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1.
Hum Immunol ; 2021 Nov 04.
Article in English | MEDLINE | ID: covidwho-1499900

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patient's immunological status and found dramatic changes in the IGH within the patient's immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion, and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones 2-3 weeks after the onset of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34, and IGHV4-39 in COVID-19 patients were more abundant than those of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.

2.
BMC Infect Dis ; 21(1): 737, 2021 Aug 03.
Article in English | MEDLINE | ID: covidwho-1435227

ABSTRACT

BACKGROUND: The serum surfactant protein D (SP-D) level is suggested to be a useful biomarker for acute lung injuries and acute respiratory distress syndrome. Whether the serum SP-D level could identify the severity of coronavirus disease 2019 (COVID-19) in the early stage has not been elucidated. METHODS: We performed an observational study on 39 laboratory-confirmed COVID-19 patients from The Fourth People's Hospital of Yiyang, Hunan, China. Receiver operating characteristic (ROC) curve analysis, correlation analysis, and multivariate logistic regression model analysis were performed. RESULTS: In the acute phase, the serum levels of SP-D were elevated significantly in severe COVID-19 patients than in mild cases (mean value ± standard deviation (SD), 449.7 ± 125.8 vs 245.9 ± 90.0 ng/mL, P<0.001), while the serum levels of SP-D in the recovery period were decreased dramatically than that in the acute phase (mean value ± SD, 129.5 ± 51.7 vs 292.9 ± 130.7 ng/ml, P<0.001), and so were for the stratified patients. The chest CT imaging scores were considerably higher in the severe group compared with those in the mild group (median value, 10.0 vs 9.0, P = 0.011), while markedly lower in the recovery period than those in the acute phase (median value, 2.0 vs 9.0, P<0.001), and so were for the stratified patients. ROC curve analysis revealed that areas under the curve of lymphocyte counts (LYM), C-reaction protein (CRP), erythrocyte sedimentation rate (ESR), interleukin-6 (IL-6), and SP-D for severe COVID-19 were 0.719, 0.833, 0.817, 0.837, and 0.922, respectively. Correlation analysis showed that the SP-D levels were negatively correlated with LYM (r = - 0.320, P = 0.047), while positively correlated with CRP (r = 0.658, P<0.001), IL-6 (r = 0.471, P = 0.002), the duration of nucleic acid of throat swab turning negative (r = 0.668, P<0.001), chest CT imaging score on admission (r = 0.695, P<0.001) and length of stay (r = 0.420, P = 0.008). Multivariate logistic regression model analysis showed that age (P = 0.041, OR = 1.093) and SP-D (P = 0.008, OR = 1.018) were risk factors for severe COVID-19. CONCLUSIONS: Elevated serum SP-D level was a potential biomarker for the severity of COVID-19; this may be useful in identifying patients whose condition worsens at an early stage.


Subject(s)
COVID-19 , Pulmonary Surfactant-Associated Protein D , Humans , Prognosis , ROC Curve , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index
3.
Ther Adv Chronic Dis ; 12: 20406223211041924, 2021.
Article in English | MEDLINE | ID: covidwho-1398819

ABSTRACT

Background: A novel coronavirus disease 2019 (COVID-19) has caused outbreaks worldwide, and the number of cases is rapidly increasing through human-to-human transmission. Because of the greater transmission capacity and possible subsequent multi-organ damage caused by the virus, it is crucial to understand precisely and manage COVID-19 patients. However, the underlying differences in the clinical features of COVID-19 with and without comorbidities are not fully understood. Aim: The objective of this study was to identify the clinical features of COVID-19 patients with and without complications to guide treatment and predict the prognosis. Method: We collected the clinical characteristics of COVID-19 patients with and without different complications, including hypertension, cardiovascular disease and diabetes. Next, we performed a baseline comparison of each index and traced the dynamic changes in these factors during hospitalization to explore the potential associations. Result: A clinical index of differential expression was used for the regression to select top-ranking factors. The top-ranking clinical characteristics varied in each subgroup, such as indices of liver function, renal function and inflammatory markers. Among them, the indices of renal function were highly ranked in all subgroups and displayed significant differences during hospitalization. Conclusion: Organ functions of COVID-19 patients, particularly renal function, should be cautiously taken care of during management and might be a crucial factor for a poor prognosis of these patients with complications.

5.
BMC Geriatr ; 21(1): 186, 2021 03 17.
Article in English | MEDLINE | ID: covidwho-1140479

ABSTRACT

BACKGROUND: A large number of studies have explored the association between frailty and mortality among COVID-19 patients, with inconsistent results. The aim of this meta-analysis was to synthesize the evidence on this issue. METHODS: Three databases, PubMed, Embase, and Cochrane Library, from inception to 20th January 2021 were searched for relevant literature. The Newcastle-Ottawa Scale (NOS) was used to assess quality bias, and STATA was employed to pool the effect size by a random effects model. Additionally, potential publication bias and sensitivity analyses were performed. RESULTS: Fifteen studies were included, with a total of 23,944 COVID-19 patients, for quantitative analysis. Overall, the pooled prevalence of frailty was 51% (95% CI: 44-59%). Patients with frailty who were infected with COVID-19 had an increased risk of mortality compared to those without frailty, and the pooled hazard ratio (HR) and odds ratio (OR) were 1.99 (95% CI: 1.66-2.38) and 2.48 (95% CI: 1.78-3.46), respectively. In addition, subgroup analysis based on population showed that the pooled ORs for hospitalized patients in eight studies and nursing home residents in two studies were 2.62 (95% CI: 1.68-4.07) and 2.09 (95% CI: 1.40-3.11), respectively. Subgroup analysis using the frailty assessment tool indicated that this association still existed when using the clinical frailty scale (CFS) (assessed in 6 studies, pooled OR = 2.88, 95% CI: 1.52-5.45; assessed in 5 studies, pooled HR = 1.99, 95% CI: 1.66-2.38) and other frailty tools (assessed in 4 studies, pooled OR = 1.98, 95% CI: 1.81-2.16). In addition, these significant positive associations still existed in the subgroup analysis based on study design and geographic region. CONCLUSION: Our study indicates that frailty is an independent predictor of mortality among patients with COVID-19. Thus, frailty could be a prognostic factor for clinicians to stratify high-risk groups and remind doctors and nurses to perform early screening and corresponding interventions urgently needed to reduce mortality rates in patients infected by SARS-CoV-2.


Subject(s)
COVID-19 , Frailty , Aged , Frail Elderly , Frailty/diagnosis , Humans , Prevalence , SARS-CoV-2
6.
Angewandte Chemie ; n/a(n/a), 2021.
Article in English | Wiley | ID: covidwho-1077184

ABSTRACT

The COVID-19 pandemic caused by SARS-CoV-2 is threating global health. Inhibiting interaction of the receptor-binding domain of SARS-CoV-2 S protein (S RBD) and human ACE2 receptor is a promising treatment strategy. However, SARS-CoV-2 neutralizing antibodies are compromised by their risk of antibody-dependent enhancement (ADE) and unfavorably large size for intranasal delivery. To avoid the limitations of neutralizing antibodies, we proposed and demonstrated an aptamer blocking strategy by engineering aptamers? binding to the region on S RBD that directly mediates ACE2 receptor engagement, leading to block SARS-CoV-2 infection. With aptamer selection against S RBD and molecular docking, aptamer CoV2-6 was identified and successfully applied to prevent, compete, and substitute ACE2 from binding to S RBD protein. CoV2-6 was further shortened and engineered as a circular bivalent apamer CoV2-6C3 (cb-CoV2-6C3) to improve the stability, affinity, and inhibition efficacy. With its circular form, cb-CoV2-6C3 aptamer was found to be stable in serum for more than 12 hours and can be stored at room temperature for more than 14 days. The circular bivalent aptamer binds to S RBD with high affinity (Kd of 0.13 nM) and blocks authentic SARS-CoV-2 virus with a half-maximal inhibitory concentration of 0.42 nM. With its excellent affinity, stability, safety and programmability, our aptamer showed its capability to inhibit SARS-CoV-2 infection, suggesting aptamer blocking strategy as a new direction for developing therapeutic agents against COVID-19 and other emerging infectious diseases.

7.
Mediterr J Hematol Infect Dis ; 13(1): e2021015, 2021.
Article in English | MEDLINE | ID: covidwho-1045343

ABSTRACT

Background: Coronavirus disease 2019 (COVID-19) is highly contagious and deadly and is associated with coagulopathy. Pentraxin-3(PTX3) participates in innate resistance to infections and plays a role in thrombogenesis. Purpose: The present study aimed to investigate the role of PTX3 in coagulopathy in patients with COVID-19. Methods: A retrospective study, including thirty-nine COVID-19 patients, enrolled in Hunan, China, were performed. The patients were classified into the D-dimer_L (D-dimer <1mg/L) and D-dimer_H (D-dimer≥1mg/L) groups basing on the plasma D-dimer levels on admission. Serum PTX3 levels were detected by enzyme-linked immunosorbent assays and compared between those two groups, then receiver operating characteristic (ROC) curve analysis, correlation analysis, and linear regression models were performed to analyze the association between PTX3 and D-dimer. Results: Our results showed that serum PTX3 levels (median values, 10.21 vs. 3.36, P<0.001), computerized chest tomography (C.T.) scores (median values, 10.0 vs. 9.0, P<0.05), and length of stay (LOS) (mean values, 16.0 vs. 10.7, P=0.001) in the D-dimer_H group were significantly higher than that in D-dimer_L group. ROC curve analysis revealed that the AUC of white blood corpuscle counts, C-reaction protein, erythrocyte sedimentation rate, and PTX3 for COVID-19 were 0.685, 0.863, 0.846, and 0.985, respectively. Correlation analysis showed that there was a positive relationship between PTX3 and D-dimer (r=0.721, P<0.001), chest CT imaging score (r=0.418, P=0.008), and LOS (r=0.486, P=0.002). Multiple linear regression analysis showed that the coefficient of determination was 0.657 (P < 0.001). Conclusion: Serum level of PTX3 was positively correlated with disease severity and coagulopathy. Detection of serum PTX3 level could help identify severer patients on admission and may be a potential therapeutic target for coagulopathy in patients with COVID-19.

8.
Cell ; 182(2): 417-428.e13, 2020 07 23.
Article in English | MEDLINE | ID: covidwho-342735

ABSTRACT

Nucleotide analog inhibitors, including broad-spectrum remdesivir and favipiravir, have shown promise in in vitro assays and some clinical studies for COVID-19 treatment, this despite an incomplete mechanistic understanding of the viral RNA-dependent RNA polymerase nsp12 drug interactions. Here, we examine the molecular basis of SARS-CoV-2 RNA replication by determining the cryo-EM structures of the stalled pre- and post- translocated polymerase complexes. Compared with the apo complex, the structures show notable structural rearrangements happening to nsp12 and its co-factors nsp7 and nsp8 to accommodate the nucleic acid, whereas there are highly conserved residues in nsp12, positioning the template and primer for an in-line attack on the incoming nucleotide. Furthermore, we investigate the inhibition mechanism of the triphosphate metabolite of remdesivir through structural and kinetic analyses. A transition model from the nsp7-nsp8 hexadecameric primase complex to the nsp12-nsp7-nsp8 polymerase complex is also proposed to provide clues for the understanding of the coronavirus transcription and replication machinery.


Subject(s)
Betacoronavirus/chemistry , Betacoronavirus/enzymology , RNA-Dependent RNA Polymerase/chemistry , Viral Nonstructural Proteins/chemistry , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/metabolism , Adenosine Monophosphate/pharmacology , Alanine/analogs & derivatives , Alanine/chemistry , Alanine/metabolism , Alanine/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Catalytic Domain , Coronavirus RNA-Dependent RNA Polymerase , Cryoelectron Microscopy , Models, Chemical , Models, Molecular , RNA, Viral/metabolism , SARS-CoV-2 , Transcription, Genetic , Virus Replication
9.
Nat Struct Mol Biol ; 27(6): 529-532, 2020 06.
Article in English | MEDLINE | ID: covidwho-222247

ABSTRACT

The antineoplastic drug carmofur is shown to inhibit the SARS-CoV-2 main protease (Mpro). Here, the X-ray crystal structure of Mpro in complex with carmofur reveals that the carbonyl reactive group of carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30 µM) and is a promising lead compound to develop new antiviral treatment for COVID-19.


Subject(s)
Betacoronavirus/enzymology , Cysteine Endopeptidases/chemistry , Fluorouracil/analogs & derivatives , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Animals , Betacoronavirus/drug effects , COVID-19 , Chlorocebus aethiops , Coronavirus 3C Proteases , Coronavirus Infections/virology , Cysteine Endopeptidases/genetics , Cysteine Endopeptidases/metabolism , Fluorouracil/chemistry , Fluorouracil/pharmacology , Models, Molecular , Pandemics , Pneumonia, Viral/virology , SARS-CoV-2 , Vero Cells , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism
10.
Science ; 368(6492): 779-782, 2020 05 15.
Article in English | MEDLINE | ID: covidwho-47347

ABSTRACT

A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase [(RdRp), also named nsp12] is the central component of coronaviral replication and transcription machinery, and it appears to be a primary target for the antiviral drug remdesivir. We report the cryo-electron microscopy structure of COVID-19 virus full-length nsp12 in complex with cofactors nsp7 and nsp8 at 2.9-angstrom resolution. In addition to the conserved architecture of the polymerase core of the viral polymerase family, nsp12 possesses a newly identified ß-hairpin domain at its N terminus. A comparative analysis model shows how remdesivir binds to this polymerase. The structure provides a basis for the design of new antiviral therapeutics that target viral RdRp.


Subject(s)
Betacoronavirus/enzymology , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/ultrastructure , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/ultrastructure , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/metabolism , Adenosine Monophosphate/pharmacology , Alanine/analogs & derivatives , Alanine/metabolism , Alanine/pharmacology , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Catalytic Domain , Coronavirus RNA-Dependent RNA Polymerase , Cryoelectron Microscopy , Drug Design , Models, Molecular , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism , Multiprotein Complexes/ultrastructure , Protein Conformation, beta-Strand , Protein Domains , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2 , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/metabolism
11.
Preprint in English | medRxiv | ID: ppmedrxiv-20036145

ABSTRACT

Currently, there are no approved specific antiviral agents for 2019 novel coronavirus disease (COVID-19). In this study, ten severe patients confirmed by real-time viral RNA test were enrolled prospectively. One dose of 200 mL convalescent plasma (CP) derived from recently recovered donors with the neutralizing antibody titers above 1:640 was transfused to the patients as an addition to maximal supportive care and antiviral agents. The primary endpoint was the safety of CP transfusion. The second endpoints were the improvement of clinical symptoms and laboratory parameters within 3 days after CP transfusion. The median time from onset of illness to CP transfusion was 16.5 days. After CP transfusion, the level of neutralizing antibody increased rapidly up to 1:640 in five cases, while that of the other four cases maintained at a high level (1:640). The clinical symptoms were significantly improved along with increase of oxyhemoglobin saturation within 3 days. Several parameters tended to improve as compared to pre-transfusion, including increased lymphocyte counts (0.65x109/L vs. 0.76x109/L) and decreased C-reactive protein (55.98 mg/L vs. 18.13 mg/L). Radiological examinations showed varying degrees of absorption of lung lesionswithin 7 days. The viral load was undetectable after transfusion in seven patients who had previous viremia. No severe adverse effects were observed. This study showed CP therapy was welltolerated and could potentially improve the clinical outcomes through neutralizing viremia in severe COVID-19 cases. The optimal dose and time point, as well as the clinical benefit of CP therapy, needs further investigation in larger well-controlled trials. Significance StatementCOVID-19 is currently a big threat to global health. However, no specific antiviral agents are available for its treatment. In this work, we explored the feasibility of convalescent plasma (CP) transfusion to rescue severe patients. The results from 10 severe adult cases showed that one dose (200 mL) of CP was welltolerated and could significantly increase or maintain the neutralizing antibodies at a high level, leading to disappearance of viremia in 7 days. Meanwhile, clinical symptoms and paraclinical criteria rapidly improved within 3 days. Radiological examination showed varying degrees of absorption of lung lesions within 7 days. These results indicate that CP can serve as a promising rescue option for severe COVID-19 while the randomized trial is warranted.

12.
Preprint in English | medRxiv | ID: ppmedrxiv-20028068

ABSTRACT

BackgroundSARS-CoV-2-caused coronavirus disease (COVID-19) is posing a large casualty. The features of COVID-19 patients with and without pneumonia, SARS-CoV-2 transmissibility in asymptomatic carriers, and factors predicting disease progression remain unknown. MethodsWe collected information on clinical characteristics, exposure history, and laboratory examinations of all laboratory-confirmed COVID-19 patients admitted to PLA General Hospital. Cox regression analysis was applied to identify prognostic factors. The last follow-up was February 18, 2020. ResultsWe characterized 55 consecutive COVID-19 patients. The mean incubation was 8.42 (95% confidence interval [CI], 6.55-10.29) days. The mean SARS-CoV-2-positive duration from first positive test to conversion was 9.71 (95%CI, 8.21-11.22) days. COVID-19 course was approximately 2 weeks. Asymptomatic carriers might transmit SARS-CoV-2. Compared to patients without pneumonia, those with pneumonia were 15 years older and had a higher rate of hypertension, higher frequencies of having a fever and cough, and higher levels of interleukin-6 (14.61 vs. 8.06pg/mL, P=0.040), B lymphocyte proportion (13.0% vs.10.0%, P=0.024), low account (<190/{micro}L) of CD8+ T cells (33.3% vs. 0, P=0.019). Multivariate Cox regression analysis indicated that circulating interleukin-6 and lactate independently predicted COVID-19 progression, with a hazard ratio (95%CI) of 1.052 (1.000-1.107) and 1.082 (1.013-1.155), respectively. During disease course, T lymphocytes were generally lower, neutrophils higher, in pneumonia patients than in pneumonia-free patients. CD8+ lymphocytes did not increase at the 20th days after illness onset. ConclusionThe epidemiological features are important for COVID-19 prophylaxis. Circulating interleukin-6 and lactate are independent prognostic factors. CD8+ T cell exhaustion might be critical in the development of COVID-19.

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