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1.
Clin Chem ; 68(1): 143-152, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-20243230

ABSTRACT

BACKGROUND: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 , COVID-19/diagnosis , Clinical Laboratory Techniques , Humans , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Specimen Handling
2.
Eur J Gastroenterol Hepatol ; 33(3): 309-311, 2021 03 01.
Article in English | MEDLINE | ID: covidwho-20232271

ABSTRACT

On 12 March 2020, the WHO declared that the coronavirus disease 2019 (COVID-19) constitutes a pandemic. Cases of liver damage or dysfunction (mainly characterized by moderately elevated serum aspartate aminotransferase levels) have been reported among patients with COVID-19. However, it is currently uncertain whether the COVID-19 related liver damage/dysfunction is due mainly to the viral infection by itself or other coexisting conditions, such as the use of potentially hepatotoxic medications and the coexistence of systemic inflammatory response, respiratory distress syndrome-induced hypoxia, and multiple organ dysfunction. Individuals at high risk for severe COVID-19 are typical of older age and/or present with comorbid conditions such as diabetes, cardiovascular disease, and hypertension. This is also the same profile for those at increased risk for unrecognized underlying liver disease, especially nonalcoholic fatty liver disease. This could make them more susceptible to liver injury from the virus, medications used in supportive management, or hypoxia. So the aim of this review was to illustrate the clinical implications of COVID-19 on the liver in healthy and diseased states as well as the implications of common liver disorders on the outcome of COVID-19.


Subject(s)
COVID-19/virology , Liver Diseases/virology , Liver/virology , SARS-CoV-2/pathogenicity , COVID-19/diagnosis , COVID-19/epidemiology , Host-Pathogen Interactions , Humans , Liver/pathology , Liver Diseases/diagnosis , Liver Diseases/epidemiology , Prognosis , Risk Assessment , Risk Factors
3.
Eur Rev Med Pharmacol Sci ; 27(10): 4764-4771, 2023 May.
Article in English | MEDLINE | ID: covidwho-20231936

ABSTRACT

OBJECTIVE: Serum thrombin-activated fibrinolysis inhibitor (TAFI) levels were measured in coronavirus disease 2019 (COVID-19) patients requiring intensive care, clinical hospitalization, and outpatient follow-up. The relationships between serum TAFI levels and prognosis were determined. PATIENTS AND METHODS: Ninety patients who had positive COVID-19 PCR test results were randomly selected and included in the study. Subgroups were formed according to the clinical characteristics of the patients as follows: mild, moderate, and severe. Venous blood samples were taken from all patients, and serum C-reactive protein (CRP), lactate dehydrogenase (LDH), fibrinogen, D-dimer, ferritin, and TAFI levels were measured. The results were evaluated by comparing each group. RESULTS: The one-way ANOVA test to determine differences between subgroups resulted in p-values lower than 0.05 for all biochemical analytes (CRP, LDH, fibrinogen, D-dimer, ferritin, and TAFI). Regarding serum TAFI levels, there were significant differences in the severe group (853.04 ± 338.58 ng/mL) compared to the mild group (548.33 ± 264.17 ng/mL). ROC curve analysis to predict mortality revealed that TAFI levels were able to detect 85% of deaths. In addition, ROC analysis revealed that serum TAFI levels could detect 86% of intubated cases. CONCLUSIONS: The disease progression is more severe in patients with high TAFI levels, and high TAFI levels are associated with mortality and intubation rates. Further studies are needed to determine serum TAFI levels as a biomarker of prognosis in COVID-19 patients.


Subject(s)
COVID-19 , Thrombin , Humans , Thrombin/metabolism , COVID-19/diagnosis , Prognosis , Biomarkers , C-Reactive Protein/analysis , Fibrinogen
4.
J Zhejiang Univ Sci B ; 24(6): 463-484, 2023 Jun 15.
Article in English, Chinese | MEDLINE | ID: covidwho-20238798

ABSTRACT

Coronavirus disease 2019 (COVID-19) has continued to spread globally since late 2019, representing a formidable challenge to the world's healthcare systems, wreaking havoc, and spreading rapidly through human contact. With fever, fatigue, and a persistent dry cough being the hallmark symptoms, this disease threatened to destabilize the delicate balance of our global community. Rapid and accurate diagnosis of COVID-19 is a prerequisite for understanding the number of confirmed cases in the world or a region, and an important factor in epidemic assessment and the development of control measures. It also plays a crucial role in ensuring that patients receive the appropriate medical treatment, leading to optimal patient care. Reverse transcription-polymerase chain reaction (RT-PCR) technology is currently the most mature method for detecting viral nucleic acids, but it has many drawbacks. Meanwhile, a variety of COVID-19 detection methods, including molecular biological diagnostic, immunodiagnostic, imaging, and artificial intelligence methods have been developed and applied in clinical practice to meet diverse scenarios and needs. These methods can help clinicians diagnose and treat COVID-19 patients. This review describes the variety of such methods used in China, providing an important reference in the field of the clinical diagnosis of COVID-19.


Subject(s)
Artificial Intelligence , COVID-19 , Humans , China , COVID-19/diagnosis , COVID-19 Testing
5.
ACS Sens ; 8(6): 2309-2318, 2023 Jun 23.
Article in English | MEDLINE | ID: covidwho-20238622

ABSTRACT

We adapted an existing, spaceflight-proven, robust "electronic nose" (E-Nose) that uses an array of electrical resistivity-based nanosensors mimicking aspects of mammalian olfaction to conduct on-site, rapid screening for COVID-19 infection by measuring the pattern of sensor responses to volatile organic compounds (VOCs) in exhaled human breath. We built and tested multiple copies of a hand-held prototype E-Nose sensor system, composed of 64 chemically sensitive nanomaterial sensing elements tailored to COVID-19 VOC detection; data acquisition electronics; a smart tablet with software (App) for sensor control, data acquisition and display; and a sampling fixture to capture exhaled breath samples and deliver them to the sensor array inside the E-Nose. The sensing elements detect the combination of VOCs typical in breath at parts-per-billion (ppb) levels, with repeatability of 0.02% and reproducibility of 1.2%; the measurement electronics in the E-Nose provide measurement accuracy and signal-to-noise ratios comparable to benchtop instrumentation. Preliminary clinical testing at Stanford Medicine with 63 participants, their COVID-19-positive or COVID-19-negative status determined by concomitant RT-PCR, discriminated between these two categories of human breath with a 79% correct identification rate using "leave-one-out" training-and-analysis methods. Analyzing the E-Nose response in conjunction with body temperature and other non-invasive symptom screening using advanced machine learning methods, with a much larger database of responses from a wider swath of the population, is expected to provide more accurate on-the-spot answers. Additional clinical testing, design refinement, and a mass manufacturing approach are the main steps toward deploying this technology to rapidly screen for active infection in clinics and hospitals, public and commercial venues, or at home.


Subject(s)
COVID-19 , Nanostructures , Volatile Organic Compounds , Animals , Humans , Electronic Nose , Reproducibility of Results , COVID-19/diagnosis , Breath Tests/methods , Volatile Organic Compounds/analysis , Mammals
6.
Front Public Health ; 11: 1099116, 2023.
Article in English | MEDLINE | ID: covidwho-20238620

ABSTRACT

This study aims to optimize the COVID-19 screening strategies under China's dynamic zero-case policy through cost-effectiveness analysis. A total of 9 screening strategies with different screening frequencies and combinations of detection methods were designed. A stochastic agent-based model was used to simulate the progress of the COVID-19 outbreak in scenario I (close contacts were promptly quarantined) and scenario II (close contacts were not promptly quarantined). The primary outcomes included the number of infections, number of close contacts, number of deaths, the duration of the epidemic, and duration of movement restriction. Net monetary benefit (NMB) and the incremental cost-benefit ratio were used to compare the cost-effectiveness of different screening strategies. The results indicated that under China's COVID-19 dynamic zero-case policy, high-frequency screening can help contain the spread of the epidemic, reduce the size and burden of the epidemic, and is cost-effective. Mass antigen testing is not cost-effective compared with mass nucleic acid testing in the same screening frequency. It would be more cost-effective to use AT as a supplemental screening tool when NAT capacity is insufficient or when outbreaks are spreading very rapidly.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , Cost-Effectiveness Analysis , Cost-Benefit Analysis , Policy , China/epidemiology
7.
Front Public Health ; 11: 1162711, 2023.
Article in English | MEDLINE | ID: covidwho-20238393

ABSTRACT

Background: Testing was the cornerstone of the COVID-19 epidemic response in most countries until vaccination became available for the general population. Social inequalities generally affect access to healthcare and health behaviors, and COVID-19 was rapidly shown to impact deprived population more drastically. In support of the regional health agency in Provence-Alpes-Côte d'Azur (PACA) in South-Eastern France, we analyzed the relationship between testing rate and socio-demographic characteristics of the population, to identify gaps in testing coverage and improve targeting of response strategies. Methods: We conducted an ecological analysis of SARS-CoV-2/COVID-19 testing rate in the PACA region, based on data aggregated at the finest spatial resolution available in France (IRIS) and by periods defined by public health implemented measures and major epidemiological changes. Using general census data, population density, and specific deprivation indices, we used principal component analysis followed by hierarchical clustering to define profiles describing local socio-demographic characteristics. We analyzed the association between these profiles and testing rates in a generalized additive multilevel model, adjusting for access to healthcare, presence of a retirement home, and the age profile of the population. Results: We identified 6 socio-demographic profiles across the 2,306 analyzed IRIS spatial units: privileged, remote, intermediate, downtown, deprived, and very deprived (ordered by increasing social deprivation index). Profiles also ranged from rural (remote) to high density urban areas (downtown, very deprived). From July 2020 to December 2021, we analyzed SARS-CoV-2/COVID-19 testing rate over 10 periods. Testing rates fluctuated strongly but were highest in privileged and downtown areas, and lowest in very deprived ones. The lowest adjusted testing rate ratios (aTRR) between privileged (reference) and other profiles occurred after implementation of a mandatory healthpass for many leisure activities in July 2021. Periods of contextual testing near Christmas displayed the largest aTRR, especially during the last periods of 2021 after the end of free convenience testing for unvaccinated individuals. Conclusion: We characterized in-depth local heterogeneity and temporal trends in testing rates and identified areas and circumstances associated with low testing rates, which the regional health agency targeted specifically for the deployment of health mediation activities.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19 Testing , COVID-19/diagnosis , COVID-19/epidemiology , Social Deprivation , France/epidemiology
8.
Viruses ; 15(5)2023 05 17.
Article in English | MEDLINE | ID: covidwho-20238379

ABSTRACT

Multiple assays have been developed for the characterization of the functional activation of SARS-CoV-2 specific T-cells. This study was conducted to assess the post-vaccination and post-infection T cell response, as detected by the QuantiFERON-SARS-CoV-2 assay using the combination of three SARS-CoV-2 specific antigens (Ag1, Ag2 and Ag3). An amount of 75 participants with different infection and vaccination backgrounds were recruited for the evaluation of humoral and cellular immune responses. An elevated IFN-γ response in at least one Ag tube was observed in 69.2% of convalescent subjects and 63.9% of vaccinated ones. Interestingly, in a healthy unvaccinated case and three convalescents with negative IgG-RBD, we detected a positive QuantiFERON test after stimulation with Ag3. The majority of the T cell responders reacted simultaneously to the three SARS-CoV-2 specific antigens, and Ag3 demonstrated the highest rate of reactivity. At univariable analysis, the only factor that was associated with an absence of a cellular response was time from blood collection, being less than 30 days (OR:3.5, CI95% [1.15-10.50], p = 0.028). Overall, the inclusion of Ag3 improved the performance of the QuantiFERON-SARS-CoV-2 and showed a particular interest among subjects who fail to achieve a measurable antibody response after infection or vaccination.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2 , Biological Assay , Health Status , Vaccination , Antibodies, Viral
9.
Vopr Virusol ; 68(2): 105-116, 2023 05 18.
Article in Russian | MEDLINE | ID: covidwho-20238321

ABSTRACT

INTRODUCTION: The study of the mechanisms of transmission of the SARS-CoV-2 virus is the basis for building a strategy for anti-epidemic measures in the context of the COVID-19 pandemic. Understanding in what time frame a patient can spread SARS-CoV-2 is just as important as knowing the transmission mechanisms themselves. This information is necessary to develop effective measures to prevent infection by breaking the chains of transmission of the virus. The aim of the work is to identify the infectious SARS-CoV-2 virus in patient samples in the course of the disease and to determine the duration of virus shedding in patients with varying severity of COVID-19. MATERIALS AND METHODS: In patients included in the study, biomaterial (nasopharyngeal swabs) was subjected to analysis by quantitative RT-PCR and virological determination of infectivity of the virus. RESULTS: We have determined the timeframe of maintaining the infectivity of the virus in patients hospitalized with severe and moderate COVID-19. Based on the results of the study, we made an analysis of the relationship between the amount of detected SARS-CoV-2 RNA and the infectivity of the virus in vitro in patients with COVID-19. The median time of the infectious virus shedding was 8 days. In addition, a comparative analysis of different protocols for the detection of the viral RNA in relation to the identification of the infectious virus was carried out. CONCLUSION: The obtained data make it possible to assess the dynamics of SARS-CoV-2 detection and viral load in patients with COVID-19 and indicate the significance of these parameters for the subsequent spread of the virus and the organization of preventive measures.


Subject(s)
COVID-19 , Coronaviridae , Severe acute respiratory syndrome-related coronavirus , Humans , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2/genetics , RNA, Viral/genetics , Pandemics/prevention & control , Delivery of Health Care
10.
Pediatr Int ; 65(1): e15525, 2023.
Article in English | MEDLINE | ID: covidwho-20238288

ABSTRACT

BACKGROUND: The coronavirus disease 2019 outbreak has prompted some hospitals to implement screening tests upon admission since 2020. FilmArray® Respiratory 2.1 Panel (FilmArray) is a multiplex polymerase chain reaction (PCR) test with high sensitivity and specificity for detecting respiratory pathogens. We aimed to assess the clinical influence of the routine use of FilmArray for pediatric patients, including those without symptoms suggestive of an infection. METHODS: We conducted a single-center retrospective observational study, which investigated patients aged ≤15 years who underwent FilmArray on admission in 2021. We collected the patients' epidemiological information, symptoms, and FilmArray results from their electronic health records. RESULTS: A positive result was observed in 58.6% of patients admitted to the general ward or intensive care unit (ICU) but only in 1.5% of patients in the neonatal ward. Among the patients admitted to the general ward or ICU who tested positive, 93.3% had symptoms suggestive of infections, 44.6% had a sick contact before admission, and 70.5% had siblings. However, 62 (28.2%) out of 220 patients without the four (fever, respiratory, gastrointestinal, and dermal) symptoms also had positive results. Among them, 18 patients with adenovirus and three with respiratory syncytial virus were isolated to private rooms. However, 12 (57.1%) patients were discharged without symptoms suggestive of viral infection. CONCLUSION: Multiplex PCR routine use for all inpatients may lead to excessive management of positive cases because FilmArray cannot quantify microorganisms. Thus, targets for testing should be considered carefully based on patients' symptoms and histories of sick contacts.


Subject(s)
COVID-19 , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Infant, Newborn , Humans , Child , Multiplex Polymerase Chain Reaction/methods , Respiratory Tract Infections/diagnosis , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing
11.
Ter Arkh ; 94(11): 1239-1245, 2022 Dec 26.
Article in Russian | MEDLINE | ID: covidwho-20238212

ABSTRACT

BACKGROUND: Tuberculosis is a serious medical and social problem that does not lose its importance, despite all the advances in pharmacology and surgery. Diagnosis of urogenital tuberculosis (UGTB), as a rule, is delayed due to low index of suspicion to tuberculosis and the absence of pathognomonic symptoms. AIM: Determining the change in the ratio of clinical forms of renal tuberculosis from 1999 to 2020. MATERIALS AND METHODS: A retrospective cohort comparative non-interventional study on the spectrum of the incidence of extrapulmonary tuberculosis (EPTB) was carried out. Among all 13852 extrapulmonary tuberculosis patients which were diagnosed from 1999 to 2020, patients with renal tuberculosis were selected, and the spectrum of their clinical forms in three periods was analyzed: 1st period 1999-2004 (1155 patients), second period 2005-2014 (2657 patients), and the third period 2015-2020 (671 patients). The clinical features of nephrotuberculosis in 88 patients was also estimated. RESULTS: Over the 20 years of the analyzed period, the number of patients with UGTB decreased by 80.6%; for the year of the COVID-19 pandemic, this figure fell by another third. In the first period, destructive complicated forms of nephrotuberculosis prevailed (922 patients - 79.8%), while the so-called "minor forms" were diagnosed in 233 patients (20.2%). In the second period, the situation was statistically significantly more favorable: the proportion of destructive and complicated forms of renal tuberculosis decreased to 43.8% (1124 patients), "small forms" were diagnosed in 1443 patients (56.2%). In the third period, destructive and complicated forms of nephrotuberculosis were diagnosed in 531 patients (77.6%), and the proportion of "small forms" in comparison with the previous period decreased by half, to 22.4%. Analysis of the clinical features of renal tuberculosis, depending on the prevalence of the destruction, showed that an asymptomatic course is possible, and pain, dysuria, intoxication and renal colic are present with different frequencies, and the clinical picture of tuberculosis of the renal parenchyma differs significantly from the clinical picture of tuberculous papillitis, cavernous nephrotuberculosis and symptoms of renal tuberculosis as whole. CONCLUSION: Currently, there is no screening on urogenital tuberculosis at all. Patients are diagnosed by referral, with a long history, after receiving multiple courses of antibacterial treatment; mainly through the pathomorphological examination of the operating material. Thus, a sharp decrease in the proportion of UGTB patients does not mean the disappearance of tuberculosis of this localization, but only states the tragic defects in timely diagnosis and low index of suspicion of medical doctors in relation to UGTB.


Subject(s)
COVID-19 , Tuberculosis, Renal , Tuberculosis, Urogenital , Tuberculosis , Humans , Tuberculosis, Renal/diagnosis , Tuberculosis, Renal/epidemiology , Retrospective Studies , Pandemics , COVID-19/diagnosis , COVID-19/epidemiology , Tuberculosis, Urogenital/diagnosis , Tuberculosis, Urogenital/epidemiology , Tuberculosis/epidemiology
12.
Med J Malaysia ; 78(3): 279-286, 2023 05.
Article in English | MEDLINE | ID: covidwho-20237861

ABSTRACT

INTRODUCTION: Cluster-associated transmission has contributed to the majority of COVID-19 cases in Malaysia. Although widely used, the performance of the World Health Organization (WHO) case definition for suspected COVID19 in environments with high numbers of such cases has not been reported. MATERIALS AND METHODS: All suspected cases of COVID-19 that self-presented to hospitals or were cluster screened from 1st April to 31st May 2020 were included. Positive SARS-CoV-2 rRT-PCR was used as the diagnostic reference for COVID-19. RESULTS: 540 individuals with suspected COVID-19 were recruited. Two-third of patients were identified through contact screening, while the rest presented sporadically. Overall COVID-19 positivity rate was 59.4% (321/540) which was higher in the cluster screened group (85.6% vs. 11.6%, p<0.001). Overall, cluster-screened COVID-19 cases were significantly younger, had fewer comorbidities and were less likely to be symptomatic than those present sporadically. Mortality was significantly lower in the cluster-screened COVID-19 cases (0.3% vs. 4.5%, p<0.05). A third of all chest radiographs in confirmed COVID-19 cases were abnormal, with consolidation, ground-glass opacities or both predominating in the peripheral lower zones. The WHO suspected case definition for COVID-19 accurately classified 35.4% of all COVID-19 patients, a rate not improved by the addition of baseline radiographic data. Misclassification rate was higher among the cluster-associated cases (80.6%) compared to sporadic cases (35.3%). CONCLUSION: COVID-19 cases in Malaysia identified by active tracing of community cluster outbreaks had lower mortality rate. The WHO suspected COVID-19 performed poorly in this setting even when chest radiographic information was available, a finding that has implications for future spikes of the disease in countries with similar transmission characteristics.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , Malaysia/epidemiology , COVID-19 Testing , Disease Outbreaks
13.
Emerg Microbes Infect ; 12(2): 2222850, 2023 Dec.
Article in English | MEDLINE | ID: covidwho-20237574

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in wastewater. Wastewater-based epidemiology (WBE) is a practical and cost-effective tool for the assessment and controlling of pandemics and probably for examining SARS-CoV-2 presence. Implementation of WBE during the outbreaks is not without limitations. Temperature, suspended solids, pH, and disinfectants affect the stability of viruses in wastewater. Due to these limitations, instruments and techniques have been utilized to detect SARS-CoV-2. SARS-CoV-2 has been detected in sewage using various concentration methods and computer-aided analyzes. RT-qPCR, ddRT-PCR, multiplex PCR, RT-LAMP, and electrochemical immunosensors have been employed to detect low levels of viral contamination. Inactivation of SARS-CoV-2 is a crucial preventive measure against coronavirus disease 2019 (COVID-19). To better assess the role of wastewater as a transmission route, detection, and quantification methods need to be refined. In this paper, the latest improvements in quantification, detection, and inactivation of SARS-CoV-2 in wastewater are explained. Finally, limitations and future research recommendations are thoroughly described.


Subject(s)
Biosensing Techniques , COVID-19 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Wastewater , Water , Immunoassay
14.
Sensors (Basel) ; 23(10)2023 May 09.
Article in English | MEDLINE | ID: covidwho-20237544

ABSTRACT

Rapid, easy-to-use, and low-cost systems for biological sample testing are important for point-of-care diagnostics and various other health applications. The recent pandemic of Coronavirus Disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed an urgent need to rapidly and accurately identify the genetic material of SARS-CoV-2, an enveloped ribonucleic acid (RNA) virus, in upper respiratory specimens from people. In general, sensitive testing methods require genetic material extraction from the specimen. Unfortunately, current commercially available extraction kits are expensive and involve time-consuming and laborious extraction procedures. To overcome the difficulties associated with common extraction methods, we propose a simple enzymatic assay for the nucleic acid extraction step using heat mediation to improve the polymerase chain reaction (PCR) reaction sensitivity. Our protocol was tested on Human Coronavirus 229E (HCoV-229E) as an example, which comes from the large coronaviridae family of viruses that affect birds, amphibians, and mammals, of which SARS-CoV-2 is a member. The proposed assay was performed using a low-cost, custom-made, real-time PCR system that incorporates thermal cycling and fluorescence detection. It had fully customizable reaction settings to allow versatile biological sample testing for various applications, including point-of-care medical diagnosis, food and water quality testing, and emergency health situations. Our results show that heat-mediated RNA extraction is a viable extraction method when compared to commercial extraction kits. Further, our study showed that extraction has a direct impact on purified laboratory samples of HCoV-229E, but no direct impact on infected human cells. This is clinically relevant, as it allows us to circumvent the extraction step on clinical samples when using PCR.


Subject(s)
COVID-19 , Nucleic Acids , Animals , Humans , Real-Time Polymerase Chain Reaction , RNA , COVID-19/diagnosis , SARS-CoV-2/genetics , Mammals , COVID-19 Testing
15.
J Pediatric Infect Dis Soc ; 12(6): 322-331, 2023 Jun 30.
Article in English | MEDLINE | ID: covidwho-20237253

ABSTRACT

BACKGROUND: To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki disease (KD), bacterial infections, and viral infections. METHODS: Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020 and April 2021 were prospectively recruited. Whole-blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C (n = 38) to those from children with KD (n = 136), definite bacterial (DB; n = 188) and viral infections (DV; n = 138). Genes significantly differentially expressed (SDE) between MIS-C and comparator groups were identified. Feature selection was used to identify genes that optimally distinguish MIS-C from other diseases, which were subsequently translated into RT-qPCR assays and evaluated in an independent validation set comprising MIS-C (n = 37), KD (n = 19), DB (n = 56), DV (n = 43), and COVID-19 (n = 39). RESULTS: In the discovery set, 5696 genes were SDE between MIS-C and combined comparator disease groups. Five genes were identified as potential MIS-C diagnostic biomarkers (HSPBAP1, VPS37C, TGFB1, MX2, and TRBV11-2), achieving an AUC of 96.8% (95% CI: 94.6%-98.9%) in the discovery set, and were translated into RT-qPCR assays. The RT-qPCR 5-gene signature achieved an AUC of 93.2% (95% CI: 88.3%-97.7%) in the independent validation set when distinguishing MIS-C from KD, DB, and DV. CONCLUSIONS: MIS-C can be distinguished from KD, DB, and DV groups using a 5-gene blood RNA expression signature. The small number of genes in the signature and good performance in both discovery and validation sets should enable the development of a diagnostic test for MIS-C.


Subject(s)
COVID-19 , Mucocutaneous Lymph Node Syndrome , Child , Humans , COVID-19/diagnosis , COVID-19/genetics , Systemic Inflammatory Response Syndrome/diagnosis , Systemic Inflammatory Response Syndrome/genetics , Hospitals , Mucocutaneous Lymph Node Syndrome/diagnosis , Mucocutaneous Lymph Node Syndrome/genetics , COVID-19 Testing
16.
Int J Environ Res Public Health ; 20(10)2023 05 12.
Article in English | MEDLINE | ID: covidwho-20237187

ABSTRACT

INTRODUCTION: A likely mechanism of Long COVID (LC) is dysautonomia, manifesting as orthostatic intolerance (OI). In our LC service, all patients underwent a National Aeronautics and Space Administration (NASA) Lean Test (NLT), which can detect OI syndromes of Postural Tachycardia Syndrome (PoTS) or Orthostatic Hypotension (OH) in a clinic setting. Patients also completed the COVID-19 Yorkshire Rehabilitation Scale (C19-YRS), a validated LC outcome measure. Our objectives in this retrospective study were (1) to report on the findings of the NLT; and (2) to compare findings from the NLT with LC symptoms reported on the C19-YRS. METHODS: NLT data, including maximum heart rate increase, blood pressure decrease, number of minutes completed and symptoms experienced during the NLT were extracted retrospectively, together with palpitation and dizziness scores from the C19-YRS. Mann-Witney U tests were used to examine for statistical difference in palpitation or dizziness scores between patients with normal NLT and those with abnormal NLT. Spearman's rank was used to examine the correlation between the degree of postural HR and BP change with C19-YRS symptom severity score. RESULTS: Of the 100 patients with LC recruited, 38 experienced symptoms of OI during the NLT; 13 met the haemodynamic screening criteria for PoTS and 9 for OH. On the C19-YRS, 81 reported dizziness as at least a mild problem, and 68 for palpitations being at least a mild problem. There was no significant statistical difference between reported dizziness or palpitation scores in those with normal NLT and those with abnormal NLT. The correlation between symptom severity score and NLT findings was <0.16 (poor). CONCLUSIONS: We have found evidence of OI, both symptomatically and haemodynamically in patients with LC. The severity of palpitations and dizziness reported on the C19-YRS does not appear to correlate with NLT findings. We would recommend using the NLT in all LC patients in a clinic setting, regardless of presenting LC symptoms, due to this inconsistency.


Subject(s)
COVID-19 , Hypotension, Orthostatic , Orthostatic Intolerance , Postural Orthostatic Tachycardia Syndrome , Humans , Orthostatic Intolerance/diagnosis , Retrospective Studies , Post-Acute COVID-19 Syndrome , Dizziness/etiology , COVID-19/diagnosis , Postural Orthostatic Tachycardia Syndrome/diagnosis , Postural Orthostatic Tachycardia Syndrome/epidemiology , Hypotension, Orthostatic/diagnosis , Hypotension, Orthostatic/epidemiology
17.
Int J Mol Sci ; 24(11)2023 May 25.
Article in English | MEDLINE | ID: covidwho-20237163

ABSTRACT

Since the outbreak of the pandemic respiratory virus SARS-CoV-2 (COVID-19), academic communities and governments/private companies have used several detection techniques based on gold nanoparticles (AuNPs). In this emergency context, colloidal AuNPs are highly valuable easy-to-synthesize biocompatible materials that can be used for different functionalization strategies and rapid viral immunodiagnosis. In this review, the latest multidisciplinary developments in the bioconjugation of AuNPs for the detection of SARS-CoV-2 virus and its proteins in (spiked) real samples are discussed for the first time, with reference to the optimal parameters provided by three approaches: one theoretical, via computational prediction, and two experimental, using dry and wet chemistry based on single/multistep protocols. Overall, to achieve high specificity and low detection limits for the target viral biomolecules, optimal running buffers for bioreagent dilutions and nanostructure washes should be validated before conducting optical, electrochemical, and acoustic biosensing investigations. Indeed, there is plenty of room for improvement in using gold nanomaterials as stable platforms for ultrasensitive and simultaneous "in vitro" detection by the untrained public of the whole SARS-CoV-2 virus, its proteins, and specific developed IgA/IgM/IgG antibodies (Ab) in bodily fluids. Hence, the lateral flow assay (LFA) approach is a quick and judicious solution to combating the pandemic. In this context, the author classifies LFAs according to four generations to guide readers in the future development of multifunctional biosensing platforms. Undoubtedly, the LFA kit market will continue to improve, adapting researchers' multidetection platforms for smartphones with easy-to-analyze results, and establishing user-friendly tools for more effective preventive and medical treatments.


Subject(s)
COVID-19 , Metal Nanoparticles , Humans , SARS-CoV-2 , COVID-19/diagnosis , Gold , Antibodies, Viral , Immunoglobulin A , Sensitivity and Specificity , Computer Simulation , Immunoassay/methods , COVID-19 Testing
18.
Eur J Gen Pract ; 29(2): 2212904, 2023 Dec.
Article in English | MEDLINE | ID: covidwho-20236935

ABSTRACT

BACKGROUND: Access to testing during the first wave of the COVID-19 pandemic was limited, impacting patients with COVID-19-like symptoms. Current qualitative studies have been limited to one country or were conducted outside Europe. OBJECTIVES: To explore - in eight European countries - the experiences of patients consulting in primary care with COVID-19-like symptoms during the first wave of the pandemic. METHODS: Sixty-six semi-structured interviews, informed by a topic guide, were conducted by telephone or in person between April and July 2020. Patients with COVID-19-like symptoms were purposively recruited in primary care sites in eight countries and sampled based on age, gender, and symptom presentation. Deductive and inductive thematic analysis techniques were used to develop a framework representing data across settings. Data adequacy was attained by collecting rich data. RESULTS: Seven themes were identified, which described the experiences of patients consulting. Two themes are reported in this manuscript describing the role of COVID-19 testing in this experience. Patients described significant distress due to their symptoms, especially those at higher risk of complications from COVID-19, and those with severe symptoms. Patients wanted access to testing to identify the cause of their illness and minimise the burden of managing uncertainty. Some patients testing positive for COVID-19 assumed they would be immune from future infection. CONCLUSION: Patients experiencing novel and severe symptoms, particularly those with comorbidities, experienced a significant emotional and psychological burden due to concerns about COVID-19. Testing provided reassurance over health status and helped patients identify which guidance to follow. Testing positive for SARS-CoV-2 led to some patients thinking they were immune from future infection, thus influencing subsequent behaviour.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2 , Pandemics , COVID-19 Testing , Emotions
19.
PLoS One ; 18(5): e0286148, 2023.
Article in English | MEDLINE | ID: covidwho-20236835

ABSTRACT

Amidst the fourth COVID-19 wave in Viet Nam, national lockdowns necessitated the closure of numerous dental schools. To assess DDS (Doctor of Dental Surgery) graduation exams, this study analyzed their 2021 implementation in comparison to onsite exams conducted in 2020 and 2022 at the Faculty of Odonto-Stomatology, University of Medicine and Pharmacy at Ho Chi Minh City, Viet Nam (FOS-UMPH). The final online examination comprises two main sessions: a synchronous online examination using FOS-UMPH e-Learning for theories (consisting of 200 MCQs and 3 written tests with 3 clinical situations needed be solved) and a synchronous online examination using Microsoft Teams for practicum (comprising of 12 online OSCE stations). The final grades were evaluated using the same metrics in face-to-face final examinations in 2022 and 2020. A total of 114, 112 and 95 students were recruited for the first-time exams in 2020, 2021 and 2022, respectively. In order to analyze the reliability, histogram and k-mean clustering were employed. The histograms from 2020, 2021 and 2022 showed a striking similarity. However, fewer students failed in 2021 and 2022 (13% and 12.6%, respectively) compared to 2020 (28%), with clinical problem-solving part grades (belonging to theory session) being notably higher in 2021 and 2022. Intriguingly, the MCQ Score results showed the identical patterns. The courses of orthodontics, dental public health, and pediatrics subjects (in the group of prevention and development dentistry) stood out for their exceptional accuracy across both sessions. After examining data gathered over three years, we identified three distinct clusters: the first comprised of scattered average and low scores, the second characterized by high scores but unstable and scattered and the third cluster boasting consistently high and centered scores. According to our study, online and onsite traditional graduation exam results are relatively equivalent, but additional measures are necessary to standardize the final examination and adapt to the new normal trend in dental education.


Subject(s)
COVID-19 , Humans , Child , COVID-19/diagnosis , COVID-19/epidemiology , Communicable Disease Control , Reproducibility of Results , Benchmarking , Cluster Analysis
20.
J Intern Med ; 293(2): 246-258, 2023 02.
Article in English | MEDLINE | ID: covidwho-20236678

ABSTRACT

BACKGROUND: The occurrence and healthcare use trajectory of post COVID-19 condition (PCC) is poorly understood. Our aim was to investigate these aspects in SARS-CoV-2-positive individuals with and without a PCC diagnosis. METHODS: We conducted a population-based cohort study of adults in Stockholm, Sweden, with a verified infection from 1 March 2020 to 31 July 2021, stratified by the severity of the acute infection. The outcome was a PCC diagnosis registered any time 90-360 days after a positive test. We performed Cox regression models to assess baseline characteristics associated with the PCC diagnosis. Individuals diagnosed with PCC were then propensity-score matched to individuals without a diagnosis to assess healthcare use beyond the acute infection. RESULTS: Among 204,805 SARS-CoV-2-positive individuals, the proportion receiving a PCC diagnosis was 1% among individuals not hospitalized for their COVID-19 infection, 6% among hospitalized, and 32% among intensive care unit (ICU)-treated individuals. The most common new-onset symptom diagnosis codes among individuals with a PCC diagnosis were fatigue (29%) among nonhospitalized and dyspnea among both hospitalized (25%) and ICU-treated (41%) individuals. Female sex was associated with a PCC diagnosis among nonhospitalized and hospitalized individuals, with interactions between age and sex. Previous mental health disorders and asthma were associated with a PCC diagnosis among nonhospitalized and hospitalized individuals. Among individuals with a PCC diagnosis, the monthly proportion with outpatient care was substantially elevated up to 1 year after acute infection compared to before, with substantial proportions of this care attributed to PCC-related care. CONCLUSION: The differential association of age, sex, comorbidities, and healthcare use with the severity of the acute infection indicates different trajectories and phenotypes of PCC, with incomplete resolution 1 year after infection.


Subject(s)
COVID-19 , Female , Humans , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/therapy , SARS-CoV-2 , Cohort Studies , Comorbidity , Delivery of Health Care
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