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1.
Environmental Pollution ; : 119308, 2022.
Article in English | ScienceDirect | ID: covidwho-1796874

ABSTRACT

Numerous epidemiological studies have shown a close relationship between outdoor air pollution and increased risks for cancer, infection, and cardiopulmonary diseases. However, very few studies have investigated the potential health effects of coexposure to airborne particulate matter (PM) and bioaerosols through the transmission of infectious agents, particularly under the current circumstances of the coronavirus disease 2019 pandemic. In this study, we aimed to identify urinary metabolite biomarkers that might serve as clinically predictive or diagnostic standards for relevant diseases in a real-time manner. We performed an unbiased gas/liquid chromatography–mass spectroscopy (GC/LC-MS) approach to detect urinary metabolites in 92 samples from young healthy individuals collected at three different time points after exposure to clean air, polluted ambient, or purified air, as well as two additional time points after air repollution or repurification. Subsequently, we compared the metabolomic profiles between the two time points using an integrated analysis, along with Kyoto Encyclopedia of Genes and Genomes-enriched pathway and time-series analysis. We identified 33 and 155 differential metabolites (DMs) associated with PM and bioaerosol exposure using GC/LC–MS and follow-up analyses, respectively. Our findings suggest that 16-dehydroprogesterone and 4-hydroxyphenylethanol in urine samples may serve as potential biomarkers to predict or diagnose PM- or bioaerosol-related diseases, respectively. The results indicated apparent differences between PM- and bioaerosol-associated DMs at five different time points and revealed dynamic alterations in the urinary metabolic profiles of young healthy humans with cyclic exposure to clean and polluted air environments. Our findings will help in investigating the detrimental health effects of short-term coexposure to airborne PM and bioaerosols in a real-time manner and improve clinically predictive or diagnostic strategies for preventing air pollution-related diseases.

2.
Microbiol Spectr ; : e0219121, 2022 Mar 07.
Article in English | MEDLINE | ID: covidwho-1731263

ABSTRACT

SARS-CoV-2 continues adapting to human hosts during the current worldwide pandemic since 2019. This virus evolves through multiple means, such as single nucleotide mutations and structural variations, which has brought great difficulty to disease prevention and control of COVID-19. Structural variation, including multiple nucleotide changes like insertions and deletions, has a greater impact relative to single nucleotide mutation on both genome structures and protein functions. In this study, we found that deletion occurred frequently in not only SARS-CoV-2 but also in other SARS-related coronaviruses. These deletions showed obvious location bias and formed 45 recurrent deletion regions in the viral genome. Some of these deletions showed proliferation advantages, including four high-frequency deletions (nsp6 Δ106-109, S Δ69-70, S Δ144, and Δ28271) that were detected in around 50% of SARS-CoV-2 genomes and other 19 median-frequency deletions. In addition, the association between deletions and the WHO reported variants of concern (VOC) and variants of interest (VOI) of SARS-CoV-2 indicated that these variants had a unique combination of deletion patterns. In the spike (S) protein, the deletions in SARS-CoV-2 were mainly in the N-terminal domain. Some deletions, such as S Δ144/145 and S Δ243-244, have been confirmed to block the binding sites of neutralizing antibodies. Overall, this study revealed a conservative regional pattern and the potential effect of some deletions in SARS-CoV-2 over the whole genome, providing important evidence for potential epidemic control and vaccine development. IMPORTANCE Mutations in SARS-CoV-2 were studied extensively, while only the structure variations on the spike protein were discussed well in previous studies. To study the role of structural variations in virus evolution, we described the distribution of structure variations on the whole genome. Conserved patterns were found of deletions among SARS-CoV-2, SARS-CoV-2-like, and SARS-CoV-like viruses. There were 45 recurrent deletion regions (RDRs) in SARS-CoV-2 generated through the integration of deleted positions. In these regions, four high-frequency deletions parallelly appeared in multiple strains. Furthermore, in the spike protein, the deletions in SARS-CoV-2 were mainly in the N-terminal domain, blocking the binding sites of some neutralizing antibodies, while the structural variations in SARS-related coronavirus were mainly in the N-terminal domain and receptor binding domain. The receptor binding domain is highly related to hosting recognition. The deletions in the receptor binding domain may play a role in host adaption.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-312737

ABSTRACT

The SARS-CoV-2 virus has had a major impact on global human health. During the spread of SARS-CoV-2, weakened host immunity and the use of vaccines with low efficacy may result in the development of more virulent strains or strains with resistance to existing vaccines and antibodies. The prevalence of SARS-CoV-2 mutant strains differs among regions, and this variation may affect the effectiveness of vaccines. In this study, an epidemiological investigation of SARS-CoV-2 in Portugal was performed, and the VSV-ΔG-G* pseudovirus system was used to construct 12 S protein epidemic mutants, D614G, A222V+D614G, B.1.1.7, S477N+D614G, P1162R+D614G+A222V, D839Y+D614G, L176F+D614G, B.1.1.7+L216F, B.1.1.7+M740V, B.1.258, B.1.258+L1063F, and B.1.258+N751Y.The mutant pseudoviruses were used to infect four susceptible cell lines (i.e., Huh7, hACE2-293T, Vero, and LLC-MK2) and 14 cell lines overexpressing ACE2 from different species. Mutant strains did not show increased infectivity or cross-species transmission. Neutralization activity was evaluated using the newly constructed pseudoviruses, mouse serum, and 11 monoclonal antibodies. The neutralizing activity in immunized mouse serum was not significantly reduced for the mutant strains. Additionally, mutant strains in Portugal showed escape from 9 of 11 monoclonal antibodies. Neutralization resistance was mainly caused by the S477N, N439K, and N501Y mutations in the Spike receptor binding domain. These findings emphasize the importance of SARS-CoV-2 mutation tracking in different regions for epidemic prevention and control.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323786

ABSTRACT

Ethnopharmacological relevance: Novel coronavirus disease (COVID-19) outbroke in Wuhan has imposed a huge influence onto the society in term of the public heath and economy. However, so far, no effective drugs or vaccines have been developed. Whereas, the Traditional Chinese Medicine (TCM) has been considered as a promising supplementary treatment for the disease owing to its clinically proven performance on many diseases even like severe acute respiratory syndrome (SARS). Meanwhile, many side-effect (SE) reports suggest the SE of the TCM prescriptions cannot be ignored in curing the COVID-19, especially because COVID-19 always simultaneously leads to dramatic degradation of the patients’physical condition. How to evaluate the TCM regarding to their latent SE is a urgent challenge. Aim of the study: In this study, we use an ontology-based side-effect prediction framework (OSPF) developed in our previous work and Artificial Neural Network (ANN)-based deep learning to evaluate the TCM prescriptions that are officially recommended in China for novel coronavirus (COVID-19). Materials and methods: Firstly, we adopted the OSPF developed in our previous work, where an ontology-based model separate all the ingredients in a TCM prescription into two categories: hot and cold. Then, we established a database by converting each TCM prescription into a vector containing the ingredient dosage and the according hot/cold attribution as well as the safe/unsafe label. And, we trained the ANN model using this database, after which a safety indicator (SI), as the complementary percentage of side-effect (SE) possibility, is then given for each TCM prescription. According to the proposed SI from high to low, we re-organize the recommended prescription list. Secondly, by using this method, we also evaluate the safety indicators of some other famous TCM prescriptions that are not in the recommended list but are used traditionally to cure flu-like diseases for extending the potential treatments. Results: Based on the SI generated in the ANN model, FTS, PMSP, and SF are the safest ones in recommended list, which all own a more-than-0.8 SI. Whereas, JHQG, LHQW, SFJD, XBJ, and SHL are the prescriptions that are most likely unsafe, where the indicators are all below 0.2. In the extra list, the indicators of XC, XQRS, CC, and CHBX are all above 0.8, and at the meantime, XZXS, SJ, QW, and KBD’s indicators are all below 0.2. Conclusions: In total, there are seven TCM prescriptions which own the indicators more than 0.8, suggesting these prescriptions should be considered firstly in curing COVID-19, if suitable. We believe this work will provide a reasonable suggestion for the society to choose proper TCM as the supplementary treatment for COVID-19. Besides, this work also introduces a pilot and enlightening method for creating a more reasonable recommendation list of TCM to other diseases.

5.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315184

ABSTRACT

Background: Numerous epidemiological studies showed close relationships of outdoor air pollution with increased risk of cancer, infection, and cardiopulmonary diseases. However, a very limited number of studies investigate the potential biomarkers of the co-exposures of particle matters (PM) and bioaerosols, especially under current circumstances of the Coronavirus disease 2019 (COVID-19) pandemic. In the present study, we aimed to identify metabolic candidate biomarkers that are associated with co-exposure to PM and bioaerosols.Methods: We performed an unbiased gas/liquid chromatography-mass spectroscopy (GC/LC-MS) approach to detect urinary metabolites of 92 samples from young healthy individuals collected at three different time points with exposure to clean, polluted ambient, and purified air , followed by a cycling test after air re-pollution and re-purification with two additional time points. Subsequently, we compared metabolomic profiles in between two-time points via an integrated analysis, plus KEGG enriched pathway and time series analysis.Findings: We identified 33 and 155 differential metabolites (DMs) associated with PM and bioaerosol exposure, respectively. The results from KEGG data and time series analysis indicated significantly enriched pathways and dynamic alterations of metabolomic profiles, respectively. 16-Dehydroprogesterone and 4-Hydroxyphenylethanol in urine might be used as biomarkers for diagnosis of PM- or bioaerosol-relevant diseases.Interpretation: The present studies revealed dynamic alterations in urinary metabolites of young healthy humans with the cycling of the clean and polluted air environment. Our findings help to investigate detrimental health effects of airborne PM and bioaerosols in a real-time manner and improve clinically diagnostic tools for PM- and bioaerosol-related diseases.Funding Information: This work was financially supported by the National Natural Science Foundation of China [NSFC Grant no. 81673958, 82074262, and 81828010];CAMS Innovation Fund for Medical Sciences [CIFMS 2016-I2M-3-013];The Drug Innovation Major Project of China [2018ZX09711001-007-002].Declaration of Interests: The authors declare no conflicts of interest in this work.Ethics Approval Statement: Our study was approved by the Ethical Committee of Guang'anmen Hospital. All recruited subjects provided written informed consent.

6.
mBio ; : e0360021, 2022 Feb 01.
Article in English | MEDLINE | ID: covidwho-1662304

ABSTRACT

Pyroptosis, a programmed cell death, functions as an innate immune effector mechanism and plays a crucial role against microbial invasion. Gasdermin D (GSDMD), as the main pyroptosis effector, mediates pyroptosis and promotes releasing proinflammatory molecules into the extracellular environment through pore-forming activity, modifying inflammation and immune responses. While the substantial importance of GSDMD in microbial infection and cancer has been widely investigated, the role of GSDMD in virus infection, including coronaviruses, remains unclear. Enteric coronavirus transmissible gastroenteritis virus (TGEV) and porcine deltacoronavirus (PDCoV) are the major agents for lethal watery diarrhea in neonatal pigs and pose the potential for spillover from pigs to humans. In this study, we found that alphacoronavirus TGEV upregulated and activated GSDMD, resulting in pyroptosis after infection. Furthermore, the fragment of swine GSDMD from amino acids 242 to 279 (242-279 fragment) was required to induce pyroptosis. Notably, GSDMD strongly inhibited both TGEV and PDCoV infection. Mechanistically, the antiviral activity of GSDMD was mediated through promoting the nonclassical release of antiviral beta interferon (IFN-ß) and then enhancing the interferon-stimulated gene (ISG) responses. These findings showed that GSDMD dampens coronavirus infection by an uncovered GSDMD-mediated IFN secretion, which may present a novel target of coronavirus antiviral therapeutics. IMPORTANCE Coronaviruses, primarily targeting respiratory and gastrointestinal epithelia in vivo, have a serious impact on humans and animals. GSDMD, a main executioner of pyroptosis, is highly expressed in epithelial cells and involves viral infection pathogenesis. While the functions and importance of GSDMD as a critical regulator of inflammasome activities in response to intracellular bacterial infection have been extensively investigated, the roles of GSDMD during coronavirus infection remain unclear. We here show that alphacoronavirus TGEV triggered pyroptosis and upregulated GSDMD expression, while GSDMD broadly suppressed the infection of enteric coronavirus TGEV and PDCoV by its pore-forming activity via promoting unconventional release of IFN-ß. Our study highlights the importance of GSDMD as a regulator of innate immunity and may open new avenues for treating coronavirus infection.

7.
Sustain Cities Soc ; 77: 103548, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1621040

ABSTRACT

Since the Corona Virus Disease 2019 (COVID-19) outbreak, the normalization of the epidemic has posed great challenge to epidemic prevention and control in indoor environment. Ventilation systems are commonly used to prevent and control indoor transmission of disease. However, most naturally ventilated rooms are not efficient to prevent the spread of virus, i.e., classrooms. The goal of this work is to effectively adopt forced interference strategies (e.g., airflow deflector) applied to external windows to strengthen airflow diffusion performance (ADP) of natural ventilation. So far, no systematic study has been done to investigate the effectiveness of such airflow deflectors on its influence on natural ventilation and effectiveness of preventing the disease transmission in indoor environment. In this work, a case study was conducted based on cross-ventilated classrooms. Different settings of airflow deflectors (i.e., size and installation angle) were applied to the external windows. Air Diffusion Performance Index (ADPI) was utilized to evaluated airflow diffusion performance under different settings of the airflow deflectors. Then, the Wells-Riley model was applied to evaluate infection risk. According to the results, the infection risk can be reduced by 19.29% when infection source is located at the center of classroom and 17.47% when source is located near the side walls. This work would provide guidance for the design of classrooms ventilated with induced natural wind for epidemic prevention and control.

8.
Frontiers in immunology ; 12, 2021.
Article in English | EuropePMC | ID: covidwho-1610580

ABSTRACT

Background A vaccine against coronavirus disease 2019 (COVID-19) with highly effective protection is urgently needed. The anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody response and duration after vaccination are crucial predictive indicators. Objectives To evaluate the response and duration for 5 subsets of anti-SARS-CoV-2 antibodies after vaccination and their predictive value for protection. Methods We determined the response and duration for 5 subsets of anti-SARS-CoV-2 antibodies (neutralizing antibody, anti-RBD total antibody, anti-Spike IgG, anti-Spike IgM, and anti-Spike IgA) in 61 volunteers within 160 days after the CoronaVac vaccine. A logistic regression model was used to determine the predictors of the persistence of neutralizing antibody persistence. Results The seropositivity rates of neutralizing antibody, anti-RBD total antibody, anti-Spike IgG, anti-Spike IgM, and anti-Spike IgA were only 4.92%, 27.87%, 21.31%, 3.28% and 0.00%, respectively, at the end of the first dose (28 days). After the second dose, the seropositivity rates reached peaks of 95.08%, 100.00%, 100.00%, 59.02% and 31.15% in two weeks (42 days). Their decay was obvious and the seropositivity rate remained at 19.67%, 54.10%, 50.82%, 3.28% and 0.00% on day 160, respectively. The level of neutralizing antibody reached a peak of 149.40 (101.00–244.60) IU/mL two weeks after the second dose (42 days) and dropped to 14.23 (7.62–30.73) IU/mL at 160 days, with a half-life of 35.61(95% CI, 32.68 to 39.12) days. Younger participants (≤31 years) had 6.179 times more persistent neutralizing antibodies than older participants (>31 years) (P<0.05). Participants with anti-Spike IgA seropositivity had 4.314 times greater persistence of neutralizing antibodies than participants without anti-Spike IgA seroconversion (P<0.05). Conclusions Antibody response for the CoronaVac vaccine was intense and comprehensive with 95.08% neutralizing seropositivity rate, while decay was also obvious after 160 days. Therefore, booster doses should be considered in the vaccine strategies.

9.
Int J Cardiol Heart Vasc ; 38: 100938, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1587657

ABSTRACT

Purpose: This study evaluated the diagnostic values of the extent of lung injury manifested in non-contrast enhanced CT (NCCT) images, the inflammatory and immunological biomarkers C-reactive protein (CRP) and lymphocyte for detecting acute cardiac injury (ACI) in patients with COVID-19. The correlations between the NCCT-derived parameters and arterial blood oxygen level were also investigated. Methods: NCCT lung images and blood tests were obtained in 143 patients with COVID-19 in approximately two weeks after symptom onset, and arterial blood gas measurement was also acquired in 113 (79%) patients. The diagnostic values of normal, moderately and severely abnormal lung parenchyma volume relative to the whole lungs (RVNP, RVMAP, RVSAP, respectively) measured from NCCT images for detecting the heart injury confirmed with high-sensitivity troponin I assay was determined. Results: RVNP, RVMAP and RVSAP exhibited similar accuracy for detecting ACI in COVID-19 patients. RVNP was significantly lower while both RVMAP and RVSAP were significantly higher in the patients with ACI. All of the NCCT-derived parameters exhibited poor linear and non-linear correlations with PaO2 and SaO2. The patients with ACI had a significantly higher CRP level but a lower lymphocyte level compared to the patients without ACI. Combining one of these two biomarkers with any of the three NCCT-derived parameter further improved the accuracy for predicting ACI in patients with COVID-19. Conclusion: The NCCT-delineated normal and abnormal lung parenchmyma tissues were statistically significant predictors of ACI in patients with COVID-19, but both exhibited poor correlations with the arterial blood oxygen level. The incremental diagnostic values of lymphocyte and CRP suggested viral infection and inflammation were closely related to the heart injury during the acute stage of COVID-19.

10.
Signal Transduct Target Ther ; 6(1): 438, 2021 12 24.
Article in English | MEDLINE | ID: covidwho-1585880

ABSTRACT

Messenger RNA (mRNA) vaccine technology has shown its power in preventing the ongoing COVID-19 pandemic. Two mRNA vaccines targeting the full-length S protein of SARS-CoV-2 have been authorized for emergency use. Recently, we have developed a lipid nanoparticle-encapsulated mRNA (mRNA-LNP) encoding the receptor-binding domain (RBD) of SARS-CoV-2 (termed ARCoV), which confers complete protection in mouse model. Herein, we further characterized the protection efficacy of ARCoV in nonhuman primates and the long-term stability under normal refrigerator temperature. Intramuscular immunization of two doses of ARCoV elicited robust neutralizing antibodies as well as cellular response against SARS-CoV-2 in cynomolgus macaques. More importantly, ARCoV vaccination in macaques significantly protected animals from acute lung lesions caused by SARS-CoV-2, and viral replication in lungs and secretion in nasal swabs were completely cleared in all animals immunized with low or high doses of ARCoV. No evidence of antibody-dependent enhancement of infection was observed throughout the study. Finally, extensive stability assays showed that ARCoV can be stored at 2-8 °C for at least 6 months without decrease of immunogenicity. All these promising results strongly support the ongoing clinical trial.


Subject(s)
COVID-19 Vaccines/pharmacology , COVID-19/immunology , Immunogenicity, Vaccine , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , /pharmacology , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/prevention & control , COVID-19 Vaccines/immunology , Chlorocebus aethiops , Humans , Macaca fascicularis , Vero Cells , /immunology
11.
IEEE/ACM Trans Comput Biol Bioinform ; 18(6): 2775-2780, 2021.
Article in English | MEDLINE | ID: covidwho-1559565

ABSTRACT

A novel coronavirus (COVID-19) recently emerged as an acute respiratory syndrome, and has caused a pneumonia outbreak world-widely. As the COVID-19 continues to spread rapidly across the world, computed tomography (CT) has become essentially important for fast diagnoses. Thus, it is urgent to develop an accurate computer-aided method to assist clinicians to identify COVID-19-infected patients by CT images. Here, we have collected chest CT scans of 88 patients diagnosed with COVID-19 from hospitals of two provinces in China, 100 patients infected with bacteria pneumonia, and 86 healthy persons for comparison and modeling. Based on the data, a deep learning-based CT diagnosis system was developed to identify patients with COVID-19. The experimental results showed that our model could accurately discriminate the COVID-19 patients from the bacteria pneumonia patients with an AUC of 0.95, recall (sensitivity) of 0.96, and precision of 0.79. When integrating three types of CT images, our model achieved a recall of 0.93 with precision of 0.86 for discriminating COVID-19 patients from others. Moreover, our model could extract main lesion features, especially the ground-glass opacity (GGO), which are visually helpful for assisted diagnoses by doctors. An online server is available for online diagnoses with CT images by our server (http://biomed.nscc-gz.cn/model.php). Source codes and datasets are available at our GitHub (https://github.com/SY575/COVID19-CT).


Subject(s)
COVID-19/diagnostic imaging , COVID-19/diagnosis , Deep Learning , Diagnosis, Computer-Assisted/statistics & numerical data , Tomography, X-Ray Computed/statistics & numerical data , Case-Control Studies , China , Computational Biology , Diagnosis, Differential , Humans , Models, Statistical , Pneumonia, Bacterial/diagnosis , Pneumonia, Bacterial/diagnostic imaging , SARS-CoV-2
12.
IET Image Process ; 2021 Nov 18.
Article in English | MEDLINE | ID: covidwho-1526114

ABSTRACT

The rapid spread of the novel coronavirus disease 2019 (COVID-19) causes a significant impact on public health. It is critical to diagnose COVID-19 patients so that they can receive reasonable treatments quickly. The doctors can obtain a precise estimate of the infection's progression and decide more effective treatment options by segmenting the CT images of COVID-19 patients. However, it is challenging to segment infected regions in CT slices because the infected regions are multi-scale, and the boundary is not clear due to the low contrast between the infected area and the normal area. In this paper, a coarse-refine segmentation network is proposed to address these challenges. The coarse-refine architecture and hybrid loss is used to guide the model to predict the delicate structures with clear boundaries to address the problem of unclear boundaries. The atrous spatial pyramid pooling module in the network is added to improve the performance in detecting infected regions with different scales. Experimental results show that the model in the segmentation of COVID-19 CT images outperforms other familiar medical segmentation models, enabling the doctor to get a more accurate estimate on the progression of the infection and thus can provide more reasonable treatment options.

13.
Int J Infect Dis ; 113: 148-154, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1506521

ABSTRACT

BACKGROUND: Studies have shown conflicting results on the efficacy of tocilizumab (TCZ) for patients with COVID-19, with many confounders of clinical status and limited duration of the observation. Here, we evaluate the real-world long-term efficacy of TCZ in COVID-19 patients. METHODS: We conducted a retrospective study of hospitalized adult patients with COVID-19 using a large US-based multicenter COVID-19 database (Cerner Real-World Data; updated in September, 2020). The TCZ group was defined as patients who received at least one dose of the drug. Matching weight (MW) and a propensity score weighting method were used to balance confounding factors. RESULTS: A total of 20,399 patients were identified. 1,510 and 18,899 were in the TCZ and control groups, respectively. After MW adjustment, no statistically significant differences in all-cause mortality were found for the TCZ vs. control group (Hazard Ratio [HR]:0.76, p=0.06). Survival curves suggested a better trend in short-term observation, driven from a subgroup of patients requiring oxygen masks, BIPAP or CPAP. CONCLUSION: We observed a temporal (early) benefit of TCZ, especially in patients on non-invasive high-flow supplemental oxygen. However, the benefit effects faded with longer observation. The long-term benefits and risks of TCZ should be carefully evaluated with follow-up studies.


Subject(s)
COVID-19 , Adult , Antibodies, Monoclonal, Humanized , COVID-19/drug therapy , Electronic Health Records , Humans , Retrospective Studies , SARS-CoV-2 , United States/epidemiology
14.
Front Immunol ; 12: 689065, 2021.
Article in English | MEDLINE | ID: covidwho-1502324

ABSTRACT

Coronavirus disease 2019 (COVID-19) is an acute respiratory infectious disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The US FDA has approved several therapeutics and vaccines worldwide through the emergency use authorization in response to the rapid spread of COVID-19. Nevertheless, the efficacies of these treatments are being challenged by viral escape mutations. There is an urgent need to develop effective treatments protecting against SARS-CoV-2 infection and to establish a stable effect-screening model to test potential drugs. Polyclonal antibodies (pAbs) have an intrinsic advantage in such developments because they can target rapidly mutating viral strains as a result of the complexity of their binding epitopes. In this study, we generated anti-receptor-binding domain (anti-RBD) pAbs from rabbit serum and tested their safety and efficacy in response to SARS-CoV-2 infection both in vivo and ex vivo. Primary human bronchial epithelial two-dimensional (2-D) organoids were cultured and differentiated to a mature morphology and subsequently employed for SARS-CoV-2 infection and drug screening. The pAbs protected the airway organoids from viral infection and tissue damage. Potential side effects were tested in mouse models for both inhalation and vein injection. The pAbs displayed effective viral neutralization effects without significant side effects. Thus, the use of animal immune serum-derived pAbs might be a potential therapy for protection against SARS-CoV-2 infection, with the strategy developed to produce these pAbs providing new insight into the treatment of respiratory tract infections, especially for infections with viruses undergoing rapid mutation.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Animals , Antibodies, Neutralizing/administration & dosage , Antibodies, Viral/administration & dosage , Binding Sites , Bronchi/cytology , COVID-19/genetics , COVID-19/therapy , Epithelial Cells , Gene Expression Profiling , Humans , Immunization, Passive , Mice , Mutation , Neutralization Tests , Organoids , Rabbits , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
15.
Cell Res ; 31(12): 1230-1243, 2021 12.
Article in English | MEDLINE | ID: covidwho-1475291

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the ongoing global pandemic that poses substantial challenges to public health worldwide. A subset of COVID-19 patients experience systemic inflammatory response, known as cytokine storm, which may lead to death. Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is an important mediator of inflammation and cell death. Here, we examined the interaction of RIPK1-mediated innate immunity with SARS-CoV-2 infection. We found evidence of RIPK1 activation in human COVID-19 lung pathological samples, and cultured human lung organoids and ACE2 transgenic mice infected by SARS-CoV-2. Inhibition of RIPK1 using multiple small-molecule inhibitors reduced the viral load of SARS-CoV-2 in human lung organoids. Furthermore, therapeutic dosing of the RIPK1 inhibitor Nec-1s reduced mortality and lung viral load, and blocked the CNS manifestation of SARS-CoV-2 in ACE2 transgenic mice. Mechanistically, we found that the RNA-dependent RNA polymerase of SARS-CoV-2, NSP12, a highly conserved central component of coronaviral replication and transcription machinery, promoted the activation of RIPK1. Furthermore, NSP12 323L variant, encoded by the SARS-CoV-2 C14408T variant first detected in Lombardy, Italy, that carries a Pro323Leu amino acid substitution in NSP12, showed increased ability to activate RIPK1. Inhibition of RIPK1 downregulated the transcriptional induction of proinflammatory cytokines and host factors including ACE2 and EGFR that promote viral entry into cells. Our results suggest that SARS-CoV-2 may have an unexpected and unusual ability to hijack the RIPK1-mediated host defense response to promote its own propagation and that inhibition of RIPK1 may provide a therapeutic option for the treatment of COVID-19.


Subject(s)
COVID-19/pathology , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , SARS-CoV-2/physiology , Angiotensin-Converting Enzyme 2/genetics , Animals , COVID-19/drug therapy , COVID-19/mortality , COVID-19/virology , Coronavirus RNA-Dependent RNA Polymerase/genetics , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Cytokines/genetics , Cytokines/metabolism , Down-Regulation/drug effects , ErbB Receptors/metabolism , Humans , Imidazoles/pharmacology , Imidazoles/therapeutic use , Indoles/pharmacology , Indoles/therapeutic use , Lung/pathology , Lung/virology , Mice , Mice, Transgenic , Mutation , Receptor-Interacting Protein Serine-Threonine Kinases/antagonists & inhibitors , SARS-CoV-2/isolation & purification , SARS-CoV-2/metabolism , Survival Rate , Transcriptome/drug effects , Viral Load/drug effects , Virus Internalization
17.
Environ Sci Technol ; 55(17): 11557-11567, 2021 Sep 07.
Article in English | MEDLINE | ID: covidwho-1371582

ABSTRACT

The lockdown due to COVID-19 created a rare opportunity to examine the nonlinear responses of secondary aerosols, which are formed through atmospheric oxidation of gaseous precursors, to intensive precursor emission reductions. Based on unique observational data sets from six supersites in eastern China during 2019-2021, we found that the lockdown caused considerable decreases (32-61%) in different secondary aerosol components in the study region because of similar-degree precursor reductions. However, due to insufficient combustion-related volatile organic compound (VOC) reduction, odd oxygen (Ox = O3 + NO2) concentration, an indicator of the extent of photochemical processing, showed little change and did not promote more decreases in secondary aerosols. We also found that the Chinese provinces and international cities that experienced reduced Ox during the lockdown usually gained a greater simultaneous PM2.5 decrease than other provinces and cities with an increased Ox. Therefore, we argue that strict VOC control in winter, which has been largely ignored so far, is critical in future policies to mitigate winter haze more efficiently by reducing Ox simultaneously.


Subject(s)
Air Pollutants , Air Pollution , COVID-19 , Aerosols/analysis , Air Pollutants/analysis , Air Pollution/analysis , Air Pollution/prevention & control , China , Communicable Disease Control , Environmental Monitoring , Humans , Oxygen , Particulate Matter/analysis , SARS-CoV-2
18.
Brief Bioinform ; 22(2): 1267-1278, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1343631

ABSTRACT

Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1-10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.


Subject(s)
Biological Evolution , COVID-19/virology , SARS-CoV-2/metabolism , Viral Proteins/genetics , Viral Proteins/metabolism , Genes, Viral , Humans , Molecular Sequence Annotation , Open Reading Frames , Protein Interaction Maps , SARS-CoV-2/genetics
19.
Blood ; 136(Supplement 1):22-23, 2020.
Article in English | PMC | ID: covidwho-1339020

ABSTRACT

Background: A previously unknown beta-coronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. The virus was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the international committee for the classification of viruses (ICTV). The disease caused by this virus was named as coronavirus disease 2019 (COVID-19). In addition to pulmonary manifestations, hematological changes such as lymphocytopenia, thrombocytopenia, and coagulation dysfunction can also be found in COVID-19 patients, and the mechanism is still unclear.Case data and methods: A total of 633 COVID-19 patients from Wuhan hospital of China were retrospectively analyzed. Clinical case data of all patients were collected, including gender, age, chronic underlying diseases, outcome, and blood laboratory test results. The hematological features of COVID-19 patients and the factors affecting their outcome were analyzed.Results: Of 633 patients with COVID-19, the median age was 62 years (interquartile range, IQR, 51.0-70.0) and 330 (52%) were men. Lymphocytopenia (lymphocyte count, 1.0 ×109 / L [IQR, 0.7-1.4]) occurred in 317/607 patients (52%), thrombocytopenia (platelet count <100 × 109/ L) occurred in 14/62 death patients (23%), prolonged prothrombin time (13.8 seconds [IQR, 13.1-15.1]) in 289/486 patients (59%), increased D-Dimer level (0.7 mg/L[IQR, 0.2-2.9]) in 230/411 patients (57%) and increased C-reactive protein levels (10.7 mg/L [IQR, 2.2-49.7]) in 217/426 patients (51%) . Compared with the survival patients, death patients have higher white blood cell count (11.7 × 109/L [IQR, 8.4 to 15.6]), neutrophil count (10.8 × 109/L [IQR, 7.8 to 13.9]), neutrophil count/lymphocyte count (20.5 [IQR, 12.4-34.2]), activated partial thromboplastin time (36.8 seconds [IQR, 31.3-42.3]), prothrombin time (17.1 seconds [IQR, 14.7 to 19.7]), D-Dimer level (4.6 mg/L [IQR, 1.0 to 7.8]), C-reactive protein level (111.8 mg/L (IQR, 53.1 to 196.6), and low lymphocyte count (0.5 × 109/L [IQR, 0.3 to 0.7]). The results of logistic multivariate regression analysis showed that age, neutrophil count, prothrombin time, and C-reactive protein were risk factors for patients with COVID-19.Conclusion: Hematological changes are common in patients with COVID-19. The early stage of the disease is mainly characterized by lymphocytopenia, thrombocytopenia, and the late stage may be characterized by more severe lymphocytopenia, even neutrophils elevation, elevated C-reactive protein, and severe coagulation disorder. The pathogenesis may be mediated by a direct viral infection and/or indirect immunopathology.

20.
J Proteome Res ; 20(3): 1558-1570, 2021 03 05.
Article in English | MEDLINE | ID: covidwho-1324404

ABSTRACT

Dexamethasone is a synthetic glucocorticoid medication vastly used to treat abnormal immune responses and inflammation. Although the medication is well-established in the medical community, the prolonged treatment with high dosages of dexamethasone may lead to severe adverse effects through mechanisms that are not yet well-known. Lipids are a large class of hydrophobic molecules involved in energy storage, signaling, modulation of gene expression, and membranes. Hence, untargeted lipidomics may help unravel the biochemical alterations following prolonged treatment with high dosages of dexamethasone. We performed comprehensive lipidomic analyses of brain, heart, kidney, liver, and muscle samples obtained from rats that were treated with intramuscular injections of dexamethasone for 14 weeks compared to healthy controls. The employed methodology and statistical analysis showed that phosphatidic acids, glycerophospholipids, plasmalogens, and fatty acids are deeply affected by prolonged use of the medication. Brain tissue was only mildly affected, but skeletal muscle showed a strong accumulation of lipids that may be correlated with alterations in the energy metabolism, myopathy, and oxidative processes. This work provides new insights into the mechanisms of action and adverse effects for one of the most commonly prescribed class of drugs in the world.


Subject(s)
Lipidomics , Lipids , Animals , Dexamethasone/adverse effects , Fatty Acids , Glycerophospholipids , Rats
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