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1.
AMB Express ; 12(1), 2022.
Article in English | ProQuest Central | ID: covidwho-1837317

ABSTRACT

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, a series of vaccines, antibodies and drugs have been developed to combat coronavirus disease 2019 (COVID-19). High specific antibodies are powerful tool for the development of immunoassay and providing passive immunotherapy against SARS-CoV-2 and expected with large scale production. SARS-CoV-2 S1 protein was expressed in E. coli BL21 and purified by immobilized metal affinity chromatography, as antigen used to immunize hens, the specific IgY antibodies were extracted form egg yolk by PEG-6000 precipitation, and the titer of anti-S1 IgY antibody reached 1:10,000. IgY single chain variable fragment antibody (IgY-scFv) was generated by using phage display technology and the IgY-scFv showed high binding sensitivity and capacity to S1 protein of SARS-CoV-2, and the minimum detectable antigen S1 protein concentration was 6 ng/µL. The docking study showed that the multiple epitopes on the IgY-scFv interacted with multiple residues on SARS-CoV-2 S1 RBD to form hydrogen bonds. This preliminary study suggests that IgY and IgY-scFv are suitable candidates for the development of immunoassay and passive immunotherapy for COVID-19 to humans and animals.

2.
RSC advances ; 11(28):17408-17412, 2021.
Article in English | EuropePMC | ID: covidwho-1813010

ABSTRACT

Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations. The combined experimental and theoretical study can serve as a template for formulation scientists in the pharmaceutical industry. Combining microcrystal electron diffraction (MicroED) and a cloud-based and artificial intelligence implemented crystal structure prediction (CSP) platform to support selection of a stable solid form of remdesivir in quick time.

3.
mBio ; 13(3): e0068322, 2022 Jun 28.
Article in English | MEDLINE | ID: covidwho-1788919

ABSTRACT

Compared to the original ancestral strain of SARS-CoV-2, the Delta variant of concern has shown increased transmissibility and resistance toward COVID-19 vaccines and therapies. However, the pathogenesis of the disease associated with Delta is still not clear. In this study, using K18-hACE2 transgenic mice, we assessed the pathogenicity of the Delta variant by characterizing the immune response following infection. We found that Delta induced the same clinical disease manifestations as the ancestral SARS-CoV-2, but with significant dissemination to multiple tissues, such as brain, intestine, and kidney. Histopathological analysis showed that tissue pathology and cell infiltration in the lungs of Delta-infected mice were the same as in mice infected with the ancestral SARS-CoV-2. Delta infection caused perivascular inflammation in the brain and intestinal wall thinning in K18-hACE2 transgenic mice. Increased cell infiltration in the kidney was observed in both ancestral strain- and Delta-infected mice, with no clear visible tissue damage identified in either group. Interestingly, compared with mice infected with the ancestral strain, the numbers of CD45+ cells, T cells, B cells, inflammatory monocytes, and dendritic cells were all significantly lower in the lungs of the Delta-infected mice, although there was no significant difference in the levels of proinflammatory cytokines between the two groups. Our results showed distinct immune response patterns in the lungs of K18-hACE2 mice infected with either the ancestral SARS-CoV-2 or Delta variant of concern, which may help to guide therapeutic interventions for emerging SARS-CoV-2 variants. IMPORTANCE SARS-CoV-2 variants, with the threat of increased transmissibility, infectivity, and immune escape, continue to emerge as the COVID-19 pandemic progresses. Detailing the pathogenesis of disease caused by SARS-CoV-2 variants, such as Delta, is essential to better understand the clinical threat caused by emerging variants and associated disease. This study, using the K18-hACE2 mouse model of severe COVID-19, provides essential observation and analysis on the pathogenicity and immune response of Delta infection. These observations shed light on the changing disease profile associated with emerging SARS-CoV-2 variants and have potential to guide COVID-19 treatment strategies.


Subject(s)
COVID-19 , Hepatitis D , Animals , COVID-19/drug therapy , COVID-19 Vaccines , Disease Models, Animal , Humans , Melphalan , Mice , Mice, Transgenic , Pandemics , SARS-CoV-2/genetics , gamma-Globulins
4.
Proc Natl Acad Sci U S A ; 119(16): e2117142119, 2022 04 19.
Article in English | MEDLINE | ID: covidwho-1774040

ABSTRACT

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key enzyme, which extensively digests CoV replicase polyproteins essential for viral replication and transcription, making it an attractive target for antiviral drug development. However, the molecular mechanism of how Mpro of SARS-CoV-2 digests replicase polyproteins, releasing the nonstructural proteins (nsps), and its substrate specificity remain largely unknown. Here, we determine the high-resolution structures of SARS-CoV-2 Mpro in its resting state, precleavage state, and postcleavage state, constituting a full cycle of substrate cleavage. The structures show the delicate conformational changes that occur during polyprotein processing. Further, we solve the structures of the SARS-CoV-2 Mpro mutant (H41A) in complex with six native cleavage substrates from replicase polyproteins, and demonstrate that SARS-CoV-2 Mpro can recognize sequences as long as 10 residues but only have special selectivity for four subsites. These structural data provide a basis to develop potent new inhibitors against SARS-CoV-2.


Subject(s)
Coronavirus 3C Proteases , Coronavirus RNA-Dependent RNA Polymerase , SARS-CoV-2 , Antiviral Agents/chemistry , Coronavirus 3C Proteases/chemistry , Coronavirus RNA-Dependent RNA Polymerase/chemistry , Coronavirus RNA-Dependent RNA Polymerase/genetics , Polyproteins/chemistry , Protein Conformation , Proteolysis , SARS-CoV-2/enzymology , Substrate Specificity/genetics
5.
Front Immunol ; 12: 826882, 2021.
Article in English | MEDLINE | ID: covidwho-1674339

ABSTRACT

Swine enteric coronaviruses (SECoVs) including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV), account for the majority of lethal watery diarrhea in neonatal pigs and pose significant economic and public health burdens in the world. While the three SECoVs primarily infect intestinal epithelia in vivo and cause similar clinical signs, there are evident discrepancies in their cellular tropism and pathogenicity. However, the underlying mechanisms to cause the differences remain unclear. Herein, we employed porcine enteroids that are a physiologically relevant model of the intestine to assess the host epithelial responses following infection with the three SECoVs (PEDV, TGEV, and PDCoV). Although SECoVs replicated similarly in jejunal enteroids, a parallel comparison of transcriptomics datasets uncovered that PEDV and TGEV infection induced similar transcriptional profiles and exhibited a more pronounced response with more differentially expressed genes (DEGs) in jejunal enteroids compared with PDCoV infection. Notably, TGEV and PDCoV induced high levels of type I and III IFNs and IFN-stimulated gene (ISG) responses, while PEDV displayed a delayed peak and elicited a much lesser extent of IFN responses. Furthermore, TGEV and PDCoV instead of PEDV elicited a substantial upregulation of antigen-presentation genes and T cell-recruiting chemokines in enteroids. Mechanistically, we demonstrated that IFNs treatment markedly elevated the expression of NOD-like receptor (NLR) family NLRC5 and major histocompatibility complex class I (MHC-I) molecules. Together, our results indicate unique and common viral strategies for manipulating the global IFN responses and antigen presentation utilized by SECoVs, which help us a better understanding of host-SECoVs interactions.


Subject(s)
Antigen Presentation/immunology , Coronavirus Infections/veterinary , Gene Expression Regulation , Interferons/metabolism , Porcine epidemic diarrhea virus/physiology , Swine Diseases/etiology , Swine Diseases/metabolism , Animals , Gastroenteritis, Transmissible, of Swine/etiology , Gastroenteritis, Transmissible, of Swine/metabolism , Gastroenteritis, Transmissible, of Swine/pathology , Gene Expression Profiling , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Swine , Swine Diseases/pathology , Transmissible gastroenteritis virus
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.
PubMed; 2020.
Preprint in English | PubMed | ID: ppcovidwho-292784

ABSTRACT

COVID-19 emerged in late 2019 and has rapidly spread through many countries globally. The causative SARS-CoV-2 virus was not known until recently, and there is little or no natural immunity in human populations. There is an urgent need for vaccines and drugs to combat this new pandemic. In just a few months, huge efforts and resources by government, academia, and industry have been thrown into the race to develop a vaccine. This brief review summarizes and discusses the array of technologies being applied to vaccine development, highlighting the strengths and weaknesses of the various approaches.

8.
Microb Biotechnol ; 14(6): 2356-2368, 2021 11.
Article in English | MEDLINE | ID: covidwho-1522630

ABSTRACT

Salinomycin, an FDA-approved polyketide drug, was recently identified as a promising anti-tumour and anti-viral lead compound. It is produced by Streptomyces albus, and the biosynthetic gene cluster (sal) spans over 100 kb. The genetic manipulation of large polyketide gene clusters is challenging, and approaches delivering reliable efficiency and accuracy are desired. Herein, a delicate strategy to enhance salinomycin production was devised and evaluated. We reconstructed a minimized sal gene cluster (mini-cluster) on pSET152 including key genes responsible for tailoring modification, antibiotic resistance, positive regulation and precursor supply. These genes were overexpressed under the control of constitutive promoter PkasO* or Pneo . The pks operon was not included in the mini-cluster, but it was upregulated by SalJ activation. After the plasmid pSET152::mini-cluster was introduced into the wild-type strain and a chassis host strain obtained by ribosome engineering, salinomycin production was increased to 2.3-fold and 5.1-fold compared with that of the wild-type strain respectively. Intriguingly, mini-cluster introduction resulted in much higher production than overexpression of the whole sal gene cluster. The findings demonstrated that reconstitution of sal mini-cluster combined with ribosome engineering is an efficient novel approach and may be extended to other large polyketide biosynthesis.


Subject(s)
Streptomyces , Multigene Family , Pyrans , Ribosomes/genetics , Streptomyces/genetics
9.
Front Public Health ; 9: 726491, 2021.
Article in English | MEDLINE | ID: covidwho-1518568

ABSTRACT

Introduction: The roles of some indicators in the prognosis of patients with coronavirus disease-19 (COVID-19) remain unclear and controversial. This study aimed to explore the epidemiologic characteristics of and prognostic factors for COVID-19 to provide updated recommendations for its prevention, diagnosis, and treatment. Methods: For this retrospective study, demographic, epidemiologic, and clinical data were extracted from the medical records of patients admitted to the Maternal and Child Hospital of Hubei Province (Optical Valley) with COVID-19 between February 19, 2020, and March 19, 2020. The primary outcome was the prognosis that was determined at discharge as mentioned in the medical records. Descriptive statistics, univariate analyses, and stepwise logistic regression analysis were used for data analysis. Results: Of the 1,765 patients included, 93.1% were cured and the mortality was 1.8%. Univariate analyses identified 63 factors significantly associated with COVID-19 prognosis. Logistic regression analysis revealed that a poorer prognosis was associated with undergoing resuscitation, complex disease manifestations, consultation with outside specialists, elevated basophil or lymphocyte counts, an albumin (ALB)/globulin (A/G) ratio > 2.4, and elevated levels of serum aspartate aminotransferase (AST) or creatinine. Patients had a better prognosis if the following conditions were met: dry cough reported as an initial symptom, fatigue as a clinical manifestation, and a diagnosis based on laboratory testing. Conclusion: To prevent clinical deterioration, clinicians should provide special care to patients who underwent resuscitation, with a critical disease, or requiring consultation with outside specialists. Extra attention should be paid to patients with high basophil or lymphocyte counts, a high A/G ratio, and elevated AST or creatinine levels.


Subject(s)
COVID-19 , Child , Cough , Humans , Prognosis , Retrospective Studies , SARS-CoV-2
10.
Infect Dis Poverty ; 10(1): 128, 2021 Oct 24.
Article in English | MEDLINE | ID: covidwho-1482013

ABSTRACT

BACKGROUND: Coronaviruses can be isolated from bats, civets, pangolins, birds and other wild animals. As an animal-origin pathogen, coronavirus can cross species barrier and cause pandemic in humans. In this study, a deep learning model for early prediction of pandemic risk was proposed based on the sequences of viral genomes. METHODS: A total of 3257 genomes were downloaded from the Coronavirus Genome Resource Library. We present a deep learning model of cross-species coronavirus infection that combines a bidirectional gated recurrent unit network with a one-dimensional convolution. The genome sequence of animal-origin coronavirus was directly input to extract features and predict pandemic risk. The best performances were explored with the use of pre-trained DNA vector and attention mechanism. The area under the receiver operating characteristic curve (AUROC) and the area under precision-recall curve (AUPR) were used to evaluate the predictive models. RESULTS: The six specific models achieved good performances for the corresponding virus groups (1 for AUROC and 1 for AUPR). The general model with pre-training vector and attention mechanism provided excellent predictions for all virus groups (1 for AUROC and 1 for AUPR) while those without pre-training vector or attention mechanism had obviously reduction of performance (about 5-25%). Re-training experiments showed that the general model has good capabilities of transfer learning (average for six groups: 0.968 for AUROC and 0.942 for AUPR) and should give reasonable prediction for potential pathogen of next pandemic. The artificial negative data with the replacement of the coding region of the spike protein were also predicted correctly (100% accuracy). With the application of the Python programming language, an easy-to-use tool was created to implements our predictor. CONCLUSIONS: Robust deep learning model with pre-training vector and attention mechanism mastered the features from the whole genomes of animal-origin coronaviruses and could predict the risk of cross-species infection for early warning of next pandemic.


Subject(s)
Coronavirus Infections , Coronavirus , Pandemics , Animals , Coronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Deep Learning , Humans , Models, Statistical , Risk Assessment/methods
11.
J Neurol ; 269(4): 1731-1740, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1469692

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19), a contagious infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread across the world. Apart from respiratory complications, an increasing number of patients with ischemic stroke have been reporting. OBJECTIVE: This systematic review and meta-analysis aims to explore the characteristics of ischemic stroke after SARS-CoV-2 infection, and provides valuable reference materials for subsequent clinical treatment. MATERIALS AND METHODS: PubMed, Web of Science, and Ovid-Embase databases were searched up to 24th March 2021. We utilized the search strategy of medical subject headings combined with entry terms to search all related literatures. All studies identified with the electronic and manual searches were listed by citation, title, authors, and abstract. Only studies involving patients with COVID-19-related stroke were eligible. The references of included studies were also manually screened. RESULTS: The meta-analysis was conducted following the PRISMA and MOOSE reporting guidelines. Bias risk was assessed using the Newcastle-Ottawa Scale (NOS). Ten articles, including 26,691 participants and 280 patients with ischemic stroke and COVID-19, were selected. The pooled prevalence of ischemic stroke in COVID-19 was 2% (95% CI 1-2%; p < 0.01). The pooled proportions of hypertension, hyperlipidemia and diabetes in COVID-19-related ischemic stroke was 66% (95% CI 51-81%; p < 0.01), 48% (95% CI 19-76%; p < 0.01) and 40% (95% CI 29-51%; p < 0.01), respectively. Notably, the pooled proportions of female was 36% (95% CI 21-50%; p < 0.01) in patients with COVID-19 and stroke. In addition, in TOAST classification, cryptogenic stroke subtype was associated with a high trend, and its pooled proportion was 35% (95% CI 12-59%; p < 0.01). CONCLUSION: Ischemic stroke caused by COVID-19 has its own unique clinical features. Although common high-risk factors can also be observed, its importance may have changed. The major inflammatory storm of COVID-19 is more likely to occur in male patients. The increase in the proportion of cryptogenic stroke has also made stroke related to COVID-19 complicated.


Subject(s)
COVID-19 , Ischemic Stroke , Stroke , COVID-19/complications , Female , Humans , Ischemic Stroke/epidemiology , Ischemic Stroke/etiology , Male , Risk Factors , SARS-CoV-2 , Stroke/epidemiology , Stroke/etiology
12.
Front Pediatr ; 9: 686600, 2021.
Article in English | MEDLINE | ID: covidwho-1367754

ABSTRACT

Background: Smell and taste dysfunctions are common and have been reported as an early indicator of COVID-19. The prevalence of smell and taste dysfunctions among children with COVID-19 varies greatly across studies, which remains to be summarized quantitatively. This review aimed at examining the pooled prevalence of smell or taste dysfunctions among children with COVID-19, summarizing possible causes of the inconsistencies in the current estimates. Methods: Systematic searches of databases were conducted for literature published until 12 January 2021. Statistical analyses were performed using R software, the pooled prevalence was combined using random effects model. The Loney criteria were used for quality assessment. Results: A total of 18 eligible studies were included. The results showed that the pooled prevalence of smell dysfunction among children with COVID-19 was 15.97% (95% CI: 8.18-23.77%), the pooled prevalence of taste dysfunction among children with COVID-19 was 9.20% (95% CI: 4.25-14.16%), the pooled prevalence of smell or taste dysfunction among children with COVID-19 was 15.50% (95% CI: 10.30-20.70%) and the pooled prevalence of smell and taste dysfunction among children with COVID-19 was 20.21% (95% CI: 14.14-26.28%). Higher smell or taste dysfunction rates were associated with being female, younger age, smaller sample size, patients in Asia, and with comorbidities. Conclusions: Evidence suggests that smell or taste dysfunctions were common among children with COVID-19. Further research is needed to identify effective strategies for preventing and treating smell and taste dysfunctions among children with COVID-19.

13.
Information Systems Education Journal ; 19(2):4-14, 2021.
Article in English | ProQuest Central | ID: covidwho-1306119

ABSTRACT

Today's organizations are operating in a volatile, uncertain and complex digital environment. The outbreak of COVID-19 pandemic has exacerbated this situation. There is an urgent need for organizations to acquire a new generation of business and technology professionals that not only possess in-depth and current disciplinary specialization knowledge, but also are able to communicate and collaborate using skills across the organization in fields including business, innovation, leadership, and technology (BILT). It is recognized that the traditional pathway of getting a "full-fledged" master's degree within 18-24 months may not address the challenge in a timely manner. As educators working in the technology and business sectors of higher education, we aim to explore an alternative strategy to prepare the BILT workforce ready for the "new" economy. This article reviews several alternative education models that have been taken by different stakeholders to prepare the workforce to meet employers' quickly changing expectations. An "H-shaped" BILT model is illustrated as a modular curriculum structure to enhance and complement disciplinary specializations with a focus on combined skills across multiple domains. We present a case study with details on developing and implementing the BILT model at our school as an alternative pathway with greater degrees of flexibility and agility. Finally, we discuss the potential of generalizing this alternative education model in other settings and delineate several future research directions.

14.
Zhongguo Huanjing Kexue = China Environmental Science ; 41(5):1985, 2021.
Article in English | ProQuest Central | ID: covidwho-1257861

ABSTRACT

The influence of meteorological conditions on the pollution processes was investigated in this study by analyzing the changes of air quality as well as the characteristics of two persistent heavy pollution episodes during the Coronavirus Disea se 2019(COVID-19) prevention(January 24 to February 29) of 2020 winter compared with the same period of 2015~2019. Cold air intensity in 2020 winter was weaker with the cold surges frequency decreased by 50%. Air temperature was 0.73℃ higher, and wind speed and mixed layer height were 17.8% and 32.5% lower, respectively. Relative humidity and dew point temperature increased by 60. 9% and 48.1%, respectively. Northerly wind frequency reduced 7.5% while both of southerly and easterly wind increased 6.0%. As shown above, all meteorological conditions in 2020 winter were significantly more favorable for air pollution than the same historical period. Moreover, two heavy pollution episodes(January 24~29 and February 8~14) lasted for 59 and 75 hours were analyzed. At the cumulative stage, regional transport that can be divided into east and south channel greatly affected PM2.5, with the contribution of 70% and 58% for two episodes. By contrast, the contribution of local pollution was 67% and 48%, respectively, indicating the increased proportion of hygroscopic growth and secondary generation in the maintenance and aggravation stages. Under the meteorological background of "high humidity and high atmospheric stability", the combined effects of atmospheric vertical dynamics and horizontal convergence accumulated PM2.5 and water vapor in Beijing plain and prevented them from spreading beyond the boundary layer. Further bidirectional feedback between increased pollutants and meteorological factor s in stable boundary layer resulting in aggravation of pollution. According to EMI index, meteorological conditions during the epi demic prevention in 2020 winter caused an increase of 70.1% in PM2.5 concentration compared to pre-COVID-19. Emissions reduction caused by emergency measures for COVID-19 lockdown offset 53% of the adverse impact induced by meteorological conditions. As for the two episodes in 2020 winter, EMI was 26.9% and 19.7% larger than the average of other nine episodes in the correspond ing period of 2015~2019, and PM2.5 concentration was basically unchanged or slightly reduced. Overall, if the current social emission level is not changed, emission reduction caused by city blockade under special circumstances can only partially reduce the pollution concentration, however, cannot completely offset the adverse impact of meteorological conditions.

15.
RSC Adv ; 11(28): 17408-17412, 2021 May 06.
Article in English | MEDLINE | ID: covidwho-1246409

ABSTRACT

Therapeutic options in response to the coronavirus disease 2019 (COVID-19) outbreak are urgently needed. In this communication, we demonstrate how to support selection of a stable solid form of an antiviral drug remdesivir in quick time using the microcrystal electron diffraction (MicroED) technique and a cloud-based and artificial intelligence implemented crystal structure prediction platform. We present the MicroED structures of remdesivir forms II and IV and conclude that form II is more stable than form IV at ambient temperature in agreement with experimental observations. The combined experimental and theoretical study can serve as a template for formulation scientists in the pharmaceutical industry.

16.
mBio ; 12(2)2021 04 20.
Article in English | MEDLINE | ID: covidwho-1195827

ABSTRACT

Newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, which has caused extensive mortality and morbidity and wreaked havoc on socioeconomic structures. The urgent need to better understand SARS-CoV-2 biology and enable continued development of effective countermeasures is aided by the production of laboratory tools that facilitate SARS-CoV-2 research. We previously created a directly accessible SARS-CoV-2 toolkit containing user-friendly reverse genetic (RG) infectious clones of SARS-CoV-2. Here, using K18-human ACE2 (hACE2) mice, we confirmed the validity of RG-rescued SARS-CoV-2 viruses to reproduce the infection profile, clinical disease, and pathogenesis already established in mice infected with natural SARS-CoV-2 isolates, often patient derived. RG-rescued SARS-CoV-2-infected K18-hACE2 mice developed substantial clinical disease and weight loss by day 6 postinfection. RG-rescued SARS-CoV-2 was recovered from the lungs and brains of infected K18-hACE2 mice, and infection resulted in viral pneumonia with considerable changes in lung pathology, as seen previously with natural SARS-CoV-2 infection. In mice infected with RG-rescued SARS-CoV-2-mCherry, mCherry was detected in areas of lung consolidation and colocalized with clinically relevant SARS-CoV-2-assocated immunopathology. RG-rescued SARS-CoV-2 viruses successfully recapitulated many of the features of severe COVID-19 associated with the K18-hACE2 model of SARS-CoV-2 infection. With utility in vivo, the RG-rescued SARS-CoV-2 viruses will be valuable resources to advance numerous areas of SARS-CoV-2 basic research and COVID-19 vaccine development.IMPORTANCE To develop COVID-19 countermeasures, powerful research tools are essential. We produced a SARS-COV-2 reverse genetic (RG) infectious clone toolkit that will benefit a variety of investigations. In this study, we further prove the toolkit's value by demonstrating the in vivo utility of RG-rescued SARS-CoV-2 isolates. RG-rescued SARS-CoV-2 isolates reproduce disease signs and pathology characteristic of the K18-hACE2 mouse model of severe COVID-19 in infected mice. Having been validated as a model of severe COVID-19 previously using only natural SARS-CoV-2 isolated from patients, this is the first investigation of RG-rescued SARS-CoV-2 viruses in K18-hACE2 mice. The RG-rescued SARS-CoV-2 viruses will facilitate basic understanding of SARS-CoV-2 and the preclinical development of COVID-19 therapeutics.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , COVID-19/etiology , SARS-CoV-2/pathogenicity , Animals , COVID-19/pathology , COVID-19/virology , Cytokine Release Syndrome/etiology , Disease Models, Animal , Female , Host Microbial Interactions , Humans , Inflammation Mediators/metabolism , Lung/immunology , Lung/pathology , Lung/virology , Male , Mice , Mice, Transgenic , Pandemics , Pneumonia, Viral/etiology , Pneumonia, Viral/virology , Reverse Genetics/methods , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Viral Tropism , Virus Replication
17.
Water Res ; 198: 117138, 2021 Jun 15.
Article in English | MEDLINE | ID: covidwho-1174530

ABSTRACT

Intensified sanitization practices during the recent coronavirus disease-2019 (COVID-19) led to the release of chlorine-based disinfectants in surface water, potentially triggering the formation of disinfection byproducts (DBPs) in the presence of dissolved organic nitrogen (DON). Thus, a comprehensive investigation of DON's spatial distribution and its association with DBP occurrence in the surface water is urgently needed. In this study, a total of 51 water samples were collected from two rivers and four lakes in May 2020 in Wuhan to explore the regional variation of nitrogen (N) species, DON's compositional characteristics, and the three classes of DBP occurrence. In lakes, 53.0% to 86.3% of N existed as DON, with its concentration varying between 0.3-4.0 mg N/L. In contrast, NO3--N was the dominant N species in rivers. Spectral analysis revealed that DON in the lakes contained higher humic and fulvic materials with higher A254, A253/A203, SUVA254, and PIII+IV/PI+II+V ratios, while rivers had higher levels of hydrophilic compounds. Trihalomethanes (THMs) were the most prevalent DBPs in the surface waters, followed by N-nitrosamines and haloacetonitriles (HANs). The levels of N-nitrosamines (23.1-97.4 ng/L) increased significantly after the outbreak of the COVID-19 pandemic. Excessive DON in the surface waters was responsible for the formation of N-nitrosamines. This study confirmed that the presence of DON in surface water could result in DBP formation, especially N-nitrosamines, when disinfectants were discharged into surface water during the COVID-19 pandemic.


Subject(s)
COVID-19 , Disinfectants , Water Pollutants, Chemical , Water Purification , Disinfection , Halogenation , Humans , Nitrogen/analysis , Pandemics , SARS-CoV-2 , Trihalomethanes/analysis , Water Pollutants, Chemical/analysis
18.
PLoS Biol ; 19(2): e3001091, 2021 02.
Article in English | MEDLINE | ID: covidwho-1102372

ABSTRACT

The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.


Subject(s)
COVID-19 Vaccines , COVID-19/diagnosis , COVID-19/virology , Reverse Genetics , SARS-CoV-2/genetics , A549 Cells , Angiotensin-Converting Enzyme 2/metabolism , Animals , Chlorocebus aethiops , Codon , Humans , Hydrazones/pharmacology , Mice , Morpholines/pharmacology , Open Reading Frames , Plasmids/genetics , Pyrimidines/pharmacology , Serine Endopeptidases/metabolism , Vero Cells , Viral Proteins/metabolism
19.
Front Cell Infect Microbiol ; 11: 613304, 2021.
Article in English | MEDLINE | ID: covidwho-1088903

ABSTRACT

Background: The emerging Coronavirus Disease-2019 (COVID-19) has challenged the public health globally. With the increasing requirement of detection for SARS-CoV-2 outside of the laboratory setting, a rapid and precise Point of Care Test (POCT) is urgently needed. Methods: Targeting the nucleocapsid (N) gene of SARS-CoV-2, specific primers, and probes for reverse transcription recombinase-aided amplification coupled with lateral flow dipstick (RT-RAA/LFD) platform were designed. For specificity evaluation, it was tested with human coronaviruses, human influenza A virus, influenza B viruses, respiratory syncytial virus, and hepatitis B virus, respectively. For sensitivity assay, it was estimated by templates of recombinant plasmid and pseudovirus of SARS-CoV-2 RNA. For clinical assessment, 100 clinical samples (13 positive and 87 negatives for SARS-CoV-2) were tested via quantitative reverse transcription PCR (RT-qPCR) and RT-RAA/LFD, respectively. Results: The limit of detection was 1 copies/µl in RT-RAA/LFD assay, which could be conducted within 30 min at 39°C, without any cross-reaction with other human coronaviruses and clinical respiratory pathogens. Compared with RT-qPCR, the established POCT assay offered 100% specificity and 100% sensitivity in the detection of clinical samples. Conclusion: This work provides a convenient POCT tool for rapid screening, diagnosis, and monitoring of suspected patients in SARS-CoV-2 endemic areas.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , COVID-19/virology , COVID-19 Nucleic Acid Testing/instrumentation , Coronavirus Nucleocapsid Proteins/genetics , DNA Primers/genetics , Humans , Phosphoproteins/genetics , Point-of-Care Testing , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/instrumentation , Recombinases/metabolism , Reverse Transcription , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
20.
J Virol ; 94(14)2020 07 01.
Article in English | MEDLINE | ID: covidwho-922525

ABSTRACT

Porcine deltacoronavirus (PDCoV) is an economically important enteropathogen of swine with worldwide distribution. PDCoV primarily infects the small intestine instead of the large intestine in vivo However, the underlying mechanism of PDCoV tropism to different intestinal segments remains poorly understood as a result of the lack of a suitable in vitro intestinal model that recapitulates the cellular diversity and complex functions of the gastrointestinal tract. Here, we established the PDCoV infection model of crypt-derived enteroids from different intestinal segments. Enteroids were susceptible to PDCoV, and multiple types of different functional intestinal epithelia were infected by PDCoV in vitro and in vivo We further found that PDCoV favorably infected the jejunum and ileum and restrictedly replicated in the duodenum and colon. Mechanistically, enteroids from different intestinal regions displayed a distinct gene expression profile, and the differential expression of primary viral receptor host aminopeptidase N (APN) instead of the interferon (IFN) responses determined the susceptibility of different intestinal segments to PDCoV, although PDCoV substantially elicited antiviral genes production in enteroids after infection. Additional studies showed that PDCoV infection significantly induced the expression of type I and III IFNs at the late stage of infection, and exogenous IFN inhibited PDCoV replication in enteroids. Hence, our results provide critical inputs to further dissect the molecular mechanisms of PDCoV-host interactions and pathogenesis.IMPORTANCE The zoonotic potential of the PDCoV, a coronavirus efficiently infecting cells from a broad range species, including porcine, chicken, and human, emphasizes the urgent need to further study the cell and tissue tropism of PDCoV in its natural host. Herein, we generated crypt stem cell-derived enteroids from porcine different intestinal regions, which well recapitulated the events in vivo of PDCoV infection that PDCoV targeted multiple types of intestinal epithelia and preferably infected the jejunum and ileum over the duodenum and colon. Mechanistically, we demonstrated that the expression of APN receptor rather than the IFN responses determined the susceptibility of different regions of the intestines to PDCoV infection, though PDCoV infection markedly elicited the IFN responses. Our findings provide important insights into how the distinct gene expression profiles of the intestinal segments determine the cell and tissue tropism of PDCoV.


Subject(s)
CD13 Antigens/genetics , Coronavirus Infections/veterinary , Coronavirus/physiology , Gene Expression Regulation, Viral , Host-Pathogen Interactions , Swine Diseases/metabolism , Swine Diseases/virology , Viral Tropism , Animals , Enterocolitis/metabolism , Enterocolitis/pathology , Enterocolitis/virology , Interferons/metabolism , Intestinal Mucosa/metabolism , Intestinal Mucosa/pathology , Intestinal Mucosa/virology , Swine , Swine Diseases/pathology , Virus Replication
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