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2.
Virol J ; 18(1): 142, 2021 07 08.
Article in English | MEDLINE | ID: covidwho-1496196

ABSTRACT

OBJECTIVES: The aim of this study was to evaluate the role of antiviral drugs in reducing the risk of developing severe illness in patients with moderate COVID-19 pneumonia. METHODS: This retrospective cohort study included 403 adult patients with moderate COVID-19 pneumonia who were admitted to Shenzhen Third People's Hospital, China. The antiviral drugs arbidol, interferon alpha-1b, lopinavir-ritonavir and ribavirin were distributed to the patients for treatment. The primary endpoint of this study was the time to develop severe illness. RESULTS: Of the 462 patients admitted, 403 had moderate COVID-19 symptoms at hospital admission and were included in this study. 90 of the 403 (22.3%) patients progressed to severe illness. The use of arbidol was associated with a lower severity rate 3.5% compared to control group 30.5%, p-value < 0.0001; the adjusted hazard ratio was 0.28 (95% CI: 0.084-0.90, p = 0.033). The use of interferon alpha-1b was associated with a lower severity rate 15.5% compared to control group 29.3%, with p-value < 0.0001; the adjusted hazard ratio was 0.30 (95% CI: 0.15-0.58, p =  0.0005). The use of lopinavir-itonavir and ribavirin did not show significant differences in adjusted regression models. Early use of arbidol within 7 days of symptom onset was significantly associated with a reduced recovery time of - 5.2 days (IQR - 3.0 to - 7.5, p = 4e-06) compared with the control group. CONCLUSION: Treatment with arbidol and interferon alpha-1b contributes to reducing the severity of illness in patients with moderate COVID-19 pneumonia. Early use of arbidol may reduce patients' recovery time.


Subject(s)
Antiviral Agents/administration & dosage , COVID-19/drug therapy , Indoles/administration & dosage , Interferon-alpha/administration & dosage , Adult , China , Drug Therapy, Combination , Female , Hospitalization , Humans , Male , Middle Aged , Retrospective Studies , Severity of Illness Index , Treatment Outcome
3.
JAMA ; 323(16): 1582-1589, 2020 04 28.
Article in English | MEDLINE | ID: covidwho-1453469

ABSTRACT

Importance: Coronavirus disease 2019 (COVID-19) is a pandemic with no specific therapeutic agents and substantial mortality. It is critical to find new treatments. Objective: To determine whether convalescent plasma transfusion may be beneficial in the treatment of critically ill patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Design, Setting, and Participants: Case series of 5 critically ill patients with laboratory-confirmed COVID-19 and acute respiratory distress syndrome (ARDS) who met the following criteria: severe pneumonia with rapid progression and continuously high viral load despite antiviral treatment; Pao2/Fio2 <300; and mechanical ventilation. All 5 were treated with convalescent plasma transfusion. The study was conducted at the infectious disease department, Shenzhen Third People's Hospital in Shenzhen, China, from January 20, 2020, to March 25, 2020; final date of follow-up was March 25, 2020. Clinical outcomes were compared before and after convalescent plasma transfusion. Exposures: Patients received transfusion with convalescent plasma with a SARS-CoV-2-specific antibody (IgG) binding titer greater than 1:1000 (end point dilution titer, by enzyme-linked immunosorbent assay [ELISA]) and a neutralization titer greater than 40 (end point dilution titer) that had been obtained from 5 patients who recovered from COVID-19. Convalescent plasma was administered between 10 and 22 days after admission. Main Outcomes and Measures: Changes of body temperature, Sequential Organ Failure Assessment (SOFA) score (range 0-24, with higher scores indicating more severe illness), Pao2/Fio2, viral load, serum antibody titer, routine blood biochemical index, ARDS, and ventilatory and extracorporeal membrane oxygenation (ECMO) supports before and after convalescent plasma transfusion. Results: All 5 patients (age range, 36-65 years; 2 women) were receiving mechanical ventilation at the time of treatment and all had received antiviral agents and methylprednisolone. Following plasma transfusion, body temperature normalized within 3 days in 4 of 5 patients, the SOFA score decreased, and Pao2/Fio2 increased within 12 days (range, 172-276 before and 284-366 after). Viral loads also decreased and became negative within 12 days after the transfusion, and SARS-CoV-2-specific ELISA and neutralizing antibody titers increased following the transfusion (range, 40-60 before and 80-320 on day 7). ARDS resolved in 4 patients at 12 days after transfusion, and 3 patients were weaned from mechanical ventilation within 2 weeks of treatment. Of the 5 patients, 3 have been discharged from the hospital (length of stay: 53, 51, and 55 days), and 2 are in stable condition at 37 days after transfusion. Conclusions and Relevance: In this preliminary uncontrolled case series of 5 critically ill patients with COVID-19 and ARDS, administration of convalescent plasma containing neutralizing antibody was followed by improvement in their clinical status. The limited sample size and study design preclude a definitive statement about the potential effectiveness of this treatment, and these observations require evaluation in clinical trials.


Subject(s)
Antibodies, Neutralizing/therapeutic use , Antibodies, Viral/therapeutic use , Betacoronavirus/immunology , Coronavirus Infections/therapy , Pneumonia, Viral/therapy , Respiratory Distress Syndrome/therapy , Adult , Aged , Antibodies, Viral/blood , Antiviral Agents/therapeutic use , Blood Donors , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/physiopathology , Critical Illness , Female , Glucocorticoids/therapeutic use , Humans , Immunization, Passive , Immunoglobulin G/blood , Immunoglobulin M/blood , Male , Methylprednisolone/therapeutic use , Middle Aged , Organ Dysfunction Scores , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/physiopathology , SARS-CoV-2
4.
Respir Res ; 22(1): 203, 2021 Jul 09.
Article in English | MEDLINE | ID: covidwho-1300252

ABSTRACT

BACKGROUND: Thousands of Coronavirus Disease 2019 (COVID-19) patients have been discharged from hospitals Persistent follow-up studies are required to evaluate the prevalence of post-COVID-19 fibrosis. METHODS: This study involves 462 laboratory-confirmed patients with COVID-19 who were admitted to Shenzhen Third People's Hospital from January 11, 2020 to April 26, 2020. A total of 457 patients underwent thin-section chest CT scans during the hospitalization or after discharge to identify the pulmonary lesion. A total of 287 patients were followed up from 90 to 150 days after the onset of the disease, and lung function tests were conducted about three months after the onset. The risk factors affecting the persistence of pulmonary fibrosis were identified through regression analysis and the prediction model of the persistence of pulmonary fibrosis was established. RESULTS: Parenchymal bands, irregular interfaces, reticulation and traction bronchiectasis were the most common CT features in all COVID-19 patients. During the 0-30, 31-60, 61-90, 91-120 and > 120 days after onset, 86.87%, 74.40%, 79.56%, 68.12% and 62.03% patients developed with pulmonary fibrosis and 4.53%, 19.61%, 18.02%, 38.30% and 48.98% patients reversed pulmonary fibrosis, respectively. It was observed that Age, BMI, Fever, and Highest PCT were predictive factors for sustaining fibrosis even after 90 days from onset. A predictive model of the persistence with pulmonary fibrosis was developed based-on the Logistic Regression method with an accuracy, PPV, NPV, Sensitivity and Specificity of the model of 76%, 71%, 79%, 67%, and 82%, respectively. More than half of the COVID-19 patients revealed abnormal conditions in lung function after 90 days from onset, and the ratio of abnormal lung function did not differ on a statistically significant level between the fibrotic and non-fibrotic groups. CONCLUSIONS: Persistent pulmonary fibrosis was more likely to develop in patients with older age, higher BMI, severe/critical condition, fever, a longer viral clearance time, pre-existing disease and delayed hospitalization. Fibrosis developed in COVID-19 patients could be reversed in about a third of the patients after 120 days from onset. The pulmonary function of less than half of COVID-19 patients could turn to normal condition after three months from onset. An effective prediction model with an average area under the curve (AUC) of 0.84 was established to predict the persistence of pulmonary fibrosis in COVID-19 patients for early diagnosis.


Subject(s)
COVID-19/virology , Lung/virology , Patient Discharge , Pulmonary Fibrosis/virology , SARS-CoV-2/pathogenicity , Adolescent , Adult , COVID-19/complications , COVID-19/diagnosis , China , Female , Host-Pathogen Interactions , Humans , Lung/diagnostic imaging , Lung/physiopathology , Male , Middle Aged , Prognosis , Pulmonary Fibrosis/diagnostic imaging , Pulmonary Fibrosis/physiopathology , Respiratory Function Tests , Time Factors , Tomography, X-Ray Computed , Young Adult
5.
Front Immunol ; 12: 691879, 2021.
Article in English | MEDLINE | ID: covidwho-1282387

ABSTRACT

Increasing human Adenovirus (HAdV) infections complicated with acute respiratory distress syndrome (ARDS) even fatal outcome were reported in immunocompetent adolescent and adult patients. Here, we characterized the cytokine/chemokine expression profiles of immunocompetent patients complicated with ARDS during HAdV infection and identified biomarkers for disease severity/progression. Forty-eight cytokines/chemokines in the plasma samples from 19 HAdV-infected immunocompetent adolescent and adult patients (ten complicated with ARDS) were measured and analyzed in combination with clinical indices. Immunocompetent patients with ARDS caused by severe acute respiratory disease coronavirus (SARS-CoV)-2, 2009 pandemic H1N1 (panH1N1) or bacteria were included for comparative analyses. Similar indices of disease course/progression were found in immunocompetent patients with ARDS caused by HAdV, SARS-CoV-2 or panH1N infections, whereas the HAdV-infected group showed a higher prevalence of viremia, as well as increased levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and creatine kinase (CK). Expression levels of 33 cytokines/chemokines were increased significantly in HAdV-infected patients with ARDS compared with that in healthy controls, and many of them were also significantly higher than those in SARS-CoV-2-infected and panH1N1-infected patients. Expression of interferon (IFN)-γ, interleukin (IL)-1ß, hepatocyte growth factor (HGF), monokine induced by IFN-γ (MIG), IL-6, macrophage-colony stimulating factor (M-CSF), IL-10, IL-1α and IL-2Ra was significantly higher in HAdV-infected patients with ARDS than that in those without ARDS, and negatively associated with the ratio of the partial pressure of oxygen in arterial blood/fraction of inspired oxygen (PaO2/FiO2). Analyses of the receiver operating characteristic curve (ROC) showed that expression of IL-10, M-CSF, MIG, HGF, IL-1ß, IFN-γ and IL-2Ra could predict the progression of HAdV infection, with the highest area under the curve (AUC) of 0.944 obtained for IL-10. Of note, the AUC value for the combination of IL-10, IFN-γ, and M-CSF reached 1. In conclusion, the "cytokine storm" occurred during HAdV infection in immunocompetent patients, and expression of IL-10, M-CSF, MIG, HGF, IL-1ß, IFN-γ and IL-2Ra was closely associated with disease severity and could predict disease progression.


Subject(s)
Adenovirus Infections, Human/blood , Cytokines/blood , Respiratory Distress Syndrome/blood , Adenovirus Infections, Human/complications , Adenovirus Infections, Human/pathology , Adenoviruses, Human , Adolescent , Adult , Bacteria , Bacterial Infections/blood , Bacterial Infections/complications , Bacterial Infections/pathology , Biomarkers/blood , COVID-19/blood , COVID-19/complications , COVID-19/pathology , Disease Progression , Female , Humans , Influenza A Virus, H1N1 Subtype , Influenza, Human/blood , Influenza, Human/complications , Influenza, Human/pathology , Male , Respiratory Distress Syndrome/complications , Respiratory Distress Syndrome/pathology , SARS-CoV-2 , Severity of Illness Index , Viremia/blood , Viremia/complications , Viremia/pathology , Young Adult
6.
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
7.
Front Med ; 15(4): 507-527, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1188167

ABSTRACT

The avian influenza A (H7N9) virus is a zoonotic virus that is closely associated with live poultry markets. It has caused infections in humans in China since 2013. Five waves of the H7N9 influenza epidemic occurred in China between March 2013 and September 2017. H7N9 with low-pathogenicity dominated in the first four waves, whereas highly pathogenic H7N9 influenza emerged in poultry and spread to humans during the fifth wave, causing wide concern. Specialists and officials from China and other countries responded quickly, controlled the epidemic well thus far, and characterized the virus by using new technologies and surveillance tools that were made possible by their preparedness efforts. Here, we review the characteristics of the H7N9 viruses that were identified while controlling the spread of the disease. It was summarized and discussed from the perspectives of molecular epidemiology, clinical features, virulence and pathogenesis, receptor binding, T-cell responses, monoclonal antibody development, vaccine development, and disease burden. These data provide tools for minimizing the future threat of H7N9 and other emerging and re-emerging viruses, such as SARS-CoV-2.


Subject(s)
COVID-19 , Influenza A Virus, H7N9 Subtype , Influenza in Birds , Influenza, Human , Animals , China/epidemiology , Humans , Influenza in Birds/epidemiology , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Poultry , SARS-CoV-2
8.
Front Cell Infect Microbiol ; 11: 641920, 2021.
Article in English | MEDLINE | ID: covidwho-1170079

ABSTRACT

Pseudomonas aeruginosa is a biofilm-forming opportunistic pathogen which causes chronic infections in immunocompromised patients and leads to high mortality rate. It is identified as a common coinfecting pathogen in COVID-19 patients causing exacerbation of illness. In our hospital, P. aeruginosa is one of the top coinfecting bacteria identified among COVID-19 patients. We collected a strong biofilm-forming P. aeruginosa strain displaying small colony variant morphology from a severe COVID-19 patient. Genomic and transcriptomic sequencing analyses were performed with phenotypic validation to investigate its adaptation in SARS-CoV-2 infected environment. Genomic characterization predicted specific genomic islands highly associated with virulence, transcriptional regulation, and DNA restriction-modification systems. Epigenetic analysis revealed a specific N6-methyl adenine (m6A) methylating pattern including methylation of alginate, flagellar and quorum sensing associated genes. Differential gene expression analysis indicated that this isolate formed excessive biofilm by reducing flagellar formation (7.4 to 1,624.1 folds) and overproducing extracellular matrix components including CdrA (4.4 folds), alginate (5.2 to 29.1 folds) and Pel (4.8-5.5 folds). In summary, we demonstrated that P. aeuginosa clinical isolates with novel epigenetic markers could form excessive biofilm, which might enhance its antibiotic resistance and in vivo colonization in COVID-19 patients.


Subject(s)
Adaptation, Physiological/physiology , COVID-19/complications , Coinfection/complications , Pseudomonas Infections/complications , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/metabolism , Adhesins, Bacterial/genetics , Adhesins, Bacterial/metabolism , Alginates , Bacteria , Biofilms/growth & development , DNA Methylation , Epigenomics , Gene Expression Profiling , Gene Expression Regulation, Bacterial , Genome, Bacterial , Humans , Pseudomonas Infections/immunology , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/classification , Quorum Sensing/genetics , SARS-CoV-2 , Transcriptome , Virulence
9.
Innovation (N Y) ; 1(3): 100061, 2020 11 25.
Article in English | MEDLINE | ID: covidwho-1164618

ABSTRACT

The worldwide epidemic of coronavirus disease 2019 (COVID-19) is ongoing. Rapid and accurate detection of the causative virus SARS-CoV-2 is vital for the treatment and control of COVID-19. In this study, the comparative sensitivity of different respiratory specimen types were retrospectively analyzed using 3,552 clinical samples from 410 COVID-19 patients confirmed by Guangdong CDC (Center for Disease Control and Prevention). Except for bronchoalveolar lavage fluid (BALF), the sputum possessed the highest positive rate (73.4%-87.5%), followed by nasal swabs (53.1%-85.3%) for both severe and mild cases during the first 14 days after illness onset (d.a.o.). Viral RNA could be detected in all BALF samples collected from the severe group within 14 d.a.o. and lasted up to 46 d.a.o. Moreover, although viral RNA was negative in the upper respiratory samples, it was also positive in BALF samples in most cases from the severe group during treatment. Notably, no viral RNA was detected in BALF samples from the mild group. Despite typical ground-glass opacity observed via computed tomographic scans, no viral RNA was detected in the first three or all upper respiratory tract specimens from some COVID-19 patients. In conclusion, sputum is most sensitive for routine laboratory diagnosis of COVID-19, followed by nasal swabs. Detection of viral RNA in BALF improves diagnostic accuracy in severe COVID-19 patients.

10.
Clin Infect Dis ; 71(16): 2027-2034, 2020 11 19.
Article in English | MEDLINE | ID: covidwho-1153138

ABSTRACT

BACKGROUND: The novel coronavirus SARS-CoV-2 is a newly emerging virus. The antibody response in infected patients remains largely unknown, and the clinical value of antibody testing has not been fully demonstrated. METHODS: 173 patients with SARS-CoV-2 infection were enrolled. Their serial plasma samples (n = 535) collected during hospitalization were tested for total antibodies (Ab), IgM, and IgG against SARS-CoV-2. The dynamics of antibodies with disease progress were analyzed. RESULTS: Among 173 patients, the seroconversion rates for Ab, IgM, and IgG were 93.1%, 82.7%, and 64.7%, respectively. The reason for the negative antibody findings in 12 patients might be due to the lack of blood samples at the later stage of illness. The median seroconversion times for Ab, IgM, and then IgG were days 11, 12, and 4, respectively. The presence of antibodies was <40% among patients within 1 week of onset, and rapidly increased to 100.0% (Ab), 94.3% (IgM), and 79.8% (IgG) by day 15 after onset. In contrast, RNA detectability decreased from 66.7% (58/87) in samples collected before day 7 to 45.5% (25/55) during days 15-39. Combining RNA and antibody detection significantly improved the sensitivity of pathogenic diagnosis for COVID-19 (P < .001), even in the early phase of 1 week from onset (P = .007). Moreover, a higher titer of Ab was independently associated with a worse clinical classification (P = .006). CONCLUSIONS: Antibody detection offers vital clinical information during the course of SARS-CoV-2 infection. The findings provide strong empirical support for the routine application of serological testing in the diagnosis and management of COVID-19 patients.


Subject(s)
COVID-19/immunology , COVID-19/virology , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Adult , Aged , Antibodies, Viral/metabolism , Antibody Formation/physiology , Enzyme-Linked Immunosorbent Assay , Female , Humans , Immunoglobulin G/metabolism , Immunoglobulin M/metabolism , Male , Middle Aged , Pandemics , Serologic Tests
11.
PLoS Comput Biol ; 16(12): e1008489, 2020 12.
Article in English | MEDLINE | ID: covidwho-1004405

ABSTRACT

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus poses serious threats to the global public health and leads to worldwide crisis. No effective drug or vaccine is readily available. The viral RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target. A hybrid drug screening procedure was proposed and applied to identify potential drug candidates targeting RdRp from 1906 approved drugs. Among the four selected market available drug candidates, Pralatrexate and Azithromycin were confirmed to effectively inhibit SARS-CoV-2 replication in vitro with EC50 values of 0.008µM and 9.453 µM, respectively. For the first time, our study discovered that Pralatrexate is able to potently inhibit SARS-CoV-2 replication with a stronger inhibitory activity than Remdesivir within the same experimental conditions. The paper demonstrates the feasibility of fast and accurate anti-viral drug screening for inhibitors of SARS-CoV-2 and provides potential therapeutic agents against COVID-19.


Subject(s)
Aminopterin/analogs & derivatives , Antiviral Agents/pharmacology , Drug Evaluation, Preclinical/methods , Drug Repositioning , RNA-Dependent RNA Polymerase/antagonists & inhibitors , SARS-CoV-2/physiology , Aminopterin/chemistry , Aminopterin/pharmacology , Animals , Azithromycin/chemistry , Azithromycin/pharmacology , COVID-19/drug therapy , Chlorocebus aethiops , Computer Simulation , Deep Learning , Molecular Dynamics Simulation , RNA-Dependent RNA Polymerase/chemistry , Vero Cells , Virus Replication/drug effects
13.
J Inflamm Res ; 13: 985-993, 2020.
Article in English | MEDLINE | ID: covidwho-952959

ABSTRACT

Purpose: Novel coronavirus disease has become such an escalating epidemic that the exponential growth of infected patients has overloaded the health-care systems in many countries. Determination of early assessments for patients with a risk of clinical deterioration would benefit the management of COVID-19 outbreaks. Patients and Methods: A total of 214 confirmed COVID-19 patients were enrolled from January 11th to February 11th 2020. Medical records including laboratory parameters, clinical outcomes and other characteristics of the admitted patients were analyzed retrospectively. Results: The critical patients experienced a significantly prolonged onset-admission interval and presented with lymphopenia (r=-0.547, p=0.015) and lower albumin level (p<0.001) 6 days after symptom onset. Early admission of critical patients significantly reduced the duration of hormone therapy. Starting from 9 days of hospital stay, the reduced lymphocyte counts exhibited linear growth. Furthermore, on days 9 and 12, significant correlations were demonstrated between immunological manifestations and duration of hormone therapy in critical patients, and length of hospital stay in severe patients. In addition, the virus negative conversion rate was more significantly correlated with increased lymphocytes in critical patients. Conclusion: Early intervention, within 6 days of symptom onset, benefited patients' recovery from critical illness. The 9-12 days of hospital care represented a valuable window during which to evaluate the therapeutic effects on physical recovery and virus clearance.

14.
Engineering (Beijing) ; 2020 Nov 28.
Article in English | MEDLINE | ID: covidwho-947208

ABSTRACT

Coronavirus disease 2019 (COVID-19) has become a worldwide pandemic. Hospitalized patients of COVID-19 suffer from a high mortality rate, motivating the development of convenient and practical methods that allow clinicians to promptly identify high-risk patients. Here, we have developed a risk score using clinical data from 1479 inpatients admitted to Tongji Hospital, Wuhan, China (development cohort) and externally validated with data from two other centers: 141 inpatients from Jinyintan Hospital, Wuhan, China (validation cohort 1) and 432 inpatients from The Third People's Hospital of Shenzhen, Shenzhen, China (validation cohort 2). The risk score is based on three biomarkers that are readily available in routine blood samples and can easily be translated into a probability of death. The risk score can predict the mortality of individual patients more than 12 d in advance with more than 90% accuracy across all cohorts. Moreover, the Kaplan-Meier score shows that patients can be clearly differentiated upon admission as low, intermediate, or high risk, with an area under the curve (AUC) score of 0.9551. In summary, a simple risk score has been validated to predict death in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); it has also been validated in independent cohorts.

16.
Emerg Microbes Infect ; 9(1): 2368-2378, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-910382

ABSTRACT

Managing recovered COVID-19 patients with recurrent-positive SARS-CoV-2 RNA test results is challenging. We performed a population-based observational study to characterize the viral RNA level and serum antibody responses in recurrent-positive patients and evaluate their viral transmission risk. Of 479 recovered COVID-19 patients, 93 (19%) recurrent-positive patients were identified, characterized by younger age, with a median discharge-to-recurrent-positive length of 8 days. After readmission, recurrent-positive patients exhibited mild (28%) or absent (72%) symptoms, with no disease progression. The viral RNA level in recurrent-positive patients ranged from 1.8 to 5.7 log10 copies/mL (median: 3.2), which was significantly lower than the corresponding values at disease onset. There are generally no significant differences in antibody levels between recurrent-positive and non-recurrent-positive patients, or in recurrent-positive patients over time (before, during, or after recurrent-positive detection). Virus isolation of nine representative specimens returned negative results. Whole genome sequencing of six specimens yielded only genomic fragments. 96 close contacts and 1,200 candidate contacts of 23 recurrent-positive patients showed no clinical symptoms; their viral RNA (1,296/1,296) and antibody (20/20) tests were negative. After full recovery (no longer/never recurrent-positive), 60% (98/162) patients had neutralizing antibody titers of ≥1:32. Our findings suggested that an intermittent, non-stable excretion of low-level viral RNA may result in recurrent-positive occurrence, rather than re-infection. Recurrent-positive patients pose a low transmission risk, a relatively relaxed management of recovered COVID-19 patients is recommended.


Subject(s)
Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Adult , Betacoronavirus/genetics , Betacoronavirus/immunology , COVID-19 , COVID-19 Testing , Coronavirus Infections/therapy , Coronavirus Infections/transmission , Female , Genome, Viral/genetics , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/therapy , Pneumonia, Viral/transmission , Recurrence , SARS-CoV-2 , Whole Genome Sequencing , Young Adult
17.
Clin Infect Dis ; 71(15): 799-806, 2020 07 28.
Article in English | MEDLINE | ID: covidwho-909328

ABSTRACT

BACKGROUND: An outbreak of coronavirus disease 2019 (COVID-19) is becoming a public health emergency. Data are limited on the duration and host factors related to viral shedding. METHODS: In this retrospective study, risk factors associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding were evaluated in a cohort of 113 symptomatic patients from 2 hospitals outside Wuhan. RESULTS: The median (interquartile range) duration of SARS-CoV-2 RNA detection was 17 (13-22) days as measured from illness onset. When comparing patients with early (<15 days) and late (≥15 days after illness onset) viral RNA clearance, prolonged SARS-CoV-2 RNA shedding was associated with male sex (P = .009), old age (P = .033), concomitant hypertension (P = .009), delayed admission to hospital after illness onset (P = .001), severe illness at admission (P = .049), invasive mechanical ventilation (P = .006), and corticosteroid treatment (P = .025). Patients with longer SARS-CoV-2 RNA shedding duration had slower recovery of body temperature (P < .001) and focal absorption on radiograph images (P < .001) than patients with early SARS-CoV-2 RNA clearance. Male sex (OR, 3.24; 95% CI, 1.31-8.02), delayed hospital admission (OR, 1.30; 95% CI, 1.10-1.54), and invasive mechanical ventilation (OR, 9.88; 95% CI, 1.11-88.02) were independent risk factors for prolonged SARS-CoV-2 RNA shedding. CONCLUSIONS: Male sex, delayed admission to hospital after illness onset, and invasive mechanical ventilation were associated with prolonged SARS-CoV-2 RNA shedding. Hospital admission and general treatments should be started as soon as possible in symptomatic COVID-19 patients, especially male patients.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Pneumonia, Viral/virology , RNA, Viral/isolation & purification , Virus Shedding , Adult , Betacoronavirus/pathogenicity , COVID-19 , China/epidemiology , Cohort Studies , Coronavirus Infections/epidemiology , Disease Progression , Female , Hospitalization , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/epidemiology , Respiration, Artificial/adverse effects , Retrospective Studies , Risk Factors , SARS-CoV-2 , Sex Factors , Time Factors , Time-to-Treatment
18.
Structure ; 28(11): 1218-1224.e4, 2020 11 03.
Article in English | MEDLINE | ID: covidwho-872505

ABSTRACT

The ongoing global pandemic of coronavirus disease 2019 (COVID-19) resulted from the outbreak of SARS-CoV-2 in December 2019. Currently, multiple efforts are being made to rapidly develop vaccines and treatments to fight COVID-19. Current vaccine candidates use inactivated SARS-CoV-2 viruses; therefore, it is important to understand the architecture of inactivated SARS-CoV-2. We have genetically and structurally characterized ß-propiolactone-inactivated viruses from a propagated and purified clinical strain of SARS-CoV-2. We observed that the virus particles are roughly spherical or moderately pleiomorphic. Although a small fraction of prefusion spikes are found, most spikes appear nail shaped, thus resembling a postfusion state, where the S1 protein of the spike has disassociated from S2. Cryoelectron tomography and subtomogram averaging of these spikes yielded a density map that closely matches the overall structure of the SARS-CoV postfusion spike and its corresponding glycosylation site. Our findings have major implications for SARS-CoV-2 vaccine design, especially those using inactivated viruses.


Subject(s)
Betacoronavirus/ultrastructure , Disinfectants/pharmacology , Propiolactone/pharmacology , Virion/drug effects , Animals , Betacoronavirus/drug effects , Betacoronavirus/immunology , COVID-19 Vaccines , Chlorocebus aethiops , Coronavirus Infections/immunology , Coronavirus Infections/prevention & control , Cryoelectron Microscopy , Electron Microscope Tomography , Humans , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/ultrastructure , Vaccines, Inactivated/immunology , Vero Cells , Viral Vaccines/immunology , Virion/ultrastructure
19.
China Tropical Medicine ; 20(8):772-775, 2020.
Article in Chinese | GIM | ID: covidwho-860915

ABSTRACT

Objective: To analyze the clinical characteristics, cardiac injury characteristics and early warning indexes of severe type in patients with COVID-19, so as to provide data for the evaluation, clinical treatment and prognosis of COVID-19 patients.

20.
JMIR Med Inform ; 8(10): e21788, 2020 Oct 15.
Article in English | MEDLINE | ID: covidwho-862872

ABSTRACT

BACKGROUND: The novel coronavirus SARS-CoV-2 and its associated disease, COVID-19, have caused worldwide disruption, leading countries to take drastic measures to address the progression of the disease. As SARS-CoV-2 continues to spread, hospitals are struggling to allocate resources to patients who are most at risk. In this context, it has become important to develop models that can accurately predict the severity of infection of hospitalized patients to help guide triage, planning, and resource allocation. OBJECTIVE: The aim of this study was to develop accurate models to predict the mortality of hospitalized patients with COVID-19 using basic demographics and easily obtainable laboratory data. METHODS: We performed a retrospective study of 375 hospitalized patients with COVID-19 in Wuhan, China. The patients were randomly split into derivation and validation cohorts. Regularized logistic regression and support vector machine classifiers were trained on the derivation cohort, and accuracy metrics (F1 scores) were computed on the validation cohort. Two types of models were developed: the first type used laboratory findings from the entire length of the patient's hospital stay, and the second type used laboratory findings that were obtained no later than 12 hours after admission. The models were further validated on a multicenter external cohort of 542 patients. RESULTS: Of the 375 patients with COVID-19, 174 (46.4%) died of the infection. The study cohort was composed of 224/375 men (59.7%) and 151/375 women (40.3%), with a mean age of 58.83 years (SD 16.46). The models developed using data from throughout the patients' length of stay demonstrated accuracies as high as 97%, whereas the models with admission laboratory variables possessed accuracies of up to 93%. The latter models predicted patient outcomes an average of 11.5 days in advance. Key variables such as lactate dehydrogenase, high-sensitivity C-reactive protein, and percentage of lymphocytes in the blood were indicated by the models. In line with previous studies, age was also found to be an important variable in predicting mortality. In particular, the mean age of patients who survived COVID-19 infection (50.23 years, SD 15.02) was significantly lower than the mean age of patients who died of the infection (68.75 years, SD 11.83; P<.001). CONCLUSIONS: Machine learning models can be successfully employed to accurately predict outcomes of patients with COVID-19. Our models achieved high accuracies and could predict outcomes more than one week in advance; this promising result suggests that these models can be highly useful for resource allocation in hospitals.

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