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1.
Nucleic Acids Res ; 50(D1): D777-D784, 2022 01 07.
Article in English | MEDLINE | ID: covidwho-2062936

ABSTRACT

GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.


Subject(s)
Databases, Genetic , Intestinal Neoplasms/microbiology , Metagenome , Microbiota , Biomarkers/blood , Datasets as Topic , Gastrointestinal Microbiome/genetics , High-Throughput Nucleotide Sequencing , Humans , Internet , Intestinal Neoplasms/blood , Intestinal Neoplasms/genetics , Intestinal Neoplasms/pathology , Molecular Sequence Annotation , Phenotype , RNA, Ribosomal, 16S , Software
3.
Front Artif Intell ; 4: 672050, 2021.
Article in English | MEDLINE | ID: covidwho-1430749

ABSTRACT

Cohort-independent robust mortality prediction model in patients with COVID-19 infection is not yet established. To build up a reliable, interpretable mortality prediction model with strong foresight, we have performed an international, bi-institutional study from China (Wuhan cohort, collected from January to March) and Germany (Würzburg cohort, collected from March to September). A Random Forest-based machine learning approach was applied to 1,352 patients from the Wuhan cohort, generating a mortality prediction model based on their clinical features. The results showed that five clinical features at admission, including lymphocyte (%), neutrophil count, C-reactive protein, lactate dehydrogenase, and α-hydroxybutyrate dehydrogenase, could be used for mortality prediction of COVID-19 patients with more than 91% accuracy and 99% AUC. Additionally, the time-series analysis revealed that the predictive model based on these clinical features is very robust over time when patients are in the hospital, indicating the strong association of these five clinical features with the progression of treatment as well. Moreover, for different preexisting diseases, this model also demonstrated high predictive power. Finally, the mortality prediction model has been applied to the independent Würzburg cohort, resulting in high prediction accuracy (with above 90% accuracy and 85% AUC) as well, indicating the robustness of the model in different cohorts. In summary, this study has established the mortality prediction model that allowed early classification of COVID-19 patients, not only at admission but also along the treatment timeline, not only cohort-independent but also highly interpretable. This model represents a valuable tool for triaging and optimizing the resources in COVID-19 patients.

4.
Ann Hum Genet ; 85(6): 221-234, 2021 11.
Article in English | MEDLINE | ID: covidwho-1286650

ABSTRACT

In the early 2000s, emerging SARS-CoV-2, which is highly pathogenic, posed a great threat to public health. During COVID-19, epigenetic regulation is deemed to be an important part of the pathophysiology and illness severity. Using the Illumina Infinium Methylation EPIC BeadChip (850 K), we investigated genome-wide differences in DNA methylation between healthy subjects and COVID-19 patients with different disease severities. We conducted a combined analysis and selected 35 "marker" genes that could indicate a SARS-CoV-2 infection, including 12 (ATHL1, CHN2, CHST15, CPLX2, CRHR2, DCAKD, GNAI2, HECW1, HYAL1, MIR510, PDE11A, and SMG6) situated in the promoter region. The functions and pathways of differentially methylated genes were enriched in biological processes, signal transduction, and the immune system. In the "Severe versus Mild" group, differentially methylated genes, after eliminating duplicates, were used for PPI analyses. The four hub genes (GNG7, GNAS, PRKCZ, and PRKAG2) that had the highest degree of nodes were identified and among them, GNG7 and GNAS genes expressions were also downregulated in the severe group in sequencing results. Above all, the results suggest that GNG7 and GNAS may play a non-ignorable role in the progression of COVID-19. In conclusion, the identified key genes and related pathways in the current study can be used to study the molecular mechanisms of COVID-19 and may provide possibilities for specific treatments.


Subject(s)
COVID-19/genetics , COVID-19/pathology , DNA Methylation/genetics , Epigenesis, Genetic/genetics , Severity of Illness Index , Adult , Chromogranins/genetics , CpG Islands/genetics , Epigenome/genetics , Female , GTP-Binding Protein alpha Subunits, Gs/genetics , GTP-Binding Protein gamma Subunits/genetics , Genetic Markers/genetics , Humans , Inflammation/pathology , Male , Middle Aged , SARS-CoV-2
5.
BMC Public Health ; 21(1): 647, 2021 Apr 01.
Article in English | MEDLINE | ID: covidwho-1166901

ABSTRACT

BACKGROUND: In view of the ongoing coronavirus disease (COVID-19) pandemic, it remains unclear whether the severity of illness and time interval from symptom onset to release from quarantine differ between cases that originated from clusters and cases reported in other areas. This study aimed to assess epidemiological and intergenerational clinical characteristics of COVID-19 patients associated with cluster outbreaks to provide valuable data for the prevention and control of COVID-19. METHODS: We identified the first employee with COVID-19 at a supermarket and screened the close contacts of this index patient. Confirmed cases were divided into two groups according to the generation (first generation comprising supermarket employees [group A] and second or third generations comprising family members or friends of the supermarket employees [group B]). The epidemiological and clinical characteristics of the two groups were retrospectively compared. RESULTS: A total of 8437 people were screened, and 24 COVID-19 patients were identified. Seven patients (29.2%) were asymptomatic; three patients were responsible for six symptomatic cases. The interval from the confirmation of the first case to symptom onset in symptomatic patients was 5-11 days. The clinical manifestations of symptomatic patients upon admission were non-specific. All patients (including the seven asymptomatic patients) were admitted based on chest computed tomography features indicative of pneumonia. There were 11 cases in group A (first generation) and 13 cases in group B (second generation, 11 cases; third generation, 2 cases), with no significant differences in clinical and epidemiological characteristics between the two groups, except for sex, duration from symptom onset to hospitalization, and underlying disease (P > 0.05). CONCLUSIONS: For cluster outbreaks, it is important to comprehensively screen close the contacts of the index patient. Special attention should be paid to asymptomatic cases. The clinical management of cluster patients is similar to that of other COVID-19 patients.


Subject(s)
COVID-19/diagnosis , COVID-19/transmission , Contact Tracing , SARS-CoV-2 , Supermarkets , COVID-19/epidemiology , China , Female , Humans , Male , Retrospective Studies
6.
Int J Infect Dis ; 104: 685-692, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1056706

ABSTRACT

BACKGROUND: Almost a year after the outbreak of coronavirus disease 2019 (COVID-19), many hospitalized COVID-19 patients have recovered. However, little is known about the long-term follow-up (> 2 months) of discharged patients. METHODS: This study enrolled 527 discharged COVID-19 patients from 05 February to 11 March 2020. Basic characteristics, imaging features, nucleic acid detection results, and antibody levels of these patients were retrospectively reviewed. RESULTS: Of the 527 discharged patients, 32 (6.1%) had re-detectable positive (RP) nucleic acid results for SARS-CoV-2 during follow-up examinations, with 11 and four detections entailing stool samples and anal swabs, respectively, rather than respiratory samples. Juveniles were more susceptible to "infection recurrence" than other age groups, with shorter time spans for re-detectable positive (RP) RNA tests (an average of 8.8 days [6.0-9.0 days]), while the reverse was true for the middle-aged group (17.5 days on average [14.0-17.5 days]). Similar improvements in the imaging features of both RP and no RP (NRP) groups were observed. Negative antibody detections in patients at 3 and 6 months after discharge were 14.2% and 25.0%, respectively. Cases evidencing negative antibodies were more common among juvenile patients (40% vs. 15.6%, P=0.03) 6 months post-discharge. CONCLUSIONS: A total of 6.1% of 527 discharged patients showed RP status, which may be easier to be identified from stool samples than from other samples. Given the dropping rate of SARS-CoV-2 antibodies, reinfection may happen, especially in juvenile patients (aged<18 years). These findings have implications for the long-term management of recovered COVID-19 patients.


Subject(s)
COVID-19/epidemiology , SARS-CoV-2 , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/immunology , COVID-19/virology , COVID-19 Nucleic Acid Testing , COVID-19 Serological Testing , Child , Child, Preschool , China/epidemiology , Female , Follow-Up Studies , Humans , Infant , Male , Middle Aged , Patient Discharge , Retrospective Studies , Young Adult
7.
Ther Clin Risk Manag ; 17: 9-21, 2021.
Article in English | MEDLINE | ID: covidwho-1030561

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel pathogen, has caused an outbreak of coronavirus disease 2019 (COVID-19) that has spread rapidly around the world. Determining the risk factors for death and the differences in clinical features between severely ill and critically ill patients with SARS-CoV-2 pneumonia has become increasingly important. AIM: This study was intended to provide insight into the difference between severely ill and critically ill patients with SARS-CoV-2 pneumonia. METHODS: In this retrospective, multicenter cohort study, we enrolled 62 seriously ill patients with SARS-CoV-2 pneumonia who had been diagnosed by March 12, 2020. Clinical data, laboratory indexes, chest images, and treatment strategies collected from routine medical records were compared between severely ill and critically ill patients. Univariate and multivariate logistic regression analyses were also conducted to identify the risk factors associated with the progression of patients with severe COVID-19. RESULTS: Of the 62 patients with severe or critical illness, including 7 who died, 30 (48%) patients had underlying diseases, of which the most common was cardiovascular disease (hypertension, 34%, and coronary heart disease, 5%). Compared to patients with severe disease, those with critical disease had distinctly higher white blood cell counts, procalcitonin levels, and D-dimer levels, and lower hemoglobin levels and lymphocyte counts. Multivariate regression showed that a lymphocyte count less than 109/L (odds ratio 20.92, 95% CI 1.76-248.18; p=0.02) at admission increased the risk of developing a critical illness. CONCLUSION: Based on multivariate regression analysis, a lower lymphocyte count (<109/L) on admission is the most critical independent factor that is closely associated with an increased risk of progression to critical illness. Age, underlying diseases, especially hypertension and coronary heart disease, elevated D-dimer, decreased hemoglobin, and SOFA score, and APACH score also need to be taken into account for predicting disease progression. Blood cell counts and procalcitonin levels for the later secondary bacterial infection have a certain reference values.

9.
Comput Struct Biotechnol J ; 18: 3615-3622, 2020.
Article in English | MEDLINE | ID: covidwho-938867

ABSTRACT

COVID-19 has been one of the most serious infectious diseases since the end of 2019. However, the original source, as well as the treatment and prevention of causative agent of COVID-19 (namely SARS-CoV-2) are still unclear nearly a year after its publicly report. The microbiome approach, which has emerged in recent years focusing on human-related microbes, has become one of the promising avenues for source tracking, treatment, and prevention of a variety of infectious diseases including COVID-19. In this review, we summarized the microbiome approach as a supplementary approach for source tracking, treatment, and prevention of SARS-CoV-2 infection. We first provided background information on SARS-CoV-2 and microbiome approaches. Then we illustrated current strategies of microbiome methods to assist three aspects of COVID-19 research, namely source tracking, treatment, and prevention, respectively. Finally, we summarized the microbiome approaches and provided perspectives for future studies on faster and more effective SARS-CoV-2 epidemiology and pathogenesis based on microbiome approaches.

10.
mBio ; 11(6)2020 11 06.
Article in English | MEDLINE | ID: covidwho-930294

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates throughout human airways. The polarized human airway epithelium (HAE) cultured at an airway-liquid interface (HAE-ALI) is an in vitro model mimicking the in vivo human mucociliary airway epithelium and supports the replication of SARS-CoV-2. Prior studies characterized only short-period SARS-CoV-2 infection in HAE. In this study, continuously monitoring the SARS-CoV-2 infection in HAE-ALI cultures for a long period of up to 51 days revealed that SARS-CoV-2 infection was long lasting with recurrent replication peaks appearing between an interval of approximately 7 to 10 days, which was consistent in all the tested HAE-ALI cultures derived from 4 lung bronchi of independent donors. We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detected. Notably, virus infection immediately damaged the HAE, which is demonstrated by dispersed zonula occludens-1 (ZO-1) expression without clear tight junctions and partial loss of cilia. Importantly, we identified that SARS-CoV-2 productive infection of HAE requires a high viral load of >2.5 × 105 virions per cm2 of epithelium. Thus, our studies highlight the importance of a high viral load and that epithelial renewal initiates and maintains a recurrent infection of HAE with SARS-CoV-2.IMPORTANCE The pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to >35 million confirmed cases and >1 million fatalities worldwide. SARS-CoV-2 mainly replicates in human airway epithelia in COVID-19 patients. In this study, we used in vitro cultures of polarized human bronchial airway epithelium to model SARS-CoV-2 replication for a period of 21 to 51 days. We discovered that in vitro airway epithelial cultures endure a long-lasting SARS-CoV-2 propagation with recurrent peaks of progeny virus release at an interval of approximately 7 to 10 days. Our study also revealed that SARS-CoV-2 infection causes airway epithelia damage with disruption of tight junction function and loss of cilia. Importantly, SARS-CoV-2 exhibits a polarity of infection in airway epithelium only from the apical membrane; it infects ciliated and goblet cells but not basal and club cells. Furthermore, the productive infection of SARS-CoV-2 requires a high viral load of over 2.5 × 105 virions per cm2 of epithelium. Our study highlights that the proliferation of airway basal cells and regeneration of airway epithelium may contribute to the recurrent infections.


Subject(s)
Betacoronavirus/physiology , Models, Biological , Respiratory Mucosa/virology , Bronchi/cytology , Cells, Cultured , Epithelial Cells/pathology , Epithelial Cells/virology , Humans , Kinetics , Respiratory Mucosa/cytology , Respiratory Mucosa/pathology , SARS-CoV-2 , Viral Load , Viral Tropism , Virus Release , Virus Replication
11.
bioRxiv ; 2020 Aug 28.
Article in English | MEDLINE | ID: covidwho-900750

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates throughout human airways. The polarized human airway epithelium (HAE) cultured at an airway-liquid interface (HAE-ALI) is an in vitro model mimicking the in vivo human mucociliary airway epithelium and supports the replication of SARS-CoV-2. However, previous studies only characterized short-period SARS-CoV-2 infection in HAE. In this study, continuously monitoring the SARS-CoV-2 infection in HAE-ALI cultures for a long period of up to 51 days revealed that SARS-CoV-2 infection was long lasting with recurrent replication peaks appearing between an interval of approximately 7-10 days, which was consistent in all the tested HAE-ALI cultures derived from 4 lung bronchi of independent donors. We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Notably, virus infection immediately damaged the HAE, which is demonstrated by dispersed Zonula occludens-1 (ZO-1) expression without clear tight junctions and partial loss of cilia. Importantly, we identified that SARS-CoV-2 productive infection of HAE requires a high viral load of 2.5 × 10 5 virions per cm 2 of epithelium. Thus, our studies highlight the importance of a high viral load and that epithelial renewal initiates and maintains a recurrent infection of HAE with SARS-CoV-2.

12.
Front Med (Lausanne) ; 7: 210, 2020.
Article in English | MEDLINE | ID: covidwho-456897

ABSTRACT

Objective: This study aimed to identify additional characteristics and features of coronavirus disease (COVID-19) by assessing the clinical courses among COVID-19 patients in a region outside Hubei province. Methods: We analyzed retrospective data regarding general characteristics, epidemiologic history, underlying chronic diseases, clinical symptoms and complications, chest computed tomography findings, biochemical monitoring, disease severity, treatments, and outcomes among 37 adult patients with COVID-19. According to the duration from symptom onset to release from quarantine, the patients were divided into the ≤20 and >20-day groups, and the similarities and differences between them were compared. Results: Among the 37 patients, five had mild disease, 30 had moderate disease, one had severe disease, and one was critically ill. All of the patients were released from quarantine, and no mortality was observed. The average duration from symptom onset to release from quarantine was 20.2 ± 6.6 days. The average duration from symptom onset to hospitalization was 4.1 ± 3.7 days, and the patients were hospitalized for an average of 16.1 ± 6.2 days. The average age was 44.3 ± 1.67 years, and 78.4% of cases were caused by exposure to a patient with confirmed disease or the workplace of a patient with confirmed disease. The main symptoms were cough (67.6%), fever (62.2%), shortness of breath (32.4%), fatigue (24.3%), sore throat (21.6%), vomiting, and diarrhea (21.6%). White blood cell count was decreased in 27.0% of patients, and lymphocyte count was decreased in 62.2% of the patients, among whom 43.5% patients had counts of ≤0.6 × 109/L. On admission, 86.5% of patients showed pneumonia in chest CT scans, including some asymptomatic patients, while 68.8% of patients showed bilateral infiltration. In the >20-day group, the average age was 49.9 ± 1.38 years, and the average duration from symptom onset to hospitalization was 5.5 ± 3.9 days. Compared with the ≤20-day group, patients in the >20-day group were older and the duration was longer (P < 0.05). All of the seven asymptomatic patients belonged to the ≤20-day group. When the 37 patients were released from quarantine, the white blood cell count of 16.2% of the patients was <4.0 × 109/L, the lymphocyte count of 59.5% of the patients was <1.1 × 109/L, and the absolute counts of white blood cells and lymphocytes were 5.02 ± 1.34 × 109/L and 1.03 ± 0.34 × 109/L, respectively, compared with those recorded on admission (P > 0.05). Conclusion: The majority of COVID-19 cases in the study area were mild and moderate, with good clinical outcomes. There were some special characteristics in the clinical course. The reasons for differences in the duration from symptom onset to release from quarantine were complex. There was no significant change in the number of granulocytes at the time of release from quarantine compared to that at the time of admission.

13.
Preprint in English | medRxiv | ID: ppmedrxiv-20072611

ABSTRACT

BackgroundPatients with pre-existing cirrhosis are considered at increased risk of severe coronavirus disease 2019 (COVID-19) but the clinical course in these patients has not yet been reported. This study aimed to provide a detailed report of the clinical characteristics and outcomes among COVID-19 patients with pre-existing cirrhosis. MethodsIn this retrospective, multicenter cohort study, we consecutively included all adult inpatients with laboratory-confirmed COVID-19 and pre-existing cirrhosis that had been discharged or had died by 24 March 2020 from 16 designated hospitals in China. Demographic, clinical, laboratory and radiographic findings on admission, treatment, complications during hospitalization and clinical outcomes were collected and compared between survivors and non-survivors. FindingsTwenty-one patients were included consecutively in this study, of whom 16 were cured and 5 died in hospital. Seventeen patients had compensated cirrhosis and hepatitis B virus infection was the most common etiology. Lymphocyte and platelet counts were lower, and direct bilirubin levels were higher in patients who died than those who survived (p= 0{middle dot}040, 0{middle dot}032, and 0{middle dot}006, respectively). Acute respiratory distress syndrome and secondary infection were both the most frequently observed complications. Only one patient developed acute on chronic liver failure. Of the 5 non-survivors, all patients developed acute respiratory distress syndrome and 2 patients progressed to multiple organ dysfunction syndrome. InterpretationLower lymphocyte and platelet counts, and higher direct bilirubin level might represent poor prognostic indicators in SARS-CoV-2-infected patients with pre-existing cirrhosis.

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