the host's deamination enzymes. Intriguingly, since SARS-CoV-2 is an RNA virus, it is technically impossible to distinguish SNPs and RNA modifications from the RNA-seq data alone without solid evidence, making it difficult to tell the evolutionary patterns behind the mutation spectrum. Researchers should clarify their biological significance before they automatically regard the mutations as SNPs or RNA modifications. This is not a problem for DNA organisms but should be seriously considered when we are investigating the RNA viruses.


Subject(s)
Betacoronavirus/genetics , Evolution, Molecular , Polymorphism, Single Nucleotide , RNA, Viral/genetics , Base Sequence , Coronavirus Infections , Humans , Mutation Rate , Pandemics , Pneumonia, Viral , RNA-Seq
2.
J Immunol Res ; 2020: 8624963, 2020.
Article in English | MEDLINE | ID: covidwho-721226

ABSTRACT

Single-cell RNA sequencing allows highly detailed profiling of cellular immune responses from limited-volume samples, advancing prospects of a new era of systems immunology. The power of single-cell RNA sequencing offers various opportunities to decipher the immune response to infectious diseases and vaccines. Here, we describe the potential uses of single-cell RNA sequencing methods in prophylactic vaccine development, concentrating on infectious diseases including COVID-19. Using examples from several diseases, we review how single-cell RNA sequencing has been used to evaluate the immunological response to different vaccine platforms and regimens. By highlighting published and unpublished single-cell RNA sequencing studies relevant to vaccinology, we discuss some general considerations how the field could be enriched with the widespread adoption of this technology.


Subject(s)
Betacoronavirus/immunology , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , RNA-Seq/methods , Single-Cell Analysis , Vaccinology/methods , Viral Vaccines/administration & dosage , Animals , Cell Line , Clinical Trials as Topic , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Disease Models, Animal , Drug Evaluation, Preclinical , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Humans , Immunity, Cellular/genetics , Immunity, Innate/genetics , Immunogenicity, Vaccine , Pneumonia, Viral/epidemiology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , RNA, Viral/isolation & purification , Viral Vaccines/immunology
4.
Nat Immunol ; 21(9): 1107-1118, 2020 09.
Article in English | MEDLINE | ID: covidwho-710376

ABSTRACT

In coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the relationship between disease severity and the host immune response is not fully understood. Here we performed single-cell RNA sequencing in peripheral blood samples of 5 healthy donors and 13 patients with COVID-19, including moderate, severe and convalescent cases. Through determining the transcriptional profiles of immune cells, coupled with assembled T cell receptor and B cell receptor sequences, we analyzed the functional properties of immune cells. Most cell types in patients with COVID-19 showed a strong interferon-α response and an overall acute inflammatory response. Moreover, intensive expansion of highly cytotoxic effector T cell subsets, such as CD4+ effector-GNLY (granulysin), CD8+ effector-GNLY and NKT CD160, was associated with convalescence in moderate patients. In severe patients, the immune landscape featured a deranged interferon response, profound immune exhaustion with skewed T cell receptor repertoire and broad T cell expansion. These findings illustrate the dynamic nature of immune responses during disease progression.


Subject(s)
Antigens, CD/metabolism , Antigens, Differentiation, T-Lymphocyte/metabolism , Betacoronavirus/immunology , Coronavirus Infections/immunology , Interferon Type I/metabolism , Pneumonia, Viral/immunology , Receptors, Immunologic/metabolism , Adolescent , Adult , Aged , Antigens, CD/genetics , Antigens, CD/immunology , Antigens, Differentiation, T-Lymphocyte/genetics , Antigens, Differentiation, T-Lymphocyte/immunology , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cohort Studies , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Female , GPI-Linked Proteins/genetics , GPI-Linked Proteins/immunology , GPI-Linked Proteins/metabolism , Humans , Interferon Type I/genetics , Interferon Type I/immunology , Killer Cells, Natural/immunology , Killer Cells, Natural/metabolism , Male , Middle Aged , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , RNA-Seq , Receptors, Immunologic/genetics , Receptors, Immunologic/immunology , Severity of Illness Index , Single-Cell Analysis
5.
Int J Biol Sci ; 16(13): 2464-2476, 2020.
Article in English | MEDLINE | ID: covidwho-695855

ABSTRACT

In 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused infections worldwide. However, the correlation between the immune infiltration and coronavirus disease 2019 (COVID-19) susceptibility or severity in cancer patients remains to be fully elucidated. ACE2 expressions in normal tissues, cancers and cell lines were comprehensively assessed. Furthermore, we compared ACE2 expression between cancers and matched normal tissues through Gene Expression Profiling Interactive Analysis (GEPIA). In addition, we performed gene set enrichment analysis (GSEA) to investigate the related signaling pathways. Finally, the correlations between ACE2 expression and immune infiltration were investigated via Tumor Immune Estimation Resource (TIMER) and GEPIA. We found that ACE2 was predominantly expressed in both adult and fetal tissues from the digestive, urinary and male reproductive tracts; moreover, ACE2 expressions in corresponding cancers were generally higher than that in matched healthy tissues. GSEA showed that various metabolic and immune-related pathways were significantly associated with ACE2 expression across multiple cancer types. Intriguingly, we found that ACE2 expression correlated significantly with immune cell infiltration in both normal and cancer tissues, especially in the stomach and colon. These findings proposed a possible fecal-oral and maternal-fetal transmission of SARS-CoV-2 and suggested that cancers of the respiratory, digestive or urinary tracts would be more vulnerable to SARS-CoV-2 infection.


Subject(s)
Computational Biology , Coronavirus Infections/immunology , Neoplasms/immunology , Pneumonia, Viral/immunology , Adult , Betacoronavirus , Coronavirus Infections/complications , Enterocytes/metabolism , Epithelial Cells/metabolism , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Expression Regulation, Viral , Genotype , Goblet Cells/metabolism , Hepatocytes/metabolism , Humans , Immune System , Kidney Tubules/embryology , Male , Neoplasms/complications , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/complications , Prognosis , RNA-Seq , Signal Transduction
6.
J Transl Med ; 18(1): 291, 2020 07 31.
Article in English | MEDLINE | ID: covidwho-691020

ABSTRACT

BACKGROUND: Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of targeted blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. METHODS: We designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates. RESULTS: As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: immunological relevance, therapeutic development relevance and SARS biology relevance. CONCLUSION: Altogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients.


Subject(s)
Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Transcriptome , Adult , Antibodies, Viral/blood , Betacoronavirus , Coronavirus Infections/immunology , Gene Expression Profiling , Humans , Immune System , Internet , Pandemics , Pneumonia, Viral/immunology , RNA-Seq , Software
7.
PLoS One ; 15(7): e0235987, 2020.
Article in English | MEDLINE | ID: covidwho-690896

ABSTRACT

Development of novel approaches for regulating the expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) is becoming increasingly important within the context of the ongoing COVID-19 pandemic since these enzymes play a crucial role in cell infection. In this work we searched for putative ACE2 and TMPRSS2 expression regulation networks mediated by various miRNA isoforms (isomiR) across different human organs using publicly available paired miRNA/mRNA-sequencing data from The Cancer Genome Atlas (TCGA) project. As a result, we identified several miRNA families targeting ACE2 and TMPRSS2 genes in multiple tissues. In particular, we found that lysine-specific demethylase 5B (JARID1B), encoded by the KDM5B gene, can indirectly affect ACE2 / TMPRSS2 expression by repressing transcription of hsa-let-7e / hsa-mir-125a and hsa-mir-141 / hsa-miR-200 miRNA families which are targeting these genes.


Subject(s)
Betacoronavirus , Coronavirus Infections/enzymology , Gene Expression Regulation , MicroRNAs/genetics , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/enzymology , RNA, Messenger/genetics , Serine Endopeptidases/genetics , 3' Untranslated Regions , Coronavirus Infections/virology , Databases, Genetic , Gene Regulatory Networks , Humans , Jumonji Domain-Containing Histone Demethylases/genetics , MicroRNAs/metabolism , Nuclear Proteins/genetics , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/virology , RNA Isoforms/genetics , RNA, Messenger/metabolism , RNA-Seq , Repressor Proteins/genetics , Serine Endopeptidases/metabolism , Single-Cell Analysis
8.
Sci Transl Med ; 12(556)2020 08 12.
Article in English | MEDLINE | ID: covidwho-688785

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)-based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab-to-RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Colorimetry/methods , Colorimetry/statistics & numerical data , Coronavirus Infections/epidemiology , Humans , Molecular Diagnostic Techniques/statistics & numerical data , Nucleic Acid Amplification Techniques/statistics & numerical data , Nucleocapsid Proteins/genetics , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/genetics , RNA, Viral/isolation & purification , RNA-Seq , Sensitivity and Specificity , Translational Medical Research
10.
Mol Syst Biol ; 16(7): e9610, 2020 07.
Article in English | MEDLINE | ID: covidwho-680519

ABSTRACT

The novel SARS-coronavirus 2 (SARS-CoV-2) poses a global challenge on healthcare and society. For understanding the susceptibility for SARS-CoV-2 infection, the cell type-specific expression of the host cell surface receptor is necessary. The key protein suggested to be involved in host cell entry is angiotensin I converting enzyme 2 (ACE2). Here, we report the expression pattern of ACE2 across > 150 different cell types corresponding to all major human tissues and organs based on stringent immunohistochemical analysis. The results were compared with several datasets both on the mRNA and protein level. ACE2 expression was mainly observed in enterocytes, renal tubules, gallbladder, cardiomyocytes, male reproductive cells, placental trophoblasts, ductal cells, eye, and vasculature. In the respiratory system, the expression was limited, with no or only low expression in a subset of cells in a few individuals, observed by one antibody only. Our data constitute an important resource for further studies on SARS-CoV-2 host cell entry, in order to understand the biology of the disease and to aid in the development of effective treatments to the viral infection.


Subject(s)
Peptidyl-Dipeptidase A/metabolism , Respiratory System/metabolism , Betacoronavirus , Blood Vessels/metabolism , Conjunctiva/metabolism , Enterocytes/metabolism , Female , Gallbladder/metabolism , Host Microbial Interactions , Humans , Immunohistochemistry , Kidney Tubules, Proximal/metabolism , Male , Mass Spectrometry , Myocytes, Cardiac/metabolism , Organ Specificity , Peptidyl-Dipeptidase A/genetics , Placenta/metabolism , Pregnancy , RNA-Seq , Single-Cell Analysis , Testis/metabolism
11.
J Immunother Cancer ; 8(2)2020 07.
Article in English | MEDLINE | ID: covidwho-650285

ABSTRACT

BACKGROUND: Pandemic COVID-19 by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) infection is facilitated by the ACE2 receptor and protease TMPRSS2. Modestly sized case series have described clinical factors associated with COVID-19, while ACE2 and TMPRSS2 expression analyses have been described in some cell types. Patients with cancer may have worse outcomes to COVID-19. METHODS: We performed an integrated study of ACE2 and TMPRSS2 gene expression across and within organ systems, by normal versus tumor, across several existing databases (The Cancer Genome Atlas, Census of Immune Single Cell Expression Atlas, The Human Cell Landscape, and more). We correlated gene expression with clinical factors (including but not limited to age, gender, race, body mass index, and smoking history), HLA genotype, immune gene expression patterns, cell subsets, and single-cell sequencing as well as commensal microbiome. RESULTS: Matched normal tissues generally display higher ACE2 and TMPRSS2 expression compared with cancer, with normal and tumor from digestive organs expressing the highest levels. No clinical factors were consistently identified to be significantly associated with gene expression levels though outlier organ systems were observed for some factors. Similarly, no HLA genotypes were consistently associated with gene expression levels. Strong correlations were observed between ACE2 expression levels and multiple immune gene signatures including interferon-stimulated genes and the T cell-inflamed phenotype as well as inverse associations with angiogenesis and transforming growth factor-ß signatures. ACE2 positively correlated with macrophage subsets across tumor types. TMPRSS2 was less associated with immune gene expression but was strongly associated with epithelial cell abundance. Single-cell sequencing analysis across nine independent studies demonstrated little to no ACE2 or TMPRSS2 expression in lymphocytes or macrophages. ACE2 and TMPRSS2 gene expression associated with commensal microbiota in matched normal tissues particularly from colorectal cancers, with distinct bacterial populations showing strong associations. CONCLUSIONS: We performed a large-scale integration of ACE2 and TMPRSS2 gene expression across clinical, genetic, and microbiome domains. We identify novel associations with the microbiota and confirm host immunity associations with gene expression. We suggest caution in interpretation regarding genetic associations with ACE2 expression suggested from smaller case series.


Subject(s)
Betacoronavirus/immunology , Coronavirus Infections/immunology , Neoplasms/immunology , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/immunology , Serine Endopeptidases/metabolism , Aged , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Datasets as Topic , Female , Gastrointestinal Microbiome/immunology , Gene Expression Regulation, Neoplastic/immunology , HLA Antigens/blood , HLA Antigens/immunology , Humans , Macrophages/immunology , Male , Middle Aged , Neoplasms/blood , Neoplasms/microbiology , Neoplasms/pathology , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , RNA-Seq
12.
Int J Med Sci ; 17(11): 1522-1531, 2020.
Article in English | MEDLINE | ID: covidwho-647086

ABSTRACT

The outbreak of pneumonia caused by SARS-CoV-2 posed a great threat to global human health, which urgently requires us to understand comprehensively the mechanism of SARS-CoV-2 infection. Angiotensin-converting enzyme 2 (ACE2) was identified as a functional receptor for SARS-CoV-2, distribution of which may indicate the risk of different human organs vulnerable to SARS-CoV-2 infection. Previous studies investigating the distribution of ACE2 mRNA in human tissues only involved a limited size of the samples and a lack of determination for ACE2 protein. Given the heterogeneity among humans, the datasets covering more tissues with a larger size of samples should be analyzed. Indeed, ACE2 is a membrane and secreted protein, while the expression of ACE2 in blood and common blood cells remains unknown. Herein, the proteomic data in HIPED and the antibody-based immunochemistry result in HPA were collected to analyze the distribution of ACE2 protein in human tissues. The bulk RNA-seq profiles from three separate public datasets including HPA tissue Atlas, GTEx, and FANTOM5 CAGE were also obtained to determine the expression of ACE2 in human tissues. Moreover, the abundance of ACE2 in human blood and blood cells was determined by analyzing the data in the PeptideAtlas and the HPA Blood Atlas. We found that the mRNA expression cannot reflect the abundance of ACE2 factor due to the strong differences between mRNA and protein quantities of ACE2 within and across tissues. Our results suggested that ACE2 protein is mainly expressed in the small intestine, kidney, gallbladder, and testis, while the abundance of which in brain-associated tissues and blood common cells is low. HIPED revealed enrichment of ACE2 protein in the placenta and ovary despite a low mRNA level. Further, human secretome shows that the average concentration of ACE2 protein in the plasma of males is higher than those in females. Our research will be beneficial for understanding the transmission routes and sex-based differences in susceptibility of SARS-CoV-2 infection.


Subject(s)
Coronavirus Infections/metabolism , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/metabolism , Receptors, Virus/metabolism , Betacoronavirus , Databases, Protein , Female , Humans , Immunohistochemistry , Male , Mass Spectrometry , Pandemics , Proteomics , RNA, Messenger/metabolism , RNA-Seq , Tissue Distribution , Transcriptome
13.
Sci Immunol ; 5(49)2020 07 10.
Article in English | MEDLINE | ID: covidwho-639363

ABSTRACT

Although most SARS-CoV-2-infected individuals experience mild coronavirus disease 2019 (COVID-19), some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly up-regulation of the TNF/IL-1ß-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1ß-driven inflammation, and this was not seen in patients with milder COVID-19. Interestingly, we documented type I IFN-driven inflammatory features in patients with severe influenza as well. Based on this, we propose that the type I IFN response plays a pivotal role in exacerbating inflammation in severe COVID-19.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/immunology , Coronavirus Infections/immunology , Immunophenotyping , Influenza A virus/immunology , Influenza, Human/immunology , Interferon Type I/metabolism , Pneumonia, Viral/immunology , Severity of Illness Index , Adult , Aged , Aged, 80 and over , CD8-Positive T-Lymphocytes/immunology , Cells, Cultured , Coronavirus Infections/blood , Coronavirus Infections/virology , Female , Healthy Volunteers , Humans , Inflammation/immunology , Influenza, Human/blood , Influenza, Human/virology , Interleukin-1beta/metabolism , Male , Middle Aged , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/virology , RNA-Seq , Single-Cell Analysis , Transcriptome , Tumor Necrosis Factor-alpha/metabolism
14.
Nat Med ; 26(7): 1070-1076, 2020 07.
Article in English | MEDLINE | ID: covidwho-591473

ABSTRACT

There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, which has infected more than three million people worldwide1. Approximately 20% of patients with COVID-19 develop severe disease and 5% of patients require intensive care2. Severe disease has been associated with changes in peripheral immune activity, including increased levels of pro-inflammatory cytokines3,4 that may be produced by a subset of inflammatory monocytes5,6, lymphopenia7,8 and T cell exhaustion9,10. To elucidate pathways in peripheral immune cells that might lead to immunopathology or protective immunity in severe COVID-19, we applied single-cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) from seven patients hospitalized for COVID-19, four of whom had acute respiratory distress syndrome, and six healthy controls. We identify reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene signature, HLA class II downregulation and a developing neutrophil population that appears closely related to plasmablasts appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, we found that peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines. Collectively, we provide a cell atlas of the peripheral immune response to severe COVID-19.


Subject(s)
Betacoronavirus/immunology , Coronavirus Infections , Immunity, Cellular , Leukocytes, Mononuclear , Pandemics , Pneumonia, Viral , Sequence Analysis, RNA/methods , Single-Cell Analysis/methods , Adult , Aged , Aged, 80 and over , Case-Control Studies , Coronavirus Infections/genetics , Coronavirus Infections/immunology , Coronavirus Infections/pathology , Cytokines/genetics , Cytokines/metabolism , Female , Gene Expression Profiling/methods , Humans , Killer Cells, Natural/immunology , Killer Cells, Natural/metabolism , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Leukocytes, Mononuclear/virology , Male , Middle Aged , Pneumonia, Viral/genetics , Pneumonia, Viral/immunology , Pneumonia, Viral/pathology , RNA-Seq/methods , Severity of Illness Index , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Young Adult
15.
Fertil Steril ; 113(6): 1135-1139, 2020 06.
Article in English | MEDLINE | ID: covidwho-459476

ABSTRACT

OBJECTIVE: To describe detection of severe acute respiratory syndrome (SARS)-coronavirus 2 (CoV-2) in seminal fluid of patients recovering from coronavirus disease 2019 (COVID-19) and to describe the expression profile of angiotensin-converting enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2) within the testicle. DESIGN: Observational, cross-sectional study. SETTING: Tertiary referral center. PATIENT(S): Thirty-four adult Chinese males diagnosed with COVID-19 through confirmatory quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) from pharyngeal swab samples. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Identification of SARS-CoV-2 on qRT-PCR of single ejaculated semen samples. Semen quality was not assessed. Expression patterns of ACE2 and TMPRSS2 in the human testis are explored through previously published single-cell transcriptome datasets. RESULT(S): Six patients (19%) demonstrated scrotal discomfort suggestive of viral orchitis around the time of COVID-19 confirmation. Severe acute respiratory syndrome-CoV-2 was not detected in semen after a median of 31 days (interquartile range, 29-36 days) from COVID-19 diagnosis. Single-cell transcriptome analysis demonstrates sparse expression of ACE2 and TMPRSS2, with almost no overlapping gene expression. CONCLUSION(S): Severe acute respiratory syndrome-CoV-2 was not detected in the semen of patients recovering from COVID-19 1 month after COVID-19 diagnosis. Angiotensin-converting enzyme 2-mediated viral entry of SARS-CoV-2 into target host cells is unlikely to occur within the human testicle based on ACE2 and TMPRSS2 expression. The long-term effects of SARS-CoV-2 on male reproductive function remain unknown.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Pneumonia, Viral/virology , Semen/virology , Adolescent , Adult , Betacoronavirus/genetics , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/enzymology , Coronavirus Infections/genetics , Cross-Sectional Studies , Humans , Male , Middle Aged , Pandemics , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/enzymology , Pneumonia, Viral/genetics , RNA-Seq , Real-Time Polymerase Chain Reaction , Serine Endopeptidases/genetics , Testis/enzymology , Testis/virology , Time Factors , Transcriptome , Virus Internalization , Young Adult
16.
Dev Cell ; 53(5): 514-529.e3, 2020 06 08.
Article in English | MEDLINE | ID: covidwho-276241

ABSTRACT

The factors mediating fatal SARS-CoV-2 infections are poorly understood. Here, we show that cigarette smoke causes a dose-dependent upregulation of angiotensin converting enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs. Using single-cell sequencing data, we demonstrate that ACE2 is expressed in a subset of secretory cells in the respiratory tract. Chronic smoke exposure triggers the expansion of this cell population and a concomitant increase in ACE2 expression. In contrast, quitting smoking decreases the abundance of these secretory cells and reduces ACE2 levels. Finally, we demonstrate that ACE2 expression is responsive to inflammatory signaling and can be upregulated by viral infections or interferon treatment. Taken together, these results may partially explain why smokers are particularly susceptible to severe SARS-CoV-2 infections. Furthermore, our work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that SARS-CoV-2 infections could create positive feedback loops that increase ACE2 levels and facilitate viral dissemination.


Subject(s)
Alveolar Epithelial Cells/metabolism , Coronavirus Infections/epidemiology , Interferons/metabolism , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/epidemiology , Respiratory Mucosa/metabolism , Tobacco Smoke Pollution/adverse effects , Tobacco Smoking/genetics , Adult , Aged , Animals , Caco-2 Cells , Cells, Cultured , Female , HCT116 Cells , Humans , Interferons/genetics , Male , Mice , Middle Aged , Pandemics , Peptidyl-Dipeptidase A/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Seq , Rats , Signal Transduction , Single-Cell Analysis , Tobacco Smoking/epidemiology , Tobacco Smoking/metabolism , Up-Regulation
18.
ACS Chem Neurosci ; 11(11): 1555-1562, 2020 06 03.
Article in English | MEDLINE | ID: covidwho-197238

ABSTRACT

The COVID-19 pandemic revealed that there is a loss of smell in many patients, including in infected but otherwise asymptomatic individuals. The underlying mechanisms for the olfactory symptoms are unclear. Using a mouse model, we determined whether cells in the olfactory epithelium express the obligatory receptors for entry of the SARS-CoV-2 virus by using RNAseq, RT-PCR, in situ hybridization, Western blot, and immunocytochemistry. We show that the cell surface protein ACE2 and the protease TMPRSS2 are expressed in sustentacular cells of the olfactory epithelium but not, or much less, in most olfactory receptor neurons. These data suggest that sustentacular cells are involved in SARS-CoV-2 virus entry and impairment of the sense of smell in COVID-19 patients. We also show that expression of the entry proteins increases in animals of old age. This may explain, if true also in humans, why individuals of older age are more susceptible to the SARS-CoV-2 infection.


Subject(s)
Betacoronavirus/metabolism , Olfactory Mucosa/metabolism , Olfactory Receptor Neurons/metabolism , Peptidyl-Dipeptidase A/genetics , Serine Endopeptidases/genetics , Age Factors , Animals , Coronavirus Infections , Gene Expression , Gene Expression Profiling , Immunohistochemistry , In Situ Hybridization , Mice , Olfaction Disorders , Olfactory Mucosa/cytology , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral , RNA-Seq , Reverse Transcriptase Polymerase Chain Reaction , Serine Endopeptidases/metabolism , Virus Internalization
19.
Infect Dis Poverty ; 9(1): 45, 2020 Apr 28.
Article in English | MEDLINE | ID: covidwho-133403

ABSTRACT

BACKGROUND: Since its discovery in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 2 180 000 people worldwide and has caused more than 150 000 deaths as of April 16, 2020. SARS-CoV-2, which is the virus causing coronavirus disease 2019 (COVID-19), uses the angiotensin-converting enzyme 2 (ACE2) as a cell receptor to invade human cells. Thus, ACE2 is the key to understanding the mechanism of SARS-CoV-2 infection. This study is to investigate the ACE2 expression in various human tissues in order to provide insights into the mechanism of SARS-CoV-2 infection. METHODS: We compared ACE2 expression levels across 31 normal human tissues between males and females and between younger (ages ≤ 49 years) and older (ages > 49 years) persons using two-sided Student's t test. We also investigated the correlations between ACE2 expression and immune signatures in various tissues using Pearson's correlation test. RESULTS: ACE2 expression levels were the highest in the small intestine, testis, kidneys, heart, thyroid, and adipose tissue, and were the lowest in the blood, spleen, bone marrow, brain, blood vessels, and muscle. ACE2 showed medium expression levels in the lungs, colon, liver, bladder, and adrenal gland. ACE2 was not differentially expressed between males and females or between younger and older persons in any tissue. In the skin, digestive system, brain, and blood vessels, ACE2 expression levels were positively associated with immune signatures in both males and females. In the thyroid and lungs, ACE2 expression levels were positively and negatively associated with immune signatures in males and females, respectively, and in the lungs they had a positive and a negative correlation in the older and younger groups, respectively. CONCLUSIONS: Our data indicate that SARS-CoV-2 may infect other tissues aside from the lungs and infect persons with different sexes, ages, and races equally. The different host immune responses to SARS-CoV-2 infection may partially explain why males and females, young and old persons infected with this virus have markedly distinct disease severity. This study provides new insights into the role of ACE2 in the SARS-CoV-2 pandemic.


Subject(s)
Betacoronavirus , Peptidyl-Dipeptidase A/genetics , Receptors, Virus/genetics , Adult , Age Factors , Aged , Brain/enzymology , Cardiovascular System/enzymology , Cardiovascular System/immunology , Digestive System/enzymology , Digestive System/immunology , Endocrine Glands/enzymology , Endocrine Glands/immunology , Female , Gene Expression Profiling , Humans , Immune System/enzymology , Interferons/immunology , Lung/enzymology , Lung/immunology , Lymphocytes/immunology , Male , Middle Aged , Organ Specificity , Peptidyl-Dipeptidase A/blood , RNA-Seq , Receptors, Virus/blood , Sex Factors , Urogenital System/enzymology
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