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1.
Phytother Res ; 35(7): 3447-3483, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1323905

ABSTRACT

The pandemic of viral diseases like novel coronavirus (2019-nCoV) prompted the scientific world to examine antiviral bioactive compounds rather than nucleic acid analogous, protease inhibitors, or other toxic synthetic molecules. The emerging viral infections significantly associated with 2019-nCoV have challenged humanity's survival. Further, there is a constant emergence of new resistant viral strains that demand novel antiviral agents with fewer side effects and cell toxicity. Despite significant progress made in immunization and regenerative medicine, numerous viruses still lack prophylactic vaccines and specific antiviral treatments that are so often influenced by the generation of viral escape mutants. Of importance, medicinal herbs offer a wide variety of therapeutic antiviral chemotypes that can inhibit viral replication by preventing viral adsorption, adhering to cell receptors, inhibiting virus penetration in the host cell, and competing for pathways of activation of intracellular signals. The present review will comprehensively summarize the promising antiviral activities of medicinal plants and their bioactive molecules. Furthermore, it will elucidate their mechanism of action and possible implications in the treatment/prevention of viral diseases even when their mechanism of action is not fully understood, which could serve as the base for the future development of novel or complementary antiviral treatments.


Subject(s)
Antiviral Agents , Plants, Medicinal , Virus Diseases , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19 , Humans , Plants, Medicinal/chemistry , Virus Diseases/drug therapy
2.
Protein Expr Purif ; 186: 105908, 2021 10.
Article in English | MEDLINE | ID: covidwho-1243167

ABSTRACT

The current standard for the diagnosis of COVID-19 is the nucleic acid test of SARS-CoV-2 RNA, however, virus antibody detection has the advantages of convenient sample collection, high throughout, and low cost. When combining detection with nucleic acid detection, antibody detection can effectively compensate for nucleic acid detection. Virus infection always induce high antibody titer against SARS-CoV-2 nucleocapsid protein (N protein), which can be used to detect COVID-19 at both infected and convalescent patients. In this study we reported the expression and purification of N protein in E.coli from inclusion bodies by a combination of two cation exchange chromatography, and the yield of N protein was around 50 mg/L fermentation broth with more than 90% purity. A corresponding colloidal gold detection kit prepared with our purified N protein was used to verify the efficiency and accuracy our N protein in antibody detection method. Of the 58 COVID-19 PCR positive patients' inactivated serum samples, 40 samples were IgM positive (69.0%), and 42 samples were IgG positive (72.4%), and all 95 COVID-19 negative patients' inactivated serum samples were both IgM and IgG negative. Our results indicates that the refolded soluble N protein could be used for the preliminary detection of IgG and IgM antibodies against SARS-CoV- 2.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus Nucleocapsid Proteins/immunology , SARS-CoV-2/immunology , Coronavirus Nucleocapsid Proteins/biosynthesis , Coronavirus Nucleocapsid Proteins/isolation & purification , Escherichia coli/genetics , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Inclusion Bodies , Phosphoproteins/biosynthesis , Phosphoproteins/genetics , Phosphoproteins/immunology , Phosphoproteins/isolation & purification , Recombinant Proteins/biosynthesis , Recombinant Proteins/immunology , Recombinant Proteins/isolation & purification , SARS-CoV-2/genetics , Sensitivity and Specificity
3.
ISA Trans ; 124: 21-30, 2022 May.
Article in English | MEDLINE | ID: covidwho-1237731

ABSTRACT

The COVID-19 outbreak is an epidemic disease caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). When a new virus emerges, generally, little is known about it, and no vaccines or other pharmaceutical interventions are available. In the case of a person-to-person transmission virus with no vaccines or other pharmaceutical interventions, the only way to control the virus outbreak is by keeping a sustained physical distancing between the individuals. However, to adjust the level of the physical distancing accurately can be so complicated. Any level above the necessary can compromise the economic activity, and any level below can collapse the health care system. This work proposes a controller to keep the number of hospitalized individuals below a limit, and a new group-structured model to describe the COVID-19 outbreak. The proposed controller is robust to the uncertainties in the parameters of the model and keeps the number of infected individuals controlled only by adjusting the social distancing level. Numerical simulations, to show the behavior of the proposed controller and model, are done.


Subject(s)
COVID-19 , Epidemics , COVID-19/epidemiology , COVID-19/prevention & control , Epidemics/prevention & control , Humans , Pharmaceutical Preparations , Physical Distancing , SARS-CoV-2
4.
Bol Med Hosp Infant Mex ; 78(1): 66-74, 2021.
Article in English | MEDLINE | ID: covidwho-1116360

ABSTRACT

Background: The coronavirus disease 2019 (COVID-19) pandemic has posed significant challenges globally. Continuous transmission of the virus is mostly due to insufficient infection control measures and a lack of vaccines. Therefore, this review aimed to identify and describe possible vaccines for the prevention of COVID-19. Methods: A systematic review of the scientific literature was performed through electronic searches of the main databases to identify published reports or studies on vaccines under development against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Websites from international organizations, institutes of health and research, Google, and references from identified studies were also reviewed. Studies examining the mechanisms of infection, immunopathology, and genomics were excluded. Results: A total of 141 vaccines in development against SARS-CoV-2 were identified. The technologies used include weakened and inactive viruses, viral vectors, nucleic acids, and proteins. So far, 13 vaccines (9.2%) are under clinical evaluation; only the AZD1222 vaccine is under clinical evaluation Phase II-III. Ad5-nCoV and mRNA-1273 vaccines showed to produce neutralizing antibodies and also to be safe. Conclusions: Despite efforts invested in developing SARS-CoV-2 vaccines, more research is still required. The vaccine developers, international health organizations, and the decision-makers of health policies must carry out conjunct cooperation to face the different challenges and guarantee the development of an effective vaccine.


Introducción: La pandemia de COVID-19 ha planteado grandes retos en todo el mundo. La transmisión continua del virus se debe, en gran parte, a las medidas deficientes para el control de infecciones y a la falta de vacunas. El objetivo de esta revisión fue identificar y describir las posibles vacunas para la prevención de la COVID-19. Métodos: Se realizó una revisión sistemática de la literatura científica mediante búsquedas en las principales bases de datos electrónicas, para identificar informes o estudios publicados sobre las vacunas en proceso de desarrollo contra el SARS-CoV-2. También se revisaron páginas web de organismos internacionales, institutos de salud e investigación, Google y las referencias de los estudios identificados. Se excluyeron los estudios que examinaron los mecanismos de infección, inmunopatológicos y de genómica. Resultados: En total se identificaron 141 vacunas en desarrollo contra el SARS-CoV-2. Las tecnologías utilizadas incluyen virus debilitados e inactivos, vectores virales, ácidos nucleicos y proteínas. Hasta el momento solo 13 vacunas (9.2%) se encuentran en proceso de evaluación clínica y solo la vacuna AZD1222 se encuentra en fase II-III. Las vacunas Ad5-nCoV y mRNA-1273 han mostrado producción de anticuerpos neutralizantes, además de ser seguras. Conclusiones: A pesar de los esfuerzos invertidos para el desarrollo de vacunas contra el SARS-CoV-2, aún se requiere más investigación. Es necesario que los desarrolladores de vacunas, los organismos internacionales de salud y los tomadores de decisiones de políticas sanitarias cooperen para afrontar los diferentes desafíos y garantizar el desarrollo de una vacuna eficaz.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , SARS-CoV-2/immunology , 2019-nCoV Vaccine mRNA-1273 , Animals , Antibodies, Neutralizing/immunology , COVID-19 Vaccines/immunology , ChAdOx1 nCoV-19 , Health Policy , Humans
5.
Lancet Microbe ; 1(5): e218-e225, 2020 09.
Article in English | MEDLINE | ID: covidwho-1087372

ABSTRACT

BACKGROUND: In December, 2019, a novel zoonotic severe acute respiratory syndrome-related coronavirus emerged in China. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became pandemic within weeks and the number of human infections and severe cases is increasing. We aimed to investigate the susceptibilty of potential animal hosts and the risk of anthropozoonotic spill-over infections. METHODS: We intranasally inoculated nine fruit bats (Rousettus aegyptiacus), ferrets (Mustela putorius), pigs (Sus scrofa domesticus), and 17 chickens (Gallus gallus domesticus) with 105 TCID50 of a SARS-CoV-2 isolate per animal. Direct contact animals (n=3) were included 24 h after inoculation to test viral transmission. Animals were monitored for clinical signs and for virus shedding by nucleic acid extraction from nasal washes and rectal swabs (ferrets), oral swabs and pooled faeces samples (fruit bats), nasal and rectal swabs (pigs), or oropharyngeal and cloacal swabs (chickens) on days 2, 4, 8, 12, 16, and 21 after infection by quantitative RT-PCR (RT-qPCR). On days 4, 8, and 12, two inoculated animals (or three in the case of chickens) of each species were euthanised, and all remaining animals, including the contacts, were euthanised at day 21. All animals were subjected to autopsy and various tissues were collected for virus detection by RT-qPCR, histopathology immunohistochemistry, and in situ hybridisation. Presence of SARS-CoV-2 reactive antibodies was tested by indirect immunofluorescence assay and virus neutralisation test in samples collected before inoculation and at autopsy. FINDINGS: Pigs and chickens were not susceptible to SARS-CoV-2. All swabs, organ samples, and contact animals were negative for viral RNA, and none of the pigs or chickens seroconverted. Seven (78%) of nine fruit bats had a transient infection, with virus detectable by RT-qPCR, immunohistochemistry, and in situ hybridisation in the nasal cavity, associated with rhinitis. Viral RNA was also identified in the trachea, lung, and lung-associated lymphatic tissue in two animals euthanised at day 4. One of three contact bats became infected. More efficient virus replication but no clinical signs were observed in ferrets, with transmission to all three direct contact animals. Mild rhinitis was associated with viral antigen detection in the respiratory and olfactory epithelium. Prominent viral RNA loads of 0-104 viral genome copies per mL were detected in the upper respiratory tract of fruit bats and ferrets, and both species developed SARS-CoV-2-reactive antibodies reaching neutralising titres of up to 1/1024 after 21 days. INTERPRETATION: Pigs and chickens could not be infected intranasally by SARS-CoV-2, whereas fruit bats showed characteristics of a reservoir host. Virus replication in ferrets resembled a subclinical human infection with efficient spread. Ferrets might serve as a useful model for further studies-eg, testing vaccines or antivirals. FUNDING: German Federal Ministry of Food and Agriculture.


Subject(s)
COVID-19 , Chiroptera , Rhinitis , Animals , Antibodies, Viral , COVID-19/veterinary , Chickens/genetics , Chiroptera/genetics , Ferrets/genetics , RNA, Viral/genetics , SARS-CoV-2
6.
Curr Pharm Des ; 26(41): 5300-5309, 2020.
Article in English | MEDLINE | ID: covidwho-1073205

ABSTRACT

BACKGROUND: Previously human society has faced various unprecedented pandemics in the history and viruses have majorly held the responsibilities of those outbreaks. Furthermore, due to amplified global connection and speedy modernization, epidemic outbreaks caused by novel and re-emerging viruses signify potential risk to community health. Despite great advancements in immunization and drug discovery processes, various viruses still lack prophylactic vaccines and efficient antiviral therapies. Although, vaccine is a prophylaxes option, but it cannot be applied to infected patients, hence therapeutic interventions are urgently needed to control the ongoing global SARS- CoV-2 pandemic condition. To spot the novel antiviral therapy is of decisive importance and Mother Nature is an excellent source for such discoveries. METHODOLOGY: In this article, prompt high through-put virtual screening for vetting the best possible drug candidates from natural compounds' databases has been implemented. Herein, time tested rigorous multi-layered drug screening process to narrow down 66,969 natural compounds for the identification of potential lead(s) is implemented. Druggability parameters, different docking approaches and neutralization tendency of the natural products were employed in this study to screen the best possible natural compounds from the digital libraries. CONCLUSION: The results of this study conclude that compounds PALA and HMCA are potential inhibitors of SARS-CoV-2 spike protein and can be further explored for experimental validation. Overall, the methodological approach reported in this article can be suitably used to find the potential drug candidates against SARS-CoV2 in the burning situation of COVID-19 with less expenditure and a concise span of time.


Subject(s)
Antiviral Agents , COVID-19 , Antiviral Agents/pharmacology , Humans , Molecular Docking Simulation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus
7.
Front Cardiovasc Med ; 7: 618651, 2020.
Article in English | MEDLINE | ID: covidwho-1058410

ABSTRACT

The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus requires reliable assays for studying viral entry mechanisms which remains poorly understood. This knowledge is important for the development of therapeutic approaches to control SARS-CoV-2 infection by permitting the screening for neutralizing antibodies and other agents that can block infection. This is particularly important for patients who are at high risk for severe outcomes related to COVID-19. The production of pseudotyped viral particles may seem like a daunting task for a non-virology laboratory without experience in the two most commonly used pseudotyping systems, namely retro/lentiviruses and vesicular stomatitis virus (VSV) which lacks the VSV envelope glycoprotein (VSVΔG). By incorporating the most up-to-date knowledge, we have developed a detailed, easy-to-follow novel protocol for producing SARS-CoV-2 spike-bearing pseudovirus using the VSV-ΔG system. We describe the infection assay which uses GFP fluorescence as a measure of infection in a 24-well live imaging system. We present results of our optimization of the system to enhance viral infection levels through the over-expression of human ACE2 receptor and the overexpression of at least one of two proteases - TMPRSS2 or Furin, as well as, supplementation with Poloxamer 407 (P407) and Prostaglandin E2 (PGE2) as adjuvants. We show that the system works efficiently in three unrelated, clinically relevant cell lines: human 293T (renal epithelial) cells, human Calu-3 (lung epithelial) cells, and the non-human primate (African Green Monkey) cell line, Vero-E6 (renal epithelial) cells. In addition, we have used this system to show infection of human induced pluripotent stem cell-derived cardiomyocytes (iPS-CMs). This system is efficient (virus generation, titration, and infection assays can be performed in 1 week), quantitative, inexpensive, and readily scalable for application in drug development and therapeutic screening approaches.

8.
Cancers (Basel) ; 13(1)2020 Dec 24.
Article in English | MEDLINE | ID: covidwho-1016105

ABSTRACT

The COVID-19 pandemic has significantly affected the surgical units, especially those operating on the airways. This study evaluates the series of patients with tumors of the head and neck treated by our unit during Phase-1 of the pandemic and the efficacy of the preventive measures implemented for protecting both the patients and staff. A screening program was administered to all the patients who had to undergo surgery. None of the patients tested and operated during Phase 1, between 10 March and 18 May 2020, were positive for COVID-19. A significant portion of the patients was suffering from tumors in advanced stages (T3 and T4). Two patients developed respiratory symptoms during their stay at the unit, so they were put in precautionary isolation and tested, but resulted negative for COVID-19. All the surgical department staff followed the Italian Ministry of Health's prevention protocol and underwent serological testing. IgG and IgM were negative in everyone, thus confirming that nobody had been exposed to the virus. This study highlights the commitment to efficiently treating patients suffering from tumors of the head and neck region and confirms the effectiveness of the safety measures used to protect our patients and staff's health.

9.
Lancet ; 396(10247): 320-332, 2020 08 01.
Article in English | MEDLINE | ID: covidwho-981695

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of an ongoing pandemic, with increasing deaths worldwide. To date, documentation of the histopathological features in fatal cases of the disease caused by SARS-CoV-2 (COVID-19) has been scarce due to sparse autopsy performance and incomplete organ sampling. We aimed to provide a clinicopathological report of severe COVID-19 cases by documenting histopathological changes and evidence of SARS-CoV-2 tissue tropism. METHODS: In this case series, patients with a positive antemortem or post-mortem SARS-CoV-2 result were considered eligible for enrolment. Post-mortem examinations were done on 14 people who died with COVID-19 at the King County Medical Examiner's Office (Seattle, WA, USA) and Snohomish County Medical Examiner's Office (Everett, WA, USA) in negative-pressure isolation suites during February and March, 2020. Clinical and laboratory data were reviewed. Tissue examination was done by light microscopy, immunohistochemistry, electron microscopy, and quantitative RT-PCR. FINDINGS: The median age of our cohort was 73·5 years (range 42-84; IQR 67·5-77·25). All patients had clinically significant comorbidities, the most common being hypertension, chronic kidney disease, obstructive sleep apnoea, and metabolic disease including diabetes and obesity. The major pulmonary finding was diffuse alveolar damage in the acute or organising phases, with five patients showing focal pulmonary microthrombi. Coronavirus-like particles were detected in the respiratory system, kidney, and gastrointestinal tract. Lymphocytic myocarditis was observed in one patient with viral RNA detected in the tissue. INTERPRETATION: The primary pathology observed in our cohort was diffuse alveolar damage, with virus located in the pneumocytes and tracheal epithelium. Microthrombi, where observed, were scarce and endotheliitis was not identified. Although other non-pulmonary organs showed susceptibility to infection, their contribution to the pathogenesis of SARS-CoV-2 infection requires further examination. FUNDING: None.


Subject(s)
Coronavirus Infections/pathology , Pneumonia, Viral/pathology , Adult , Aged , Aged, 80 and over , Alveolar Epithelial Cells/pathology , Alveolar Epithelial Cells/ultrastructure , Alveolar Epithelial Cells/virology , Autopsy , Betacoronavirus , COVID-19 , Coronavirus Infections/epidemiology , Female , Gastrointestinal Tract/pathology , Gastrointestinal Tract/ultrastructure , Gastrointestinal Tract/virology , Heart/virology , Humans , Kidney/pathology , Kidney/ultrastructure , Kidney/virology , Liver/pathology , Liver/ultrastructure , Liver/virology , Male , Middle Aged , Myocardium/pathology , Myocardium/ultrastructure , Pandemics , Pneumonia, Viral/epidemiology , Pulmonary Alveoli/pathology , Pulmonary Alveoli/ultrastructure , Respiratory Mucosa/pathology , Respiratory Mucosa/ultrastructure , Respiratory Mucosa/virology , SARS-CoV-2 , Spleen/pathology , Spleen/ultrastructure , Spleen/virology , Thrombosis/pathology , Trachea/pathology , Trachea/ultrastructure , Trachea/virology , Washington/epidemiology
10.
PLoS One ; 15(12): e0236304, 2020.
Article in English | MEDLINE | ID: covidwho-962373

ABSTRACT

MOTIVATION: Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. RESULTS: We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks, and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.


Subject(s)
Host Microbial Interactions/physiology , Protein Interaction Maps/physiology , SARS-CoV-2/metabolism , COVID-19/virology , Coronavirus/metabolism , Coronavirus Infections/virology , Humans , Models, Theoretical , Pandemics , Pneumonia, Viral/virology , Programming, Linear , Protein Binding/physiology , Proteins/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Virus Replication/physiology
11.
Front Immunol ; 11: 586984, 2020.
Article in English | MEDLINE | ID: covidwho-909205

ABSTRACT

The recently emerged SARS-CoV-2 causing the ongoing COVID-19 pandemic is particularly virulent in the elderly while children are largely spared. Here, we explored the potential role of cross-reactive immunity acquired from pediatric vaccinations and exposure to common human pathogens in the protection and pathology of COVID-19. To that end, we sought for peptide matches to SARS-CoV-2 (identity ≥ 80%, in at least eight residues) in the proteomes of 25 human pathogens and in vaccine antigens, and subsequently predicted their T and B cell reactivity to identify potential cross-reactive epitopes. We found that viruses subject to pediatric vaccinations do not contain cross-reactive epitopes with SARS-CoV-2, precluding that they can provide any general protection against COVID-19. Likewise, common viruses including rhinovirus, respiratory syncytial virus, influenza virus, and several herpesviruses are also poor or null sources of cross-reactive immunity to SARS-CoV-2, discarding that immunological memory against these viruses can have any general protective or pathological role in COVID-19. In contrast, we found combination vaccines for treating diphtheria, tetanus, and pertussis infectious diseases (DTP vaccine) to be significant sources of potential cross-reactive immunity to SARS-CoV-2. DTP cross-reactive epitopes with SARS-CoV-2 include numerous CD8 and CD4 T cell epitopes with broad population protection coverage and potentially neutralizing B cell epitopes in SARS-CoV-2 Spike protein. Worldwide, children receive several DTP vaccinations, including three-four doses the first year of life and one at 4-6 years of age. Moreover, a low antigenic Tdap dose is also given at ages 9-14. Thereby, children may well be protected from SARS-CoV-2 through cross-reactive immunity elicited by DTP vaccinations, supporting testing in the general population to prevent COVID-19.


Subject(s)
COVID-19/immunology , Diphtheria-Tetanus-Pertussis Vaccine/immunology , Host-Pathogen Interactions/immunology , SARS-CoV-2/immunology , Viral Vaccines/immunology , Adolescent , B-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Child , Child, Preschool , Cross Reactions , Epitopes, B-Lymphocyte/immunology , Epitopes, T-Lymphocyte/immunology , Female , Humans , Immunologic Memory , Infant , Male , Spike Glycoprotein, Coronavirus/immunology , Vaccination/trends
12.
Microb Pathog ; 149: 104586, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-907907

ABSTRACT

SARS-CoV-2 remains a medical and economic challenge, due to the lack of a suitable drug or vaccine. The glycans in some proteins play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport so the hindering of N-linked glycosylation of glycoproteins will prevent assembly of the virion. Tunicamycin an anticancer drug inhibit the N- linked glycans. Our study aimed to find out the mechanism action of tunicamycin on the viral glycoproteins. The growth of coronavirus in the presence inhibitor tunicamycin resulted in the production of spikeless, non-infectious virions which were devoid of S protein. We concluded that tunicamycin inhibits E2, S, and M glycoproteins of coronaviruses. Tunicamycin is also diminished glycosylation of PTMs such as HE, and 8 ab of SARS-CoV. Finally, we recommend using this drug to treat the SARS-CoV-2.


Subject(s)
SARS-CoV-2/drug effects , Tunicamycin/pharmacology , Animals , COVID-19/metabolism , Glycosylation/drug effects , Humans , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Viral Matrix Proteins/metabolism
13.
Wellcome Open Res ; 5: 141, 2020.
Article in English | MEDLINE | ID: covidwho-895726

ABSTRACT

Background: COVID-19 is a respiratory disease caused by a novel coronavirus (SARS-CoV-2) and causes substantial morbidity and mortality. There is currently no vaccine to prevent COVID-19 or therapeutic agent to treat COVID-19. This clinical trial is designed to evaluate chloroquine as a potential therapeutic for the treatment of hospitalised people with COVID-19. We hypothesise that chloroquine slows viral replication in patients with COVID-19, attenuating the infection, and resulting in more rapid decline of viral load in throat/nose swabs. This viral attenuation should be associated with improved patient outcomes. Method: The study will start with a 10-patient prospective observational pilot study following the same entry and exclusion criteria as for the randomized trial and undergoing the same procedures. The main study is an open label, randomised, controlled trial with two parallel arms of standard of care (control arm) versus standard of care with 10 days of chloroquine (intervention arm) with a loading dose over the first 24 hours, followed by 300mg base orally once daily for nine days. The study will recruit patients in three sites in Ho Chi Minh City, Vietnam: the Hospital for Tropical Diseases, the Cu Chi Field Hospital, and the Can Gio COVID hospital. The primary endpoint is the time to viral clearance from throat/nose swab, defined as the time following randomization until the midpoint between the last positive and the first of the negative throat/nose swabs. Viral presence will be determined using RT-PCR to detect SARS-CoV-2 RNA. Discussion: The results of the study will add to the evidence-based guidelines for management of COVID-19. Given the enormous experience of its use in malaria chemoprophylaxis, excellent safety and tolerability profile, and its very low cost, if proved effective then chloroquine would be a readily deployable and affordable treatment for patients with COVID-19. Trial registration: Clinicaltrials.gov NCT04328493 31/03/2020.

14.
Glycobiology ; 31(4): 358-371, 2021 05 03.
Article in English | MEDLINE | ID: covidwho-889549

ABSTRACT

The emergence of a new human coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has imposed great pressure on the health system worldwide. The presence of glycoproteins on the viral envelope opens a wide range of possibilities for the application of lectins to address some urgent problems involved in this pandemic. In this work, we discuss the potential contributions of lectins from nonmammalian sources in the development of several fields associated with viral infections, most notably COVID-19. We review the literature on the use of nonmammalian lectins as a therapeutic approach against members of the Coronaviridae family, including recent advances in strategies of protein engineering to improve their efficacy. The applications of lectins as adjuvants for antiviral vaccines are also discussed. Finally, we present some emerging strategies employing lectins for the development of biosensors, microarrays, immunoassays and tools for purification of viruses from whole blood. Altogether, the data compiled in this review highlight the importance of structural studies aiming to improve our knowledge about the basis of glycan recognition by lectins and its repercussions in several fields, providing potential solutions for complex aspects that are emerging from different health challenges.


Subject(s)
Antiviral Agents/pharmacology , COVID-19/drug therapy , Carbohydrate Metabolism/drug effects , Lectins/metabolism , Polysaccharides/metabolism , SARS-CoV-2/drug effects , COVID-19/virology , Humans
15.
Front Microbiol ; 11: 587317, 2020.
Article in English | MEDLINE | ID: covidwho-883856

ABSTRACT

The emerging coronavirus disease (COVID-19) caused by SARS-CoV-2 has led to social and economic disruption globally. It is urgently needed to understand the structure and function of the viral proteins for understanding of the viral infection and pathogenesis and development of prophylaxis and treatment strategies. Coronavirus non-structural protein 1 (nsp1) is a notable virulence factor with versatile roles in virus-host interactions and exhibits unique characteristics on sequence, structure, and function mode. However, the roles and characteristics of SARS-CoV-2 nsp1 are currently unclear. Here, we analyze the nsp1 of SARS-CoV-2 from the following perspectives: (1) bioinformatics analysis reveals that the novel nsp1 is conserved among SARS-CoV-2 strains and shares significant sequence identity with SARS-CoV nsp1; (2) structure modeling shows a 3D α/ß-fold of SARS-CoV-2 nsp1 highly similar to that of the SARS-CoV homolog; (3) by detailed, functional review of nsp1 proteins from other coronaviruses (especially SARS-CoV) and comparison of the protein sequence and structure, we further analyzed the potential roles of SARS-CoV-2 nsp1 in manipulating host mRNA translation, antiviral innate immunity and inflammation response and thus likely promoting viral infection and pathogenesis, which are merited to be tested in the future. Finally, we discussed how understanding of the novel nsp1 may provide valuable insights into the designs of drugs and vaccines against the unprecedented coronavirus pandemic.

16.
EMBO J ; 39(21): e106057, 2020 11 02.
Article in English | MEDLINE | ID: covidwho-846583

ABSTRACT

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 and has spread across the globe. SARS-CoV-2 is a highly infectious virus with no vaccine or antiviral therapy available to control the pandemic; therefore, it is crucial to understand the mechanisms of viral pathogenesis and the host immune responses to SARS-CoV-2. SARS-CoV-2 is a new member of the betacoronavirus genus like other closely related viruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Both SARS-CoV and MERS-CoV have caused serious outbreaks and epidemics in the past eighteen years. Here, we report that one of the interferon-stimulated genes (ISGs), cholesterol 25-hydroxylase (CH25H), is induced by SARS-CoV-2 infection in vitro and in COVID-19-infected patients. CH25H converts cholesterol to 25-hydrocholesterol (25HC) and 25HC shows broad anti-coronavirus activity by blocking membrane fusion. Furthermore, 25HC inhibits USA-WA1/2020 SARS-CoV-2 infection in lung epithelial cells and viral entry in human lung organoids. Mechanistically, 25HC inhibits viral membrane fusion by activating the ER-localized acyl-CoA:cholesterol acyltransferase (ACAT) which leads to the depletion of accessible cholesterol from the plasma membrane. Altogether, our results shed light on a potentially broad antiviral mechanism by 25HC through depleting accessible cholesterol on the plasma membrane to suppress virus-cell fusion. Since 25HC is a natural product with no known toxicity at effective concentrations, it provides a potential therapeutic candidate for COVID-19 and emerging viral diseases in the future.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Cholesterol/metabolism , Coronavirus Infections/drug therapy , Pneumonia, Viral/drug therapy , Respiratory Mucosa/virology , Steroid Hydroxylases/pharmacology , Virus Internalization/drug effects , Acetyl-CoA C-Acetyltransferase/metabolism , Animals , COVID-19 , Cell Line , Cell Membrane/drug effects , Cell Membrane/metabolism , Chlorocebus aethiops , Enzyme Activation/drug effects , Humans , Middle East Respiratory Syndrome Coronavirus/drug effects , Organoids/virology , Pandemics , Respiratory Mucosa/drug effects , SARS-CoV-2 , Vero Cells
17.
Viruses ; 12(2)2020 02 14.
Article in English | MEDLINE | ID: covidwho-831427

ABSTRACT

The genomes of coronaviruses carry accessory genes known to be associated with viral virulence. The single accessory gene of porcine epidemic diarrhea virus (PEDV), ORF3, is dispensable for virus replication in vitro, while viral mutants carrying ORF3 truncations exhibit an attenuated phenotype of which the underlying mechanism is unknown. Here, we studied the effect of ORF3 deletion on the proliferation of PEDV in Vero cells. To this end, four recombinant porcine epidemic diarrhea viruses (PEDVs) were rescued using targeted RNA recombination, three carrying the full-length ORF3 gene from different PEDV strains, and one from which the ORF3 gene had been deleted entirely. Our results showed that PEDVs with intact or naturally truncated ORF3 replicated to significantly higher titers than PEDV without an ORF3. Further characterization revealed that the extent of apoptosis induced by PEDV infection was significantly lower with the viruses carrying an intact or C-terminally truncated ORF3 than with the virus lacking ORF3, indicating that the ORF3 protein as well as its truncated form interfered with the apoptosis process. Collectively, we conclude that PEDV ORF3 protein promotes virus proliferation by inhibiting cell apoptosis caused by virus infection. Our findings provide important insight into the role of ORF3 protein in the pathogenicity of PEDV.


Subject(s)
Apoptosis , Open Reading Frames/genetics , Porcine epidemic diarrhea virus/genetics , Porcine epidemic diarrhea virus/pathogenicity , Viral Proteins/genetics , Virus Replication , Animals , Cell Proliferation , Chlorocebus aethiops , Porcine epidemic diarrhea virus/physiology , Vero Cells , Virulence
18.
J Virol ; 94(17)2020 08 17.
Article in English | MEDLINE | ID: covidwho-831425

ABSTRACT

Accessory genes occurring between the S and E genes of coronaviruses have been studied quite intensively during the last decades. In porcine epidemic diarrhea virus (PEDV), the only gene at this location, ORF3, encodes a 224-residue membrane protein shown to exhibit ion channel activity and to enhance virus production. However, little is known about its intracellular trafficking or about its function during PEDV infection. In this study, two recombinant PEDVs were rescued by targeted RNA recombination, one carrying the full-length ORF3 gene and one from which the gene had been deleted entirely. These viruses as well as a PEDV encoding a naturally truncated ORF3 protein were employed to study the ORF3 protein's subcellular trafficking. In addition, ORF3 expression vectors were constructed to study the protein's independent transport. Our results show that the ORF3 protein uses the exocytic pathway to move to and accumulate in the Golgi area of the cell similarly in infected and transfected cells. Like the S protein, but unlike the other structural proteins M and N, the ORF3 protein was additionally observed at the surface of PEDV-infected cells. In addition, the C-terminally truncated ORF3 protein entered the exocytic pathway but it was unable to leave the endoplasmic reticulum (ER) and ER-to-Golgi intermediate compartment (ERGIC). Consistently, a YxxØ motif essential for ER exit was identified in the C-terminal domain. Finally, despite the use of sensitive antibodies and assays no ORF3 protein could be detected in highly purified PEDV particles, indicating that the protein is not a structural virion component.IMPORTANCE Coronaviruses typically express several accessory proteins. They vary in number and nature, and only one is conserved among most of the coronaviruses, pointing at an important biological function for this protein. PEDV is peculiar in that it expresses just this one accessory protein, termed the ORF3 protein. While its analogs in other coronaviruses have been studied to different extents, and these studies have indicated that they share an ion channel property, little is still known about the features and functions of the PEDV ORF3 protein except for its association with virulence. In this investigation, we studied the intracellular trafficking of the ORF3 protein both in infected cells and when expressed independently. In addition, we analyzed the effects of mutations in five sorting motifs in its C-terminal domain and investigated whether the protein, found to follow the same exocytic route by which the viral structural membrane proteins travel, is also incorporated into virions.


Subject(s)
Coronavirus Infections/veterinary , Exocytosis , Host-Pathogen Interactions , Open Reading Frames , Porcine epidemic diarrhea virus/genetics , Swine Diseases/metabolism , Swine Diseases/virology , Viral Proteins/metabolism , Amino Acid Sequence , Animals , Genetic Engineering , Metabolic Networks and Pathways , Plasmids/genetics , Protein Transport , Proteomics , Swine , Viral Proteins/chemistry , Viral Proteins/genetics
19.
NAR Genom Bioinform ; 2(1): lqz022, 2020 Mar.
Article in English | MEDLINE | ID: covidwho-824972

ABSTRACT

The order Nidovirales is a diverse group of (+)RNA viruses, classified together based on their common genome organisation and conserved replicative enzymes, despite drastic differences in size and complexity. One such difference pertains to the mechanisms and enzymes responsible for generation of the proposed viral 5' RNA cap. Within the Coronaviridae family, two separate methytransferases (MTase), nsp14 and nsp16, perform the RNA-cap N7-guanine and 2'-OH methylation respectively for generation of the proposed m7GpppNm type I cap structure. For the majority of other families within the Nidovirales order, the presence, structure and key enzymes involved in 5' capping are far less clear. These viruses either lack completely an RNA MTase signature sequence, or lack an N7-guanine methyltransferase signature sequence, obscuring our understanding about how RNA-caps are N7-methylated for these families. Here, we report the discovery of a putative Rossmann fold RNA methyltransferase in 10 Tobaniviridae members in Orf1a, an unusual genome locus for this gene. Multiple sequence alignments and structural analyses lead us to propose this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.

20.
Front Bioeng Biotechnol ; 8: 862, 2020.
Article in English | MEDLINE | ID: covidwho-732919

ABSTRACT

Virus-like particle (VLP) is a self-assembled nanostructure incorporating key viral structural proteins. VLP resembles molecular and morphological features of authentic viruses but is non-infectious and non-replicating due to lack of genetic materials. Successful applications of VLP has been shown in vaccinological and virological research. As an accessibly safe and relevant substitute of naturally pathogenic viruses, the construction of SARS-CoV-2 VLPs is much in demand in the ongoing fight against 2019 Coronavirus disease (COVID-19) pandemics. In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Our data demonstrate that SARS-CoV-2 VLPs possess molecular and morphological properties of native virion particles, which endow such VLPs with a promising vaccine candidate and a powerful tool for the research of SARS-CoV-2.

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