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1.
Bioengineering (Basel) ; 9(4)2022 Mar 25.
Article in English | MEDLINE | ID: covidwho-1809683

ABSTRACT

OBJECTIVE: Pulmonary function parameters play a pivotal role in the assessment of respiratory diseases. However, the accuracy of the existing methods for the prediction of pulmonary function parameters is low. This study proposes a combination algorithm to improve the accuracy of pulmonary function parameter prediction. METHODS: We first established a system to collect volumetric capnography and then processed the data with a combination algorithm to predict pulmonary function parameters. The algorithm consists of three main parts: a medical feature regression structure consisting of support vector machines (SVM) and extreme gradient boosting (XGBoost) algorithms, a sequence feature regression structure consisting of one-dimensional convolutional neural network (1D-CNN), and an error correction structure using improved K-nearest neighbor (KNN) algorithm. RESULTS: The root mean square error (RMSE) of the pulmonary function parameters predicted by the combination algorithm was less than 0.39L and the R2 was found to be greater than 0.85 through a ten-fold cross-validation experiment. CONCLUSION: Compared with the existing methods for predicting pulmonary function parameters, the present algorithm can achieve a higher accuracy rate. At the same time, this algorithm uses specific processing structures for different features, and the interpretability of the algorithm is ensured while mining the feature depth information.

2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323557

ABSTRACT

Background: The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has gradually become a global public health crisis. Some patients who have recovered from COVID-19 subsequently tested positive again for SARS-CoV-2 after discharge (retesting-positive, RTP). However, the underlying mechanism is unknown.Methods: Here, 30 RTP patients, 20 convalescent patients, and 20 healthy controls were enrolled for analysis of the immunological characteristics of their peripheral blood mononuclear cells (PBMCs). Furthermore, we sought to comprehensively characterize the transcriptional changes in the three groups by transcriptome sequencing.Findings: It was found that the absolute numbers of CD4+ T cells, CD8+ T cells, and NK cells were not decreased remarkably, while the expression of activation markers on these cells was significantly decreased in RTP patients. Furthermore, the percentage of granzyme B-producing T cells was also decreased in RTP patients compared with that in convalescent patients. Moreover, the high expression of inhibitor of differentiation-1 (ID1) and the low expression of IFITM10 may be associated with the insufficient activation of immune cells and RTP occurrence.Interpretation: Our findings provide insights into the impaired immune function and pathogenesis of RTP occurrence in COVID-19, which may contribute to the development of immunotherapy for RTP patients.Funding Statement: This work was supported by China National Center for Biotechnology Development (2020YFC0843800 and 2020YFC0846800), Ministry of Science and Technology of China (2020TFC0844100), and China Postdoctoral Science Foundation (2020T130112ZX).Declaration of Interests: The authors declare no potential conflict of interest.Ethics Approval Statement: The studies were approved by the Ethics Committee of the First Affiliated Hospital of the University of Science & Technology of China (2020-XG(H)-005) and Peking University First Hospital (2020-Research-112) for Emerging Infectious Diseases. Experiments were conducted in accordance with the ethical guidelines of the 1975 Declaration of Helsinki, the Principles of Good Clinical Practice, and the guidelines of China’s regulatory requirements.

3.
J Mol Cell Biol ; 13(10): 748-759, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-1483467

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has become a global public health crisis. Some patients who have recovered from COVID-19 subsequently test positive again for SARS-CoV-2 RNA after discharge from hospital. How such retest-positive (RTP) patients become infected again is not known. In this study, 30 RTP patients, 20 convalescent patients, and 20 healthy controls were enrolled for the analysis of immunological characteristics of their peripheral blood mononuclear cells. We found that absolute numbers of CD4+ T cells, CD8+ T cells, and natural killer cells were not substantially decreased in RTP patients, but the expression of activation markers on these cells was significantly reduced. The percentage of granzyme B-producing T cells was also lower in RTP patients than in convalescent patients. Through transcriptome sequencing, we demonstrated that high expression of inhibitor of differentiation 1 (ID1) and low expression of interferon-induced transmembrane protein 10 (IFITM10) were associated with insufficient activation of immune cells and the occurrence of RTP. These findings provide insight into the impaired immune function associated with COVID-19 and the pathogenesis of RTP, which may contribute to a better understanding of the mechanisms underlying RTP.


Subject(s)
COVID-19/immunology , Convalescence , Reinfection/immunology , SARS-CoV-2/immunology , Transcriptome/immunology , Adult , Aged , Aged, 80 and over , Antigens, CD/genetics , Antigens, CD/immunology , COVID-19/genetics , COVID-19/virology , COVID-19 Nucleic Acid Testing , Case-Control Studies , Female , Healthy Volunteers , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Humans , Inhibitor of Differentiation Protein 1/genetics , Inhibitor of Differentiation Protein 1/immunology , Male , Middle Aged , Patient Readmission , RNA, Viral/isolation & purification , Reinfection/genetics , Reinfection/virology , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Young Adult
4.
Int Immunopharmacol ; 97: 107702, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1198831

ABSTRACT

BACKGROUND: The clinical characteristics and treatment of patients who tested positive for COVID-19 after recovery remained elusive. Effective antiviral therapy is important for tackling these patients. We assessed the efficacy and safety of favipiravir for treating these patients. METHODS: This is a multicenter, open-label, randomized controlled trial in SARS-CoV-2 RNA re-positive patients. Patients were randomly assigned in a 2:1 ratio to receive either favipiravir, in addition to standard care, or standard care alone. The primary outcome was time to achieve a consecutive twice (at intervals of more than 24 h) negative RT-PCR result for SARS-CoV-2 RNA in nasopharyngeal swab and sputum sample. RESULTS: Between March 27 and May 9, 2020, 55 patients underwent randomization; 36 were assigned to the favipiravir group and 19 were assigned to the control group. Favipiravir group had a significantly shorter time from start of study treatment to negative nasopharyngeal swab and sputum than control group (median 17 vs. 26 days); hazard ratio 2.1 (95% CI [1.1-4.0], p = 0.038). The proportion of virus shedding in favipiravir group was higher than control group (80.6% [29/36] vs. 52.6% [10/19], p = 0.030, respectively). C-reactive protein decreased significantly after treatment in the favipiravir group (p = 0.016). The adverse events were generally mild and self-limiting. CONCLUSION: Favipiravir was safe and superior to control in shortening the duration of viral shedding in SARS-CoV-2 RNA recurrent positive after discharge. However, a larger scale and randomized, double-blind, placebo-controlled trial is required to confirm our conclusion.


Subject(s)
Amides/administration & dosage , Antiviral Agents/administration & dosage , COVID-19/drug therapy , Pyrazines/administration & dosage , Reinfection/drug therapy , Administration, Oral , Adult , Aged , Amides/adverse effects , Antiviral Agents/adverse effects , COVID-19/blood , Female , Humans , Lymphocyte Subsets/drug effects , Male , Middle Aged , Patient Discharge , Pyrazines/adverse effects , RNA, Viral/analysis , RNA, Viral/drug effects , Reinfection/blood , SARS-CoV-2/drug effects , Treatment Outcome
5.
Infect Dis Poverty ; 10(1): 45, 2021 Mar 31.
Article in English | MEDLINE | ID: covidwho-1166939

ABSTRACT

BACKGROUND: The management of discharge COVID-19 patients with recurrent positive SARS-CoV-2 RNA is challenging. However, there are fewer scientific dissertations about the risk of recurrent positive. The aim of this study was to explore the relationship between SARS-COV-2 RNA positive duration (SPD) and the risk of recurrent positive. METHODS: This case-control multi-center study enrolled participants from 8 Chinese hospital including 411 participants (recurrent positive 241). Using unadjusted and multivariate-adjusted logistic regression analyses, generalized additive model with a smooth curve fitting, we evaluated the associations between SPD and risk of recurrent positive. Besides, subgroup analyses were performed to explore the potential interactions. RESULTS: Among recurrent positive patients, there were 121 females (50.2%), median age was 50 years old [interquartile range (IQR): 38-63]. In non-adjusted model and adjusted model, SPD was associated with an increased risk of recurrent positive (fully-adjusted model: OR = 1.05, 95% CI: 1.02-1.08, P = 0.001); the curve fitting was not significant (P = 0.286). Comparing with SPD < 14 days, the risk of recurrent positive in SPD > 28 days was risen substantially (OR = 3.09, 95% CI: 1.44-6.63, P = 0.004). Interaction and stratified analyses showed greater effect estimates of SPD and risk of recurrent positive in the hypertension, low monocyte count and percentage patients (P for interaction = 0.008, 0.002, 0.036, respectively). CONCLUSION: SPD was associated with a higher risk of recurrent positive and especially SPD > 28 day had a two-fold increase in the relative risk of re-positive as compared with SPD < 14 day. What's more, the risk may be higher among those with hypertension and lower monocyte count or percentage.


Subject(s)
COVID-19/virology , RNA, Viral/isolation & purification , SARS-CoV-2/isolation & purification , Adult , COVID-19/epidemiology , COVID-19/pathology , Case-Control Studies , Female , Hospitalization , Humans , Male , Middle Aged , Pharynx/virology , RNA, Viral/genetics , Recurrence , Risk Factors , SARS-CoV-2/genetics , Time Factors , Virus Shedding
6.
J Autoimmun ; 118: 102596, 2021 03.
Article in English | MEDLINE | ID: covidwho-1062442

ABSTRACT

Forty-seven samples of peripheral blood mononuclear cells from four groups of coronavirus disease (COVID)-19 patients (mild, severe, convalescent, retesting-positive) and healthy controls were applied to profile the immune repertoire of COVID-19 patients in acute infection or convalescence by transcriptome sequencing and immune-receptor repertoire (IRR) sequencing. Transcriptome analyses showed that genes within principal component group 1 (PC1) were associated with infection and disease severity whereas genes within PC2 were associated with recovery from COVID-19. A "dual-injury mechanism" of COVID-19 severity was related to an increased number of proinflammatory pathways and activated hypercoagulable pathways. A machine-learning model based on the genes associated with inflammatory and hypercoagulable pathways had the potential to be employed to monitor COVID-19 severity. Signature analyses of B-cell receptors (BCRs) and T-cell receptors (TCRs) revealed the dominant selection of longer V-J pairs (e.g., IGHV3-9-IGHJ6 and IGHV3-23-IGHJ6) and continuous tyrosine motifs in BCRs and lower diversity of TCRs. These findings provide potential predictors for COVID-19 outcomes, and new potential targets for COVID-19 treatment.


Subject(s)
COVID-19/genetics , Receptors, Antigen, B-Cell/genetics , Receptors, Antigen, T-Cell/genetics , Adult , COVID-19/drug therapy , COVID-19/immunology , Female , Humans , Male , Middle Aged , Receptors, Antigen, B-Cell/immunology , Receptors, Antigen, T-Cell/immunology
7.
Biomed Pharmacother ; 133: 110825, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1002354

ABSTRACT

BACKGROUND: Since December 2019, COVID-19 has spread to almost every corner of the world. In theory, tocilizumab and favipiravir are considered to be reliable drugs for the treatment of COVID-19 with elevated IL-6. We aimed to assess the efficacy and safety of tocilizumab combined with favipiravir in patients with COVID-19. METHODS: This was a multicenter trial in adults with COVID-19. Patients were randomly assigned (3:1:1) to a 14-day combination of favipiravir combined with tocilizumab (combination group), favipiravir, and tocilizumab. The primary outcome was the cumulative lung lesion remission rate (lung CT examination indicated absorption of lung inflammation). RESULTS: Between Feb 2 and March 15, 2020, 26 patients were recruited; 14 were randomly assigned to the combination group, 7 were assigned to the favipiravir group and 5 were assigned to the tocilizumab group. The cumulative lung lesion remission rate at day 14 was significantly higher in combination group as compared with favipiravir group (P = 0.019, HR 2.66 95 % CI [1.08-6.53]). And there was also a significant difference between tocilizumab and favipivavir (P = 0.034, HR 3.16, 95 % CI 0.62-16.10). In addition, there was no significant difference between the combination group and the tocilizumab group (P = 0.575, HR 1.28 95 %CI 0.39-4.23). Furthermore, combined therapy can also significantly relieve clinical symptoms and help blood routine to return to normal. No serious adverse events were reported. CONCLUSION: Tocilizumab combined with or without favipiravir can effectively improve the pulmonary inflammation of COVID-19 patients and inhibit the deterioration of the disease.


Subject(s)
Amides/therapeutic use , Antibodies, Monoclonal, Humanized/therapeutic use , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Pyrazines/therapeutic use , SARS-CoV-2/drug effects , Adult , Aged , Aged, 80 and over , Amides/administration & dosage , Amides/adverse effects , Antibodies, Monoclonal, Humanized/administration & dosage , Antibodies, Monoclonal, Humanized/adverse effects , Antiviral Agents/administration & dosage , Antiviral Agents/adverse effects , COVID-19/diagnostic imaging , COVID-19/pathology , COVID-19/therapy , Drug Therapy, Combination , Female , Humans , Interleukin-6/blood , Kaplan-Meier Estimate , Lung/diagnostic imaging , Lung/pathology , Male , Middle Aged , Models, Immunological , Pyrazines/administration & dosage , Pyrazines/adverse effects , Receptors, Interleukin-6/antagonists & inhibitors , Respiration, Artificial/statistics & numerical data , Sample Size , Treatment Outcome
8.
SSRN; 2020.
Preprint | SSRN | ID: ppcovidwho-731

ABSTRACT

Background: Wuhan, China was the epicenter of the 2019 coronavirus outbreak. As a designated hospital, Wuhan Pulmonary Hospital has received over 700 COVID-19 p

12.
PLoS One ; 15(9): e0239695, 2020.
Article in English | MEDLINE | ID: covidwho-792712

ABSTRACT

Wuhan, China was the epicenter of the 2019 coronavirus outbreak. As a designated hospital for COVID-19, Wuhan Pulmonary Hospital has received over 700 COVID-19 patients. With the COVID-19 becoming a pandemic all over the world, we aim to share our epidemiological and clinical findings with the global community. We studied 340 confirmed COVID-19 patients with clear clinical outcomes from Wuhan Pulmonary Hospital, including 310 discharged cases and 30 death cases. We analyzed their demographic, epidemiological, clinical and laboratory data and implemented our findings into an interactive, free access web application to evaluate COVID-19 patient's severity level. Our results show that baseline T cell subsets results differed significantly between the discharged cases and the death cases in Mann Whitney U test: Total T cells (p < 0.001), Helper T cells (p <0.001), Suppressor T cells (p <0.001), and TH/TSC (Helper/Suppressor ratio, p<0.001). Multivariate logistic regression model with death or discharge as the outcome resulted in the following significant predictors: age (OR 1.05, 95% CI, 1.00 to 1.10), underlying disease status (OR 3.42, 95% CI, 1.30 to 9.95), Helper T cells on the log scale (OR 0.22, 95% CI, 0.12 to 0.40), and TH/TSC on the log scale (OR 4.80, 95% CI, 2.12 to 11.86). The AUC for the logistic regression model is 0.90 (95% CI, 0.84 to 0.95), suggesting the model has a very good predictive power. Our findings suggest that while age and underlying diseases are known risk factors for poor prognosis, patients with a less damaged immune system at the time of hospitalization had higher chance of recovery. Close monitoring of the T cell subsets might provide valuable information of the patient's condition change during the treatment process. Our web visualization application can be used as a supplementary tool for the evaluation.


Subject(s)
Coronavirus Infections/diagnosis , Coronavirus Infections/mortality , Pneumonia, Viral/diagnosis , Pneumonia, Viral/mortality , Severity of Illness Index , T-Lymphocyte Subsets/cytology , Adult , Aged , Betacoronavirus , COVID-19 , China , Humans , Internet , Logistic Models , Middle Aged , Pandemics , Patient Discharge , Risk Factors , SARS-CoV-2 , Tertiary Care Centers
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