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1.
Mater Sci Eng C Mater Biol Appl ; 116: 111260, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-1452344

ABSTRACT

Polymeric nanoparticulate systems allow the encapsulation of bio-active substances, giving them protection against external agents and increasing the drug's bioavailability. The use of biocompatible and biodegradable polymers usually guarantees the harmless character of the formulation, and a controlled drug release is also assured. A relatively easy procedure to obtain polymeric formulations of bioactive agents is ionotropic gelation, which allows the synthesis of chitosan (CS) - sodium tri-polyphosphate nanoparticles (NPs) loading encapsulated proteins. In this work, Bovine serum albumin (BSA) model protein and a recombinant porcine alpha interferon variant were used to obtain nanoparticulate formulations. The internalization of the encapsulated material by cells was studied using a BSA-fluorescein system; the fluorescent conjugate was observable inside the cells after 20 h of incubation. The therapeutic CS-alpha interferon formulation showed a maximum of protein released in vitro at around 90 h. This system was found to be safe in a cytotoxicity assay, while biological activity experiments in vitro showed antiviral protection of cells in the presence of encapsulated porcine alpha interferon. In vivo experiments in pigs revealed a significant and sustained antiviral response through overexpression of the antiviral markers OAS2 and PKR. This proves the preservation of porcine alpha interferon biological activity, and also that a lasting response was obtained. This procedure is an effective and safe method to formulate drugs in nanoparticulate systems, representing a significant contribution to the search for more effective drug delivery strategies.


Subject(s)
Chitosan , Nanoparticles , Pharmaceutical Preparations , Animals , Antiviral Agents/pharmacology , Biological Availability , Cattle , Drug Carriers , Drug Delivery Systems , Interferon-alpha , Particle Size , Polymers , Swine
2.
Clin Exp Dent Res ; 7(5): 772-785, 2021 10.
Article in English | MEDLINE | ID: covidwho-1479394

ABSTRACT

OBJECTIVES: Clinical validation of a bioluminescence imaging system (Cis) as measured by the level of agreement between clinician visual and tactile assessment of carious lesion presence and activity and the presence/absence of elevated luminescence on a tooth surface determined from intraoral image mapping. MATERIALS AND METHODS: This was a regulatory clinical study designed in consultation with the FDA. The design was a prospective, five-investigator, nonrandomized, post-approval, clinical study utilizing the Cis to provide images of elevated calcium ion concentration (indicative of active demineralization) on tooth surfaces via use of a photoprotein. Imaged teeth were identified as "sound" or having "active lesions." Images were scored independently for luminescence. RESULTS: A total of 110 participants aged 7-74 years were imaged. Of the 90 teeth assessed as "sound," 88 were deemed to show no luminescence by the reviewing investigator, a negative percentage agreement of 97.8% (significantly >50% agreement [p < .0001]; one-sided 97.5% confidence interval [CI]: 0.9220). Of the 86 teeth initially assessed as having an "active lesion," 78 were deemed to show luminescence by the reviewing investigator, a positive percentage agreement of 90.7% (significantly >50% agreement [p < .0001]; 97.5% CI: 0.8249). There were no patient-related adverse events. CONCLUSIONS: Results show, with a high level of agreement, that Cis can differentiate tooth surfaces clinically identified as involving active enamel lesions (ICDAS code 2/3), from sound sites (biochemically equivalent to inactive lesions) and that the system is safe for clinical use.


Subject(s)
Dental Caries , Tooth , Dental Caries/diagnostic imaging , Dental Enamel , Humans , Prospective Studies , Technology
3.
AACE Clin Case Rep ; 7(5): 288-292, 2021.
Article in English | MEDLINE | ID: covidwho-1397116

ABSTRACT

OBJECTIVE: During the ongoing coronavirus disease 2019 pandemic, procalcitonin (PCT) levels have proven useful in assisting clinicians to diagnose bacterial superinfection. However, in the absence of signs of infection or at the resolution thereof, inappropriately and persistently high PCT levels may suggest and reveal the presence of other pathologies. We report a patient with severe acute respiratory syndrome coronavirus 2 pneumonia with initially elevated PCT levels that persisted during recovery, prompting the diagnosis of medullary thyroid carcinoma (MTC). METHODS: A 43-year-old man presented with a 2-day history of fever, sneezing, sore throat, and dry cough. His PCT was 94 ng/mL (normal value, 0.00-0.10 ng/mL), and he was positive for severe acute respiratory syndrome coronavirus 2 RNA. RESULTS: Empirical antibiotic therapy was administered for 7 days, but despite a clinical improvement, serum PCT remained high (84 ng/mL). Serum calcitonin (CTN) was 2120 pg/mL (normal, ≤12 pg/mL). Cytologic examination of thyroid nodules and CTN measurement of the aspiration needle washout confirmed MTC. The patient underwent total thyroidectomy with bilateral cervical lymph node dissection. Lowered CTN (986 pg/mL) and PCT (16 ng/mL) levels were observed 48 hours after surgery. A close follow-up was planned following the results of RET gene analysis. CONCLUSION: PCT can be a useful biochemical marker of MTC suspicion in patients with inflammatory conditions and persistently elevated PCT, even after resolution. In our case, high levels of PCT in a patient with coronavirus disease 2019 pneumonia without signs of bacterial infection led to MTC diagnosis.

4.
PLoS One ; 15(11): e0242305, 2020.
Article in English | MEDLINE | ID: covidwho-1388894

ABSTRACT

Containment measures have been applied in several countries in order to limit the diffusion of the SARS-CoV-2 epidemic. The scope of this study is to analyze the evolution of the first wave of the SARS-CoV-2 epidemic throughout Italy and factors associated to the different way it spread in the Italian Regions, starting from the day that the first indigenous cases were detected through day 81 (6 days after the end of the strict lockdown). Data were obtained from daily reports and are represented as number (and percentage) of cases/100,000 persons. A lockdown with movement restrictions, especially across Regions, was declared at day 20. At day 81, 219,070 cases (363/100,000 persons) were diagnosed. A regression analysis based on the Gompertz model predicts a total number 233,606 cases (386/100,000 persons) at the end of the epidemic. The 21 areas, divided into Italian Regions and autonomous Provinces, showed a wide range in the frequency of cases at day 81 (58-921, median 258/100,000 persons) and total predicted cases (58-946, median 267/100,000 persons). Similarly, the predicted time for the end of the wave of the epidemic (considering as surrogate marker the time at which 99% of the total cases are predicted to occur) was highly variable, ranging from 64 to 136 (median 99) days. We analyzed the impact of local and interventional variables on the epidemic curve in each Region. The number of cases correlated inversely with the distance from the area in which first cases were detected and directly also with the gross domestic product pro capite (as a marker of industrial activity) of the Region. Moreover, an earlier start of the lockdown (i.e. in the presence of a lower number of cases) and wider testing were associated with a lower final number of total cases. In conclusion, this analysis shows that population-wide testing and early lockdown enforcement appear effective in limiting the spreading of the SARS-CoV-2 epidemic.


Subject(s)
Communicable Disease Control/methods , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Betacoronavirus , COVID-19 , Coronavirus Infections/prevention & control , Data Interpretation, Statistical , Humans , Italy/epidemiology , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Regression Analysis , SARS-CoV-2
5.
Nature ; 583(7818): 834-838, 2020 07.
Article in English | MEDLINE | ID: covidwho-1387423

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus with high nucleotide identity to SARS-CoV and to SARS-related coronaviruses that have been detected in horseshoe bats, has spread across the world and had a global effect on healthcare systems and economies1,2. A suitable small animal model is needed to support the development of vaccines and therapies. Here we report the pathogenesis and transmissibility of SARS-CoV-2 in golden (Syrian) hamsters (Mesocricetus auratus). Immunohistochemistry assay demonstrated the presence of viral antigens in nasal mucosa, bronchial epithelial cells and areas of lung consolidation on days 2 and 5 after inoculation with SARS-CoV-2, followed by rapid viral clearance and pneumocyte hyperplasia at 7 days after inoculation. We also found viral antigens in epithelial cells of the duodenum, and detected viral RNA in faeces. Notably, SARS-CoV-2 was transmitted efficiently from inoculated hamsters to naive hamsters by direct contact and via aerosols. Transmission via fomites in soiled cages was not as efficient. Although viral RNA was continuously detected in the nasal washes of inoculated hamsters for 14 days, the communicable period was short and correlated with the detection of infectious virus but not viral RNA. Inoculated and naturally infected hamsters showed apparent weight loss on days 6-7 post-inoculation or post-contact; all hamsters returned to their original weight within 14 days and developed neutralizing antibodies. Our results suggest that features associated with SARS-CoV-2 infection in golden hamsters resemble those found in humans with mild SARS-CoV-2 infections.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/transmission , Coronavirus Infections/virology , Disease Models, Animal , Lung/pathology , Lung/virology , Mesocricetus/virology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Aerosols , Alveolar Epithelial Cells/pathology , Alveolar Epithelial Cells/virology , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Antigens, Viral/immunology , Antigens, Viral/isolation & purification , Antigens, Viral/metabolism , Betacoronavirus/immunology , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Bronchi/pathology , Bronchi/virology , COVID-19 , Coronavirus Infections/immunology , Duodenum/virology , Fomites/virology , Housing, Animal , Kidney/virology , Male , Mesocricetus/immunology , Nasal Mucosa/virology , Pandemics , Pneumonia, Viral/immunology , RNA, Viral/analysis , SARS-CoV-2 , Viral Load , Weight Loss
6.
J Nucl Med ; 61(12): 1717-1719, 2020 12.
Article in English | MEDLINE | ID: covidwho-1369627

ABSTRACT

The true impact and long-term damage to organs such as the lungs after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain to be determined. Noninvasive molecularly targeted imaging may play a critical role in aiding visualization and understanding of the systemic damage. We have identified αvß6 as a molecular target; an epithelium-specific cell surface receptor that is low or undetectable in healthy adult epithelium but upregulated in select injured tissues, including fibrotic lung. Herein we report the first human PET/CT images using the integrin αvß6-binding peptide (18F-αvß6-BP) in a patient 2 mo after the acute phase of infection. Minimal uptake of 18F-αvß6-BP was noted in normal lung parenchyma, with uptake being elevated in areas corresponding to opacities on CT. This case suggests that 18F-αvß6-BP PET/CT is a promising noninvasive approach to identify the presence and potentially monitor the persistence and progression of lung damage.


Subject(s)
Antigens, Neoplasm/metabolism , COVID-19/diagnostic imaging , COVID-19/metabolism , Integrins/metabolism , Lung/diagnostic imaging , Positron Emission Tomography Computed Tomography , Aged , Humans , Male
7.
J Pediatric Infect Dis Soc ; 10(6): 706-713, 2021 Aug 14.
Article in English | MEDLINE | ID: covidwho-1358465

ABSTRACT

BACKGROUND: Recently, cases of multisystem inflammatory syndrome in children (MIS-C) associated with coronavirus disease 2019 (COVID-19) have been reported worldwide. Negative polymerase chain reaction (RT-PCR) testing associated with positive serology in most of the cases suggests a postinfectious syndrome. Because the pathophysiology of this syndrome is still poorly understood, extensive virological and immunological investigations are needed. METHODS: We report a series of 4 pediatric patients admitted to Geneva University Hospitals with persistent fever and laboratory evidence of inflammation meeting the published definition of MIS-C related to COVID-19, to whom an extensive virological and immunological workup was performed. RESULTS: RT-PCRs on multiple anatomical compartments were negative, whereas anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin A (IgA) and immunoglobulin G (IgG) were strongly positive by enzyme-linked immunosorbent assay and immunofluorescence. Both pseudoneutralization and full virus neutralization assays showed the presence of neutralizing antibodies in all children, confirming a recent infection with SARS-CoV-2. The analyses of cytokine profiles revealed an elevation in all cytokines, as reported in adults with severe COVID-19. Although differing in clinical presentation, some features of MIS-C show phenotypic overlap with hemophagocytic lymphohistiocytosis (HLH). In contrast to patients with primary HLH, our patients showed normal perforin expression and natural killer (NK) cell degranulation. The levels of soluble interleukin (IL)-2 receptor (sIL-2R) correlated with the severity of disease, reflecting recent T-cell activation. CONCLUSION: Our findings suggest that MIS-C related to COVID-19 is caused by a postinfectious inflammatory syndrome associated with an elevation in all cytokines, and markers of recent T-cell activation (sIL-2R) occurring despite a strong and specific humoral response to SARS-CoV-2. Further functional and genetic analyses are essential to better understand the mechanisms of host-pathogen interactions.


Subject(s)
COVID-19 , Antibodies, Neutralizing , Child , Humans , SARS-CoV-2 , Systemic Inflammatory Response Syndrome
8.
Brief Bioinform ; 22(2): 1215-1224, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1343625

ABSTRACT

The pandemic of coronavirus disease 2019 (COVID-19) urgently calls for more sensitive molecular diagnosis to improve sensitivity of current viral nuclear acid detection. We have developed an anchor primer (AP)-based assay to improve viral RNA stability by bioinformatics identification of RNase-binding site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and implementing AP dually targeting the N gene of SARS-CoV-2 RNA and RNase 1, 3, 6. The arbitrarily primed polymerase chain reaction (AP-PCR) improvement of viral RNA integrity was supported by (a) the AP increased resistance of the targeted gene (N gene) of SARS-CoV-2 RNA to RNase treatment; (b) the detection of SARS-CoV-2 RNA by AP-PCR with lower cycle threshold values (-2.7 cycles) compared to two commercially available assays; (c) improvement of the viral RNA stability of the ORF gene upon targeting of the N gene and RNase. Furthermore, the improved sensitivity by AP-PCR was demonstrated by detection of SARS-CoV-2 RNA in 70-80% of sputum, nasal, pharyngeal swabs and feces and 36% (4/11) of urine of the confirmed cases (n = 252), 7% convalescent cases (n = 54) and none of 300 negative cases. Lastly, AP-PCR analysis of 306 confirmed and convalescent cases revealed prolonged presence of viral loading for >20 days after the first positive diagnosis. Thus, the AP dually targeting SARS-CoV-2 RNA and RNase improves molecular detection by preserving SARS-CoV-2 RNA integrity and reveals the prolonged viral loading associated with older age and male gender in COVID-19 patients.


Subject(s)
COVID-19/virology , Polymerase Chain Reaction/methods , Ribonucleases/metabolism , SARS-CoV-2/metabolism , Aged , Binding Sites , Female , Humans , Male , RNA, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viral Load
9.
Chimia (Aarau) ; 75(5): 446-452, 2021 May 28.
Article in English | MEDLINE | ID: covidwho-1314525

ABSTRACT

Serological testing for antibodies directed against SARS-CoV-2 in patients may serve as a diagnostic tool to verify a previous infection and as surrogate for an elicited humoral immune response, ideally conferring immunity after infection or vaccination. Here, we present the recombinant expression of an extended receptor binding domain (RBD) of the SARS-CoV-2 Spike protein used as capture antigen in a unique rapid immunoassay to detect the presence of RBD binding antibodies with high sensitivity and specificity. As currently available vaccines focus on the Spike RBD as target, the developed test can also be used to monitor a successful immune response after vaccination with an RBD based vaccine.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Antibodies, Viral , Humans , SARS-CoV-2
10.
Methods Mol Biol ; 2099: 21-37, 2020.
Article in English | MEDLINE | ID: covidwho-1292545

ABSTRACT

The coronavirus spike envelope glycoprotein is an essential viral component that mediates virus entry events. Biochemical assessment of the spike protein is critical for understanding structure-function relationships and the roles of the protein in the viral life cycle. Coronavirus spike proteins are typically proteolytically processed and activated by host cell enzymes such as trypsin-like proteases, cathepsins, or proprotein-convertases. Analysis of coronavirus spike proteins by western blot allows the visualization and assessment of proteolytic processing by endogenous or exogenous proteases. Here, we present a method based on western blot analysis to investigate spike protein proteolytic cleavage by transient transfection of HEK-293 T cells allowing expression of the spike protein of the highly pathogenic Middle East respiratory syndrome coronavirus in the presence or absence of a cellular trypsin-like transmembrane serine protease, matriptase. Such analysis enables the characterization of cleavage patterns produced by a host protease on a coronavirus spike glycoprotein.


Subject(s)
Coronavirus Infections/virology , Middle East Respiratory Syndrome Coronavirus/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Blotting, Western , Cell Line , Humans , Middle East Respiratory Syndrome Coronavirus/pathogenicity , Protein Processing, Post-Translational , Proteolysis , Serine Endopeptidases/metabolism , Virus Internalization
11.
IDCases ; 25: e01187, 2021.
Article in English | MEDLINE | ID: covidwho-1267690

ABSTRACT

BACKGROUND: SARS-CoV-2 uses the human cell receptor angiotensin-converting enzyme (ACE2). ACE2 is widely present in the cardiovascular system including the myocardium and the conduction system. COVID-19 patients that present severe symptoms have been reported to have complications involving myocardial injuries caused by the virus. Here we report the detection of SARS-CoV-2 by whole genome sequencing in the endocardium of a patient with severe bradycardia. CASE PRESENTATION: We report a case of a 34-year-old male patient with COVID-19 tested by PCR, he started with gastrointestinal symptoms, however, he quickly deteriorated his hemodynamic state by means of myocarditis and bradycardia. After performing an endocardium biopsy, it was possible to identify the presence of SARS-CoV-2 in the heart tissue and to sequence its whole genome using the ARTIC-Network protocol and a modified tissue RNA extraction method. The patient's outcome was improved after a permanent pacemaker was implanted. CONCLUSIONS: It was possible to identify a SARS-CoV-2 clade 20A in the endocardium of the reported patient.

12.
BMJ Case Rep ; 14(6)2021 Jun 11.
Article in English | MEDLINE | ID: covidwho-1266369

ABSTRACT

A 61-year-old obese man who had recently tested positive for COVID-19 presented to the emergency department following an unwitnessed collapse, with a brief period of unresponsiveness. CT pulmonary angiography confirmed the presence of extensive bilateral pulmonary embolism despite the patient reporting full compliance with long-term dabigatran. The patient was initially anticoagulated with low-molecular-weight heparin and was treated with non-invasive ventilation and dexamethasone for COVID-19 pneumonia. He made a full recovery and was discharged on oral rivaroxaban. His case highlighted some of the common problems encountered when selecting an anticoagulation strategy for obese patients, as well as the lack of definitive evidence to guide treatment decisions. These challenges were further complicated by our incomplete understanding of the underlying mechanisms of COVID-19 coagulopathy, with limited data available regarding the optimal management of thromboembolic complications.


Subject(s)
COVID-19 , Pulmonary Embolism , Venous Thromboembolism , Anticoagulants/adverse effects , Humans , Male , Middle Aged , Obesity/complications , Pulmonary Embolism/complications , Pulmonary Embolism/drug therapy , SARS-CoV-2 , Venous Thromboembolism/complications , Venous Thromboembolism/drug therapy
13.
Br J Radiol ; 94(1123): 20210264, 2021 Jul 01.
Article in English | MEDLINE | ID: covidwho-1262534

ABSTRACT

OBJECTIVES: Early in the coronavirus 2019 (COVID-19) pandemic, a high frequency of pulmonary embolism was identified. This audit aims to assess the frequency and severity of pulmonary embolism in 2020 compared to 2019. METHODS: In this retrospective audit, we compared computed tomography pulmonary angiography (CTPA) frequency and pulmonary embolism severity in April and May 2020, compared to 2019. Pulmonary embolism severity was assessed with the Modified Miller score and the presence of right heart strain was assessed. Demographic information and 30-day mortality was identified from electronic health records. RESULTS: In April 2020, there was a 17% reduction in the number of CTPA performed and an increase in the proportion identifying pulmonary embolism (26%, n = 68/265 vs 15%, n = 47/320, p < 0.001), compared to April 2019. Patients with pulmonary embolism in 2020 had more comorbidities (p = 0.026), but similar age and sex compared to 2019. There was no difference in pulmonary embolism severity in 2020 compared to 2019, but there was an increased frequency of right heart strain in May 2020 (29 vs 12%, p = 0.029). Amongst 18 patients with COVID-19 and pulmonary embolism, there was a larger proportion of males and an increased 30 day mortality (28% vs 6%, p = 0.008). CONCLUSION: During the COVID-19 pandemic, there was a reduction in the number of CTPA scans performed and an increase in the frequency of CTPA scans positive for pulmonary embolism. Patients with both COVID-19 and pulmonary embolism had an increased risk of 30-day mortality compared to those without COVID-19. ADVANCES IN KNOWLEDGE: During the COVID-19 pandemic, the number of CTPA performed decreased and the proportion of positive CTPA increased. Patients with both pulmonary embolism and COVID-19 had worse outcomes compared to those with pulmonary embolism alone.


Subject(s)
COVID-19/complications , Computed Tomography Angiography/statistics & numerical data , Pulmonary Embolism/diagnostic imaging , Pulmonary Embolism/etiology , Aged , COVID-19/mortality , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , Pneumonia, Viral/mortality , Pneumonia, Viral/virology , Pulmonary Embolism/mortality , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index
14.
Analyst ; 146(13): 4340-4347, 2021 Jun 28.
Article in English | MEDLINE | ID: covidwho-1262015

ABSTRACT

Sensitive, reliable and cost-effective detection of pathogens has wide ranging applications in clinical diagnostics and therapeutics, water and food safety, environmental monitoring, biosafety and epidemiology. Nucleic acid amplification tests (NAATs) such as PCR and isothermal amplification methods provide excellent analytical performance and significantly faster turnaround times than conventional culture-based methods. However, the inherent cost and complexity of NAATs limit their application in resource-limited settings and the developing world. To help address this urgent need, we have developed a sensitive method for nucleic acid analysis based on padlock probe rolling circle amplification (PLRCA), nuclease protection (NP) and lateral flow detection (LFA), referred to as PLAN-LFA, that can be used in resource-limited settings. The assay involves solution-phase hybridization of a padlock probe to target, sequence-specific ligation of the probe to form a circular template that undergoes isothermal rolling circle amplification in the presence of a polymerase and a labeled probe DNA. The RCA product is a long, linear concatenated single-stranded DNA that contains binding sites for the labeled probe. The sample is then exposed to a nuclease which selectively cleaves single-stranded DNA, the double-stranded labeled probe is protected from nuclease digestion and detected in a lateral flow immunoassay format to provide a visual, colorimetric readout of results. We have developed specific assays targeting beta-lactamase resistance gene for monitoring of antimicrobial resistance and Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2, the novel coronavirus discovered in 2019) using the PLAN-LFA platform. The assay provides a limit of detection of 1.1 pM target DNA (or 1.3 × 106 copies per reaction). We also demonstrate the versatility and robustness of the method by performing analysis on DNA and RNA targets, and perform analysis in complex sample matrices like saliva, plant tissue extract and bacterial culture without any sample pretreatment steps.


Subject(s)
COVID-19 , SARS-CoV-2 , DNA Probes , Humans , Nucleic Acid Amplification Techniques , Nucleic Acid Hybridization
15.
J Proteome Res ; 20(7): 3404-3413, 2021 07 02.
Article in English | MEDLINE | ID: covidwho-1253877

ABSTRACT

SARS-CoV-2 infection has become a major public health burden and affects many organs including lungs, kidneys, the liver, and the brain. Although the virus is readily detected and diagnosed using nasopharyngeal swabs by reverse transcriptase polymerase chain reaction (RT-PCR), detection of its presence in body fluids is fraught with difficulties. A number of published studies have failed to detect viral RNA by RT-PCR methods in urine. Although microbial identification in clinical microbiology using mass spectrometry is undertaken after culture, here we undertook a mass spectrometry-based approach that employed an enrichment step to capture and detect SARS-CoV-2 nucleocapsid protein directly from urine of COVID-19 patients without any culture. We detected SARS-CoV-2 nucleocapsid protein-derived peptides from 13 out of 39 urine samples. Further, a subset of COVID-19 positive and COVID-19 negative urine samples validated by mass spectrometry were used for the quantitative proteomics analysis. Proteins with increased abundance in urine of SARS-CoV-2 positive individuals were enriched in the acute phase response, regulation of complement system, and immune response. Notably, a number of renal proteins such as podocin (NPHS2), an amino acid transporter (SLC36A2), and sodium/glucose cotransporter 5 (SLC5A10), which are intimately involved in normal kidney function, were decreased in the urine of COVID-19 patients. Overall, the detection of viral antigens in urine using mass spectrometry and alterations of the urinary proteome could provide insights into understanding the pathogenesis of COVID-19.


Subject(s)
Body Fluids , COVID-19 , Antigens, Viral , Humans , Immunity , Mass Spectrometry , Phosphoproteins , RNA, Viral , SARS-CoV-2
16.
Mol Cell Probes ; 58: 101744, 2021 08.
Article in English | MEDLINE | ID: covidwho-1253367

ABSTRACT

To increase the repertoire of PCR based laboratory developed tests (LDTs) for the detection of SARS-CoV-2, we describe a new multiplex assay (SORP), targeting the SARS-CoV-2's, Spike and ORF8 genes. The widely used human RNaseP internal control was modified to specifically co-amplify the RNaseP mRNA. The SORP triplex assay was tested on a cohort (n = 372; POS = 144/NEG = 228) of nasopharyngeal flocked swab (NPFS) specimens, previously tested for the presence of SARS-CoV-2 using a PCR assay targeting E and RdRp genes. The overall sensitivity and specificity of the SORP assay was: 99.31% (95% CI: 96.22-99.98%), 100.0% (95% CI: 98.4-100%) respectively. The SORP assay could also detect a panel of variants of concern (VOC) from the B1.1.7 (UK) and B1.351 (SA) lineage. In summary, access to a repertoire of new SARS-CoV-2 LDT's would assist diagnostic laboratories in developing strategies to overcome some of the testing issues encountered during high-throughput SARS-CoV-2 testing.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Multiplex Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , COVID-19/virology , DNA Primers/genetics , DNA Probes/genetics , Humans , Molecular Diagnostic Techniques/methods , Reproducibility of Results , Ribonuclease P/genetics , SARS-CoV-2/physiology , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
17.
Biochem Biophys Res Commun ; 565: 8-13, 2021 08 06.
Article in English | MEDLINE | ID: covidwho-1252489

ABSTRACT

Amidst infectious disease outbreaks, a practical tool that can quantitatively monitor individuals' antibodies to pathogens is vital for disease control. The currently used serological lateral flow immunoassays (LFIAs) can only detect the presence of antibodies for a single antigen. Here, we fabricated a multiplexed circular flow immunoassay (CFIA) test strip with YOLO v4-based object recognition that can quickly quantify and differentiate antibodies that bind membrane glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or hemagglutinin of influenza A (H1N1) virus in the sera of immunized mice in one assay using one sample. Spot intensities were found to be indicative of antibody titers to membrane glycoprotein of SARS-CoV-2 and were, thus, quantified relative to spots from immunoglobulin G (IgG) reaction in a CFIA to account for image heterogeneity. Quantitative intensities can be displayed in real time alongside an image of CFIA that was captured by a built-in camera. We demonstrate for the first time that CFIA is a specific, multi-target, and quantitative tool that holds potential for digital and simultaneous monitoring of antibodies recognizing various pathogens including SARS-CoV-2.


Subject(s)
Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/immunology , Coronavirus M Proteins/immunology , Immunoassay/methods , SARS-CoV-2/immunology , Animals , COVID-19/virology , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Immunoglobulin G/blood , Immunoglobulin G/immunology , Mice , SARS-CoV-2/isolation & purification
18.
Chem Commun (Camb) ; 57(51): 6229-6232, 2021 Jun 24.
Article in English | MEDLINE | ID: covidwho-1246405

ABSTRACT

Tracking the viral progression of SARS-CoV-2 in COVID-19 infected body tissues is an emerging need of the current pandemic. Imaging at near infrared second biological window (NIR-II) offers striking benefits over the other technologies to explore deep-tissue information. Here we design, synthesise and characterise a molecular probe that selectively targets the N-gene of SARS-CoV-2. Highly specific antisense oligonucleotides (ASOs) were conjugated to lead sulfide quantum dots using a UV-triggered thiol-ene click chemistry for the recognition of viral RNA. Our ex vivo imaging studies demonstrated that the probe exhibits aggregation induced NIR-II emission only in presence of SARS-CoV-2 RNA which can be attributed to the efficient hybridisation of the ASOs with their target RNA strands.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , Fluorescent Dyes/chemistry , Oligonucleotides, Antisense/chemistry , Quantum Dots/chemistry , SARS-CoV-2/isolation & purification , Spectroscopy, Near-Infrared/methods , Animals , COVID-19/diagnostic imaging , COVID-19/metabolism , Click Chemistry/methods , Fluorescent Dyes/chemical synthesis , Humans , Lung/diagnostic imaging , Lung/metabolism , Lung/virology , Metal Nanoparticles/chemistry , Mice , Mice, Inbred BALB C , Models, Animal , SARS-CoV-2/genetics , SARS-CoV-2/metabolism
19.
BMC Med Inform Decis Mak ; 21(1): 170, 2021 05 25.
Article in English | MEDLINE | ID: covidwho-1243809

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) has become a pandemic since its first appearance in late 2019. Deaths caused by COVID-19 are still increasing day by day and early diagnosis has become crucial. Since current diagnostic methods have many disadvantages, new investigations are needed to improve the performance of diagnosis. METHODS: A novel method is proposed to automatically diagnose COVID-19 by using Electrocardiogram (ECG) data with deep learning for the first time. Moreover, a new and effective method called hexaxial feature mapping is proposed to represent 12-lead ECG to 2D colorful images. Gray-Level Co-Occurrence Matrix (GLCM) method is used to extract features and generate hexaxial mapping images. These generated images are then fed into a new Convolutional Neural Network (CNN) architecture to diagnose COVID-19. RESULTS: Two different classification scenarios are conducted on a publicly available paper-based ECG image dataset to reveal the diagnostic capability and performance of the proposed approach. In the first scenario, ECG data labeled as COVID-19 and No-Findings (normal) are classified to evaluate COVID-19 classification ability. According to results, the proposed approach provides encouraging COVID-19 detection performance with an accuracy of 96.20% and F1-Score of 96.30%. In the second scenario, ECG data labeled as Negative (normal, abnormal, and myocardial infarction) and Positive (COVID-19) are classified to evaluate COVID-19 diagnostic ability. The experimental results demonstrated that the proposed approach provides satisfactory COVID-19 prediction performance with an accuracy of 93.00% and F1-Score of 93.20%. Furthermore, different experimental studies are conducted to evaluate the robustness of the proposed approach. CONCLUSION: Automatic detection of cardiovascular changes caused by COVID-19 can be possible with a deep learning framework through ECG data. This not only proves the presence of cardiovascular changes caused by COVID-19 but also reveals that ECG can potentially be used in the diagnosis of COVID-19. We believe the proposed study may provide a crucial decision-making system for healthcare professionals. SOURCE CODE: All source codes are made publicly available at: https://github.com/mkfzdmr/COVID-19-ECG-Classification.


Subject(s)
COVID-19 , Deep Learning , Electrocardiography , Humans , Neural Networks, Computer , SARS-CoV-2
20.
Ann Med Surg (Lond) ; 66: 102405, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1242865

ABSTRACT

This article aims to present the case of a man affected by SARS CoV-2 and to discuss the association between this manifestation, viral infection and Open Abodmen. A 52 years old Caucasian man, affected by SARS CoV-2 infection, was admitted to the Emergency department of Arcispedale Sant'Anna of Ferrara for epigastralgia followed by syncopal episode, vomiting and diarrhea with bloody stools. The next day the patient underwent colonoscopy, which detected an ulceration proximally to the ileocecal valve without active bleeding. Subsequently an initial non-operative management and two pharyngeal swabs negative, for another rectorrhagia and hypotensive episode, underwent emerging surgery and an Open Abdomen was performed. The patient was discharged in 12th post-surgery day without complications. The IHC analysis with anti-SARS-CoV-2 nucleocapsid-protein revealed the presence of viral protein expression in epithelial cell of ulcerated intestinal mucosa. In this case report, we showed the presence of viral inclusion in small intestinal wall after two negative pharyngeal swabs for SARS-CoV-2 RNA. We can also say that the largest amount of viral inclusions was in the tissue of ulceration of the last ileal loop. This case report showed that SARS-CoV-2 can be unseen also after clinical healing. It's probably can be expelled with stools and rectal swabs search for SARS-Cov-2 RNA after pharyngeal swabs could be mandatory for declare heled a patient. Moreover, damage control surgery and Open Abdomen as a surgical technique can be a valid alternative in case of uncertainty of the bleeding source and when a second surgical look is necessary.

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