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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.
Arq. ciências saúde UNIPAR ; 27(3): 1322-1333, 2023.
Article in Portuguese | WHO COVID, LILACS (Americas) | ID: covidwho-20242962

ABSTRACT

Introdução: Com a emergência do SARS-CoV-2 foi disponibilizado uma grande quantidade de ferramentas de diagnóstico. Neste contexto, a falta de vacina, de tratamento e o grande número de casos graves e morte, possibilitou a aprovação emergencial de diversos testes, que ainda necessitam de estudos populacionais para seu registro definitivo. Objetivo: Realizar uma revisão de literatura para avaliar as metodologias de diagnóstico disponíveis no Brasil, de acordo com a realidade local de saúde, explorando o momento epidemiológico a complexidade do teste e a finalidade da sua aplicação. Metodologia: Trata-se de um estudo bibliográfico, descritivo do tipo revisão de literatura. Foram utilizadas as seguintes bases de dados científicos para buscas: PUBMED, MEDLINE, LILACS E COCHRANE LIBRARY, através de descritores selecionados na plataforma DECS. Resultados: O cenário de diversos ensaios, baseados em diferentes metodologias, como os testes baseados em RNA viral, em detecção de antígenos virais ou de anticorpos, associados ao conhecimento da história natural do vírus, possibilita uma análise crítica do melhor diagnóstico de acordo com a clínica do paciente, os epidemiológicos, o objetivo do diagnóstico e a acurácia do ensaio. Atualmente, há mudança no padrão imunológico da população e a descrição de tipos e subtipos de SARS-CoV-2 com mudanças gênicas, que podem levar a mudanças na acurácia diagnóstica ou a re-emergência em surtos de doença grave. Conclusão: Ainda é incerto o caminho evolutivo da história natural da Covid-19 e os ensaios diagnósticos estão em diferentes estágios de desenvolvimento, validação e produção e cada tipo de teste tem suas próprias vantagens e desvantagens distintas inerentes a plataforma tecnológica de origem e uma combinação de tipos de testes usados em momentos diferentes pode ser útil para a condução clínica dos pacientes e no controle da pandemia por SARS-CoV-2.


Introduction: With the emergence of SARS-CoV-2, a large number of diagnostic tools were made available. In this context, the lack of vaccine, treatment and the large number of severe cases and death, allowed the emergency approval of several tests, which still require population studies for their definitive registration. Objective: To carry out a literature review to evaluate the diagnostic methodologies available in Brazil, according to the local health reality, exploring the epidemiological moment, the complexity of the test and the purpose of its application. Methodology: This is a bibliographic, descriptive study of the literature review type. The following scientific databases were used for searches: PUBMED, MEDLINE, LILACS AND COCHRANE LIBRARY, through selected descriptors on the DECS platform. Results: The scenario of several tests, based on different methodologies, such as tests based on viral RNA, on detection of viral antigens or antibodies, associated with knowledge of the natural history of the virus, allows a critical analysis of the best diagnosis according to the patient's clinical, epidemiological, diagnostic objective and assay accuracy. Currently, there is a change in the immune pattern of the population and the description of types and subtypes of SARS-CoV-2 with genetic changes, which can lead to changes in diagnostic accuracy or the re-emergence in outbreaks of severe disease. Conclusion: The evolutionary path of the natural history of Covid-19 is still uncertain and diagnostic assays are at different stages of development, validation and production and each type of test has its own distinct advantages and disadvantages inherent in the technology platform of origin and a combination of types of tests used at different times can be useful for the clinical management of patients and in the control of the SARS-CoV-2 pandemic.


Introducción: Con la aparición del SARS-CoV-2, se dispuso de un gran número de herramientas diagnósticas. En este contexto, la falta de vacuna, tratamiento y el gran número de casos graves y muerte, permitieron la aprobación de urgencia de varias pruebas, que aún requieren estudios poblacionales para su registro definitivo. Objetivo: Realizar una revisión bibliográfica para evaluar las metodologías diagnósticas disponibles en Brasil, de acuerdo con la realidad sanitaria local, explorando el momento epidemiológico, la complejidad de la prueba y la finalidad de su aplicación. Metodología: Se trata de un estudio bibliográfico, descriptivo, del tipo revisión de literatura. Para las búsquedas se utilizaron las siguientes bases de datos científicas PUBMED, MEDLINE, LILACS Y COCHRANE LIBRARY, a través de descriptores seleccionados en la plataforma DECS. Resultados: El escenario de varias pruebas, basadas en diferentes metodologías, como pruebas basadas en el ARN viral, en la detección de antígenos virales o anticuerpos, asociado al conocimiento de la historia natural del virus, permite un análisis crítico del mejor diagnóstico de acuerdo con la clínica del paciente, epidemiológica, objetivo diagnóstico y precisión de la prueba. Actualmente, hay un cambio en el patrón inmunológico de la población y la descripción de tipos y subtipos de SARS-CoV-2 con cambios genéticos, que pueden conducir a cambios en la precisión diagnóstica o la reaparición en brotes de enfermedad grave. Conclusiones: El camino evolutivo de la historia natural del Covid-19 es aún incierto y los ensayos de diagnóstico se encuentran en diferentes etapas de desarrollo, validación y producción y cada tipo de prueba tiene sus propias ventajas y desventajas distintas inherentes a la plataforma tecnológica de origen y una combinación de tipos de pruebas utilizadas en diferentes momentos puede ser útil para el manejo clínico de los pacientes y en el control de la pandemia de SARS- CoV-2.


Subject(s)
Systematic Reviews as Topic , COVID-19 Serological Testing/methods , COVID-19 Testing/methods , COVID-19 Nucleic Acid Testing/methods , Health Services Research , Antibodies/analysis , Antigens/analysis
3.
J Appl Microbiol ; 130(1): 2-13, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-2299665

ABSTRACT

AIMS: Providing a ready-to-use reverse transcriptase qPCR (RT-qPCR) method fully validated to detect the SARS-CoV-2 with a higher exclusivity than this shown by early published RT-qPCR designs. METHODS AND RESULTS: The specificity of the GPS™ CoVID-19 dtec-RT-qPCR test by analysis of sequence alignments was approached and compared with other RT-qPCR designs. The GPS™ CoVID-19 dtec-RT-qPCR test was validated following criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III, (Madrid, Spain), the Public Health England (Colindale, London, UK), and received the label CE-IVD. The GPS design showed the highest exclusivity and passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by using reference methods and showed 100% of diagnostic sensitivity and specificity. CONCLUSIONS: The CE-IVD GPS™ CoVID-19 dtec-RT-qPCR test, available worldwide with full analytical and diagnostic validation, is the more exclusive for SARS-CoV-2 by far. SIGNIFICANCE AND IMPACT OF THE STUDY: Considering the CoVID-19 pandemic status, the exclusivity of RT-qPCR tests is crucial to avoid false positives due to related coronaviruses. This work provides of a highly specific and validated RT-qPCR method for detection of SARS-CoV-2, which represents a case of efficient transfer of technology successfully used since the pandemic was declared.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , COVID-19 Nucleic Acid Testing/standards , Computer Simulation , Humans , Pandemics , Real-Time Polymerase Chain Reaction , Reproducibility of Results , SARS-CoV-2/classification , SARS-CoV-2/genetics , Sensitivity and Specificity , Sequence Alignment
4.
Science ; 375(6585): 1100-1104, 2022 Mar 11.
Article in English | MEDLINE | ID: covidwho-2285693
5.
Epidemiol Prev ; 44(5-6 Suppl 2): 193-199, 2020.
Article in English | MEDLINE | ID: covidwho-2238909

ABSTRACT

BACKGROUND: facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. Although RT-PCR is the most reliable technique to detect ongoing infections, serological tests are frequently proposed as tools in heterogeneous screening strategies. OBJECTIVES: to analyse the performance of a screening strategy proposed by the local government of Tuscany (Central Italy), which first uses qualitative rapid tests for antibody detection, and then RT-PCR tests on the positive subjects. METHODS: a simulation study is conducted to investigate the number of RT-PCR tests required by the screening strategy and the undetected ongoing infections in a pseudo-population of 500,000 subjects, under different prevalence scenarios and assuming a sensitivity of the serological test ranging from 0.50 to 0.80 (specificity 0.98). A compartmental model is used to predict the number of new infections generated by the false negatives two months after the screening, under different values of the infection reproduction number. RESULTS: assuming a sensitivity equal to 0.80 and a prevalence of 0.3%, the screening procedure would require on average 11,167 RT-PCR tests and would produce 300 false negatives, responsible after two months of a number of contagions ranging from 526 to 1,132, under the optimistic scenario of a reproduction number between 0.5 to 1. Resources and false negatives increase with the prevalence. CONCLUSIONS: the analysed screening procedure should be avoided unless the prevalence and the rate of contagion are very low. The cost and effectiveness of the screening strategies should be evaluated in the actual context of the epidemic, accounting for the fact that it may change over time.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing , COVID-19/diagnosis , Computer Simulation , Mass Screening/methods , Models, Theoretical , Pandemics , SARS-CoV-2/immunology , Basic Reproduction Number , COVID-19/epidemiology , COVID-19/transmission , COVID-19 Nucleic Acid Testing , COVID-19 Serological Testing/economics , COVID-19 Serological Testing/methods , Cost-Benefit Analysis , False Negative Reactions , False Positive Reactions , Humans , Italy/epidemiology , Mass Screening/economics , Monte Carlo Method , Point-of-Care Testing/economics , Prevalence , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
6.
Euro Surveill ; 26(13)2021 04.
Article in English | MEDLINE | ID: covidwho-2228493

ABSTRACT

Two cases of confirmed SARS-CoV-2 infection with the B.1.351 variant were reported in France in mid-January, 2020. These cases attended a gathering in Mozambique in mid-December 2020. Investigations led to the identification of five imported cases responsible for 14 transmission chains and a total 36 cases. Epidemiological characteristics seemed comparable to those described before the emergence of the South African variant B.1.351. The lack of tertiary transmission outside of the personal sphere suggests that distancing and barrier measures were effective.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , SARS-CoV-2/genetics , Travel , Adolescent , Adult , Aged , Black People , COVID-19/epidemiology , COVID-19/transmission , COVID-19 Nucleic Acid Testing , Child , Communicable Diseases, Imported , Female , France/epidemiology , Humans , Male , Middle Aged , Mozambique/ethnology , SARS-CoV-2/isolation & purification , Young Adult
7.
Diagn Interv Radiol ; 27(3): 336-343, 2021 May.
Article in English | MEDLINE | ID: covidwho-2217336

ABSTRACT

PURPOSE: This study aims to identify chest computed tomography (CT) characteristics of coronavirus disease 2019 (COVID-19), investigate the association between CT findings and laboratory or demographic findings, and compare the accuracy of chest CT with reverse transcription-polymerase chain reaction (RT-PCR). METHODS: Overall, 120 of 159 consecutive cases isolated due to suspected COVID-19 at our hospital between 17 and 25 March 2020 were included in this retrospective study. All patients underwent both chest CT and RT-PCR at first admission. The patients were divided into two groups: laboratory-confirmed COVID-19 and clinically diagnosed COVID-19. Clinical findings, laboratory findings, radiologic features and CT severity index (CT-SI) of the patients were noted. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of chest CT were calculated for the diagnosis of COVID-19, using RT-PCR as reference. RESULTS: The laboratory-confirmed and clinically diagnosed COVID-19 groups consisted of 69 (M/F 43/26, mean age 50.9±14.0 years) and 51 patients (M/F 24/27, mean age 50.9±18.8 years), respectively. Dry cough (62.3% vs. 52.9%), fever (30.4% vs. 25.5%) and dyspnea (23.2% vs. 27.5%) were the most common admission symptoms in the laboratory-confirmed and clinically diagnosed COVID-19 groups, respectively. Bilateral multilobe involvement (83.1% vs. 57.5%), peripheral distribution (96.9% vs. 97.5%), patchy shape (75.4% vs. 70.0%), ground-glass opacities (GGO) (96.9% vs. 100.0%), vascular enlargement (56.9% vs. 50.0%), intralobular reticular density (40.0% vs. 40.0%) and bronchial wall thickening (27.7% vs. 45.0%) were the most common CT findings in the laboratory-confirmed and clinically diagnosed COVID-19 subgroups, respectively. Except for the bilateral involvement and white blood cell (WBC) count, no difference was found between the clinical, laboratory, and parenchymal findings of the two groups. Positive correlation was found between CT-SI and, lactate dehydrogenase (LDH) and C-reactive protein (CRP) values in the laboratory-confirmed COVID-19 subgroup. Chest CT and RT-PCR positivity rates among patients with suspected COVID-19 were 87.5% (105/120) and 57.5% (69/120), respectively. The sensitivity, specificity, PPV, NPV and accuracy rates of chest CT were determined as 94.2% (95% confidence interval [CI], 85.8-98.4), 21.57% (95% CI, 11.3-35.3), 61.90% (95% CI, 58.2-65.5), 73.3% (95% CI, 48.2-89.1) and 63.3% (95% CI, 54.1-71.9), respectively. CONCLUSION: Chest CT has high sensitivity and low specificity in the diagnosis of COVID-19. The clinical, laboratory, and CT findings of laboratory-confirmed and clinically diagnosed COVID-19 patients are similar.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19/diagnosis , Lung/diagnostic imaging , Tomography, X-Ray Computed/methods , Adult , Aged , Aged, 80 and over , COVID-19/diagnostic imaging , Female , Humans , Laboratories , Male , Middle Aged , Patient Admission , Reproducibility of Results , Retrospective Studies , SARS-CoV-2 , Young Adult
8.
Biosensors (Basel) ; 11(2)2021 Jan 27.
Article in English | MEDLINE | ID: covidwho-2215575

ABSTRACT

Worldwide infection disease due to SARS-CoV-2 is tremendously affecting our daily lives. High-throughput detection methods for nucleic acids are emergently desired. Here, we show high-sensitivity and high-throughput metasurface fluorescence biosensors that are applicable for nucleic acid targets. The all-dielectric metasurface biosensors comprise silicon-on-insulator nanorod array and have prominent electromagnetic resonances enhancing fluorescence emission. For proof-of-concept experiment on the metasurface biosensors, we have conducted fluorescence detection of single-strand oligoDNAs, which model the partial sequences of SARS-CoV-2 RNA indicated by national infection institutes, and succeeded in the high-throughput detection at low concentrations on the order of 100 amol/mL without any amplification technique. As a direct detection method, the metasurface fluorescence biosensors exhibit high performance.


Subject(s)
Biosensing Techniques/methods , COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/genetics , High-Throughput Screening Assays/methods , Humans , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , RNA, Viral/analysis , Sensitivity and Specificity
9.
JMIR Public Health Surveill ; 7(6): e28265, 2021 06 03.
Article in English | MEDLINE | ID: covidwho-2197911

ABSTRACT

BACKGROUND: Despite the limitations in the use of cycle threshold (CT) values for individual patient care, population distributions of CT values may be useful indicators of local outbreaks. OBJECTIVE: We aimed to conduct an exploratory analysis of potential correlations between the population distribution of cycle threshold (CT) values and COVID-19 dynamics, which were operationalized as percent positivity, transmission rate (Rt), and COVID-19 hospitalization count. METHODS: In total, 148,410 specimens collected between September 15, 2020, and January 11, 2021, from the greater El Paso area were processed in the Dascena COVID-19 Laboratory. The daily median CT value, daily Rt, daily count of COVID-19 hospitalizations, daily change in percent positivity, and rolling averages of these features were plotted over time. Two-way scatterplots and linear regression were used to evaluate possible associations between daily median CT values and outbreak measures. Cross-correlation plots were used to determine whether a time delay existed between changes in daily median CT values and measures of community disease dynamics. RESULTS: Daily median CT values negatively correlated with the daily Rt values (P<.001), the daily COVID-19 hospitalization counts (with a 33-day time delay; P<.001), and the daily changes in percent positivity among testing samples (P<.001). Despite visual trends suggesting time delays in the plots for median CT values and outbreak measures, a statistically significant delay was only detected between changes in median CT values and COVID-19 hospitalization counts (P<.001). CONCLUSIONS: This study adds to the literature by analyzing samples collected from an entire geographical area and contextualizing the results with other research investigating population CT values.


Subject(s)
COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19/epidemiology , Hospitalization/statistics & numerical data , Adult , COVID-19/transmission , Female , Humans , Male , Middle Aged , Pandemics , SARS-CoV-2 , Texas , Time Factors
10.
JMIR Public Health Surveill ; 7(6): e27189, 2021 06 03.
Article in English | MEDLINE | ID: covidwho-2197904

ABSTRACT

BACKGROUND: During the COVID-19 pandemic, swab tests proved to be effective in containing the infection and served as a means for early diagnosis and contact tracing. However, little evidence exists regarding the correct timing for the execution of the swab test, especially for asymptomatic individuals and health care workers. OBJECTIVE: The objective of this study was to analyze changes in the positive findings over time in individual SARS-CoV-2 swab tests during a health surveillance program. METHODS: The study was conducted with 2071 health care workers at the University Hospital of Verona, with a known date of close contact with a patient with COVID-19, between February 29 and April 17, 2020. The health care workers underwent a health surveillance program with repeated swab tests to track their virological status. A generalized additive mixed model was used to investigate how the probability of a positive test result changes over time since the last known date of close contact, in an overall sample of individuals who tested positive for COVID-19 and in a subset of individuals with an initial negative swab test finding before being proven positive, to assess different surveillance time intervals. RESULTS: Among the 2071 health care workers in this study, 191 (9.2%) tested positive for COVID-19, and 103 (54%) were asymptomatic with no differences based on sex or age. Among 49 (25.7%) cases, the initial swab test yielded negative findings after close contact with a patient with COVID-19. Sex, age, symptoms, and the time of sampling were not different between individuals with an initial negative swab test finding and those who initially tested positive after close contact. In the overall sample, the estimated probability of testing positive was 0.74 on day 1 after close contact, which increased to 0.77 between days 5 and 8. In the 3 different scenarios for scheduled repeated testing intervals (3, 5, and 7 days) in the subgroup of individuals with an initially negative swab test finding, the probability peaked on the sixth, ninth and tenth, and 13th and 14th days, respectively. CONCLUSIONS: Swab tests can initially yield false-negative outcomes. The probability of testing positive increases from day 1, peaking between days 5 and 8 after close contact with a patient with COVID-19. Early testing, especially in this final time window, is recommended together with a health surveillance program scheduled in close intervals.


Subject(s)
COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19/diagnosis , Health Personnel/statistics & numerical data , Adult , COVID-19/epidemiology , COVID-19/transmission , Contact Tracing/methods , False Negative Reactions , Female , Humans , Infectious Disease Transmission, Patient-to-Professional/statistics & numerical data , Italy/epidemiology , Male , Middle Aged , Pandemics , SARS-CoV-2 , Time Factors
11.
Medicine (Baltimore) ; 100(21): e26143, 2021 May 28.
Article in English | MEDLINE | ID: covidwho-2191018

ABSTRACT

INTRODUCTION: Coronavirus disease 2019 (COVID-19) is a rapidly emerging infectious respiratory disease caused by severe acute respiratory syndrome coronavirus 2. Currently, more than 100 million cases of COVID-19 have been confirmed worldwide, with over 2.4 million mortalities. The pandemic affects people of all ages but older individuals and those with severe chronic illnesses, including cancer patients, are at higher risk. PATIENT CONCERNS: The impact of cancer treatment on the progression of COVID-19 is unclear. Therefore, we assessed the effects of chemotherapy on COVID-19 outcomes for 2 cancer patients. On January 24, 2020, a level I response to a major public health emergency was initiated in Hubei Province, China, which includes Enshi Autonomous Prefecture that has a population of 4.026 million people. As of April 30, 2020, 252 confirmed cases of COVID-19 and 11 asymptomatic carriers were identified in Enshi. DIAGNOSIS: Among the confirmed cases and asymptomatic carriers, 2 patients were identified who were previously diagnosed with malignant tumors, including one with hepatocellular carcinoma and the other with cardia carcinoma. INTERVENTIONS: These 2 patients were receiving or just completed chemotherapy at the time of their COVID-19 diagnosis. OUTCOMES: Both patients were followed and presented favorable outcomes. The positive outcomes for these 2 patients could be partially explained by their recent chemotherapy that impacted their immune status. Also, their relatively younger ages and lack of comorbidities were likely factors in their successful recovery from COVID-19. CONCLUSIONS: Anticancer treatment might enhance a patient's ability to respond favorably to COVID-19 infection. However, anticancer treatment is likely to impact immune function differently in different individuals, which can influence disease outcomes.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , COVID-19/immunology , Liver Neoplasms/drug therapy , SARS-CoV-2/immunology , Stomach Neoplasms/drug therapy , Adult , COVID-19/complications , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing , Cyclobutanes/therapeutic use , Docetaxel/therapeutic use , Drug Therapy, Combination/methods , Humans , Liver Neoplasms/complications , Liver Neoplasms/immunology , Lung/diagnostic imaging , Male , Middle Aged , Organoplatinum Compounds/therapeutic use , RNA, Viral/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sorafenib/therapeutic use , Stomach Neoplasms/complications , Stomach Neoplasms/immunology , Tomography, X-Ray Computed , Treatment Outcome , COVID-19 Drug Treatment
12.
Medicine (Baltimore) ; 100(21): e26034, 2021 May 28.
Article in English | MEDLINE | ID: covidwho-2191014

ABSTRACT

ABSTRACT: To determine the role of ultra-low dose chest computed tomography (uld CT) compared to chest radiographs in patients with laboratory-confirmed early stage SARS-CoV-2 pneumonia.Chest radiographs and uld CT of 12 consecutive suspected SARS-CoV-2 patients performed up to 48 hours from hospital admission were reviewed by 2 radiologists. Dosimetry and descriptive statistics of both modalities were analyzed.On uld CT, parenchymal abnormalities compatible with SARS-CoV-2 pneumonia were detected in 10/12 (83%) patients whereas on chest X-ray in, respectively, 8/12 (66%) and 5/12 (41%) patients for reader 1 and 2. The average increment of diagnostic performance of uld CT compared to chest X-ray was 29%. The average effective dose was, respectively, of 0.219 and 0.073 mSv.Uld CT detects substantially more lung injuries in symptomatic patients with suspected early stage SARS-CoV-2 pneumonia compared to chest radiographs, with a significantly better inter-reader agreement, at the cost of a slightly higher equivalent radiation dose.


Subject(s)
COVID-19/diagnosis , Lung/diagnostic imaging , Radiography, Thoracic/statistics & numerical data , SARS-CoV-2/isolation & purification , Tomography, X-Ray Computed/statistics & numerical data , Adult , Aged , Aged, 80 and over , COVID-19/virology , COVID-19 Nucleic Acid Testing , Female , Humans , Male , Middle Aged , Observer Variation , Predictive Value of Tests , RNA, Viral/isolation & purification , Radiation Dosage , Radiography, Thoracic/adverse effects , Radiography, Thoracic/methods , Radiometry/statistics & numerical data , Retrospective Studies , SARS-CoV-2/genetics , Tomography, X-Ray Computed/adverse effects , Tomography, X-Ray Computed/methods
13.
Medicine (Baltimore) ; 100(21): e25645, 2021 May 28.
Article in English | MEDLINE | ID: covidwho-2190994

ABSTRACT

ABSTRACT: Since December 2019, pneumonia caused by a novel coronavirus (SARS-CoV-2), namely 2019 novel coronavirus disease (COVID-19), has rapidly spread from Wuhan city to other cities across China. The present study was designed to describe the epidemiology, clinical characteristics, treatment, and prognosis of 74 hospitalized patients with COVID-19.Clinical data of 74 COVID-19 patients were collected to analyze the epidemiological, demographic, laboratory, radiological, and treatment data. Thirty-two patients were followed up and tested for the presence of the viral nucleic acid and by pulmonary computed tomography (CT) scan at 7 and 14 days after they were discharged.Among all COVID-19 patients, the median incubation period for patients and the median period from symptom onset to admission was all 6 days; the median length of hospitalization was 13 days. Fever symptoms were presented in 83.78% of the patients, and the second most common symptom was cough (74.32%), followed by fatigue and expectoration (27.03%). Inflammatory indicators, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) of the intensive care unit (ICU) patients were significantly higher than that of the non-ICU patients (P < .05). However, 50.00% of the ICU patients had their the ratio of T helper cells to cytotoxic T cells (CD4/CD8) ratio lower than 1.1, whose proportion is much higher than that in non-ICU patients (P < .01).Compared with patients in Wuhan, COVID-19 patients in Anhui Province seemed to have milder symptoms of infection, suggesting that there may be some regional differences in the transmission of SARS-CoV-2 between different cities.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19/diagnosis , Cough/epidemiology , Fever/epidemiology , Hyperbaric Oxygenation/statistics & numerical data , Adolescent , Adult , Aged , Antibiotic Prophylaxis/statistics & numerical data , Blood Sedimentation , C-Reactive Protein/analysis , COVID-19/complications , COVID-19/epidemiology , COVID-19/therapy , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , China/epidemiology , Cities/epidemiology , Cough/blood , Cough/therapy , Cough/virology , Female , Fever/blood , Fever/therapy , Fever/virology , Follow-Up Studies , Geography , Humans , Length of Stay/statistics & numerical data , Lung/diagnostic imaging , Male , Middle Aged , RNA, Viral/isolation & purification , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Severity of Illness Index , Tomography, X-Ray Computed , Young Adult
14.
Viruses ; 15(2)2023 01 22.
Article in English | MEDLINE | ID: covidwho-2200906

ABSTRACT

(1) Background: Rapid and accurate negative discrimination enables efficient management of scarce isolated bed resources and adequate patient accommodation in the majority of areas experiencing an explosion of confirmed cases due to Omicron mutations. Until now, methods for artificial intelligence or deep learning to replace time-consuming RT-PCR have relied on CXR, chest CT, blood test results, or clinical information. (2) Methods: We proposed and compared five different types of deep learning algorithms (RNN, LSTM, Bi-LSTM, GRU, and transformer) for reducing the time required for RT-PCR diagnosis by learning the change in fluorescence value derived over time during the RT-PCR process. (3) Results: Among the five deep learning algorithms capable of training time series data, Bi-LSTM and GRU were shown to be able to decrease the time required for RT-PCR diagnosis by half or by 25% without significantly impairing the diagnostic performance of the COVID-19 RT-PCR test. (4) Conclusions: The diagnostic performance of the model developed in this study when 40 cycles of RT-PCR are used for diagnosis shows the possibility of nearly halving the time required for RT-PCR diagnosis.


Subject(s)
COVID-19 , Deep Learning , Humans , Artificial Intelligence , COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Algorithms , COVID-19 Testing
15.
Sci Rep ; 12(1): 17221, 2022 Oct 14.
Article in English | MEDLINE | ID: covidwho-2077104

ABSTRACT

For SARS-CoV-2, R0 calculations in the range of 2-3 dominate the literature, but much higher estimates have also been published. Because capacity for RT-PCR testing increased greatly in the early phase of the Covid-19 pandemic, R0 determinations based on these incidence values are subject to strong bias. We propose to use Covid-19-induced excess mortality to determine R0 regardless of RT-PCR testing capacity. We used data from the Robert Koch Institute (RKI) on the incidence of Covid cases, Covid-related deaths, number of RT-PCR tests performed, and excess mortality calculated from data from the Federal Statistical Office in Germany. We determined R0 using exponential growth estimates with a serial interval of 4.7 days. We used only datasets that were not yet under the influence of policy measures (e.g., lockdowns or school closures). The uncorrected R0 value for the spread of SARS-CoV-2 based on RT-PCR incidence data was 2.56 (95% CI 2.52-2.60) for Covid-19 cases and 2.03 (95% CI 1.96-2.10) for Covid-19-related deaths. However, because the number of RT-PCR tests increased by a growth factor of 1.381 during the same period, these R0 values must be corrected accordingly (R0corrected = R0uncorrected/1.381), yielding 1.86 for Covid-19 cases and 1.47 for Covid-19 deaths. The R0 value based on excess deaths was calculated to be 1.34 (95% CI 1.32-1.37). A sine-function-based adjustment for seasonal effects of 40% corresponds to a maximum value of R0January = 1.68 and a minimum value of R0July = 1.01. Our calculations show an R0 that is much lower than previously thought. This relatively low range of R0 fits very well with the observed seasonal pattern of infection across Europe in 2020 and 2021, including the emergence of more contagious escape variants such as delta or omicron. In general, our study shows that excess mortality can be used as a reliable surrogate to determine the R0 in pandemic situations.


Subject(s)
Basic Reproduction Number , COVID-19 , COVID-19/epidemiology , COVID-19/mortality , COVID-19 Nucleic Acid Testing , Germany/epidemiology , Humans , Pandemics , Reproducibility of Results , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
16.
Cornea ; 40(11): 1502-1504, 2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-2063050

ABSTRACT

ABSTRACT: The coronavirus disease 2019 global pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several ophthalmic manifestations have been reported to be associated with SARS-CoV-2 infection, including conjunctivitis, acute sixth nerve palsy, and multiple cranial neuropathies. We present a unique case of unilateral phlyctenular keratoconjunctivitis in a 5-year-old boy in the setting of SARS-CoV-2 infection.


Subject(s)
COVID-19/diagnosis , Conjunctivitis, Viral/diagnosis , Eye Infections, Viral/diagnosis , Keratoconjunctivitis/diagnosis , SARS-CoV-2/pathogenicity , Administration, Oral , Anti-Bacterial Agents/administration & dosage , Ascorbic Acid/administration & dosage , Azithromycin/administration & dosage , COVID-19/virology , COVID-19 Nucleic Acid Testing , Child, Preschool , Conjunctivitis, Viral/drug therapy , Conjunctivitis, Viral/virology , Drug Therapy, Combination , Eye Infections, Viral/drug therapy , Eye Infections, Viral/virology , Fluorometholone/therapeutic use , Glucocorticoids/therapeutic use , Humans , Keratoconjunctivitis/drug therapy , Keratoconjunctivitis/virology , Male , Ophthalmic Solutions , Slit Lamp Microscopy , Tomography, Optical Coherence , Visual Acuity/physiology , COVID-19 Drug Treatment
17.
Medicina (Ribeirao Preto, Online) ; 55(2)abr. 2022. ilus, tab
Article in English | WHO COVID, LILACS (Americas) | ID: covidwho-1979695

ABSTRACT

The severity of SARS-CoV2 infection, Covid19 disease, should account for the diversity of human individual immu-noinflammatory responses. Serum immunological markers during Covid19 illness may lead to individualized thera-peutics with better outcomes. Efficient treatment for Covid19 may require: 1) early disease detection, 2) combined drug therapy for 3) targeting the virus replication cycle, and 4) individualized drug treatment for specific immu-noinflammatory human profile responses administered in a 5) timely manner. Covid19 is unlikely to be the last emergent human disease with fast pandemic potential. Gathering knowledge on the individual human host profiles of immunoinflammatory responses is an opportunity that could lead us to understand individual differences in re-sponse to infection at the individual and population level, paving the way to faster, more efficient strategies to tack-le upcoming infectious diseases. This is a position paper based on an integrative non-exhaustive literature revision (AU)


A diversidade das respostas imunoinflamatórias individuais humanas muito provavelmente tem papel na gravidade da doença Covid19 causada pela infecção pelo vírus SARS-CoV2. Marcadores imunológicos séricos durante a Covid19 po-dem guiar a escolha de terapias individualizadas com melhores resultados. O tratamento eficiente para Covid19 pode exigir: 1) detecção precoce da doença, 2) terapia medicamentosa combinada com alvo ao 3) ciclo de replicação do ví-rus e 4) terapia anti-inflamatória individualizada para perfis de respostas imunoinflamatórias humanas, administradas em tempo hábil. É improvável que a Covid19 seja a última doença humana emergente com potencial de alastramento veloz pandêmico. Reunir conhecimento sobre perfis de respostas imunoinflamatórias individuais dos hospedeiros humanos é uma oportunidade ímpar que pode nos levar a entender as diferenças dessas respostas entre indivíduos, abrindo caminho para estratégias terapêuticas mais rápidas e eficientes no combate à futuras epidemias (AU)


Subject(s)
Treatment Outcome , Essay , Severe Acute Respiratory Syndrome , Cytokine Release Syndrome , COVID-19 Nucleic Acid Testing , COVID-19/therapy , Immunity
18.
Diagn Microbiol Infect Dis ; 104(3): 115763, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-1914300

ABSTRACT

BACKGROUND: The gold standard for COVID-19 diagnosis-reverse-transcriptase polymerase chain reaction (RT-PCR)- is expensive and often slow to yield results whereas lateral flow tests can lack sensitivity. METHODS: We tested a rapid, lateral flow antigen (LFA) assay with artificial intelligence read (LFAIR) in subjects from COVID-19 treatment trials (N = 37; daily tests for 5 days) and from a population-based study (N = 88; single test). LFAIR was compared to RT-PCR from same-day samples. RESULTS: Using each participant's first sample, LFAIR showed 86.2% sensitivity (95% CI 73.6%-98.8) and 94.3% specificity (88.8%-99.7%) compared to RT-PCR. Adjusting for days since symptom onset and repeat testing, sensitivity was 97.8% (89.9%-99.5%) on the first symptomatic day and decreased with each additional day. Sensitivity improved with artificial intelligence (AI) read (86.2%) compared to the human eye (71.4%). CONCLUSION: LFAIR showed improved accuracy compared to LFA alone. particularly early in infection.


Subject(s)
Antigens, Viral , Artificial Intelligence , COVID-19 Serological Testing , COVID-19 , SARS-CoV-2 , Antigens, Viral/analysis , Antigens, Viral/immunology , COVID-19/diagnosis , COVID-19/immunology , COVID-19/virology , COVID-19 Nucleic Acid Testing , COVID-19 Serological Testing/methods , COVID-19 Serological Testing/standards , Clinical Trials as Topic , Humans , Reproducibility of Results , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Time Factors
19.
Diagn Microbiol Infect Dis ; 103(3): 115700, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1899670

ABSTRACT

We evaluated the performance of the QIAprep& Viral RNA UM Kit (Qiagen) for SARS-CoV-2 detection. It displayed specificity and sensitivity required for SARS-CoV-2 RNA detection from swab transport media without RNA extraction. This method identifies accurately patients at risk of transmission while saving time and cost of extraction.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing , Humans , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
20.
Science ; 376(6600): eabq4411, 2022 06 24.
Article in English | MEDLINE | ID: covidwho-1861571

ABSTRACT

Rapid transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has led to record-breaking incidence rates around the world. The Real-time Assessment of Community Transmission-1 (REACT-1) study has tracked SARS-CoV-2 infection in England using reverse transcription polymerase chain reaction (RT-PCR) results from self-administered throat and nose swabs from randomly selected participants aged 5 years and older approximately monthly from May 2020 to March 2022. Weighted prevalence in March 2022 was the highest recorded in REACT-1 at 6.37% (N = 109,181), with the Omicron BA.2 variant largely replacing the BA.1 variant. Prevalence was increasing overall, with the greatest increase in those aged 65 to 74 years and 75 years and older. This was associated with increased hospitalizations and deaths, but at much lower levels than in previous waves against a backdrop of high levels of vaccination.


Subject(s)
COVID-19 , Epidemics , SARS-CoV-2 , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/virology , COVID-19 Nucleic Acid Testing , England/epidemiology , Humans , Incidence , Prevalence , RNA, Viral/analysis , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
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