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1.
Acta Inform Med ; 29(1): 45-50, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1811118

ABSTRACT

BACKGROUND: Since December 2019. millions of people in the world have been affected with the novel Coronavirus disease-2019 (COVID-19) pandemic, and high economic impact has affect many countries especially low socioeconomic one like Iraq due to the high cost and limited availability of RT-PCR for diagnosis of COVID-19, so there should be predictive low cost easily available laboratory tests that can be used before proceeding to the high cost techniques. OBJECTIVE: In this retrospective study we aimed to evaluate the diagnostic accuracy of CRP, ferritin, LDH and D-dimer in predicting positive cases of COVID-19 in Iraq. METHODS: It is a retrospective observational cohort study based on STARD guidelines to determine the diagnostic accuracy of (CRP, LDH, ferritin and D dimer) for COVID-19 of electronic medical records of private medical center in Najaf city, at which 566 individuals were recruited. The investigated subjects were either in close contact with previously COVID-19 positive patients or have one or more symptoms of COVID-19. They were categorized into 2 groups, 205 subjects diagnosed with RT-PCR as COVID-19 negative, and 361 COVID-19 positive patients, results of study variables of the cohort were recruited from the medical records. RESULTS: Combining of these parameters had the following findings: CRP + ferritin; AUC: 0.77 with 55% sensitivity and 97% specificity, Ferritin + LDH; AUC: 0.83 with 65% sensitivity and 92% specificity, CRP+LDH; AUC: 0.78 with 56% sensitivity and 98% specificity, CRP + LDH + ferritin; AUC: 0.85, with 73% sensitivity and 88% specificity, CRP + LDH + ferritin + D dimer; AUC: 0.85 75% sensitivity and 87% specificity. CONCLUSION: Combination of routine laboratory biomarkers (CRP, LDH and ferritin ±D dimer) can be used to predict the diagnosis of COVID-19 with an accepted sensitivity and specificity before proceeding to definitive diagnosis by RT-PCR.

2.
Clin J Am Soc Nephrol ; 16(11): 1755-1765, 2021 11.
Article in English | MEDLINE | ID: covidwho-1526737

ABSTRACT

Despite evidence of multiorgan tropism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with coronavirus disease 2019 (COVID-19), direct viral kidney invasion has been difficult to demonstrate. The question of whether SARS-CoV2 can directly infect the kidney is relevant to the understanding of pathogenesis of AKI and collapsing glomerulopathy in patients with COVID-19. Methodologies to document SARS-CoV-2 infection that have been used include immunohistochemistry, immunofluorescence, RT-PCR, in situ hybridization, and electron microscopy. In our review of studies to date, we found that SARS-CoV-2 in the kidneys of patients with COVID-19 was detected in 18 of 94 (19%) by immunohistochemistry, 71 of 144 (49%) by RT-PCR, and 11 of 84 (13%) by in situ hybridization. In a smaller number of patients with COVID-19 examined by immunofluorescence, SARS-CoV-2 was detected in 10 of 13 (77%). In total, in kidneys from 102 of 235 patients (43%), the presence of SARS-CoV-2 was suggested by at least one of the methods used. Despite these positive findings, caution is needed because many other studies have been negative for SARS-CoV-2 and it should be noted that when detected, it was only in kidneys obtained at autopsy. There is a clear need for studies from kidney biopsies, including those performed at early stages of the COVID-19-associated kidney disease. Development of tests to detect kidney viral infection in urine samples would be more practical as a noninvasive way to evaluate SARS-CoV-2 infection during the evolution of COVID-19-associated kidney disease.


Subject(s)
COVID-19/virology , Kidney Diseases/virology , Kidney/virology , SARS-CoV-2/pathogenicity , Animals , Biopsy , COVID-19/complications , COVID-19/diagnosis , COVID-19/mortality , COVID-19 Testing , Host-Pathogen Interactions , Humans , Kidney Diseases/diagnosis , Kidney Diseases/mortality , Predictive Value of Tests , Prognosis , Risk Assessment , Risk Factors
3.
J Endocrinol Invest ; 44(12): 2675-2684, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1504521

ABSTRACT

PURPOSE: Due to relevant repercussions on reproductive medicine, we aimed to evaluate feasibility of RT-PCR as a detection method of SARS-CoV-2 RNA in seminal fluid. METHODS: A qualitative determination of the RT-PCR assays in semen was performed through different approaches: (1) efficiency of RNA extraction from sperm and seminal plasma was determined using PRM1 and PRM2 mRNA and a heterologous system as control; (2) samples obtained by diluting viral preparation from a SARS-CoV-2 panel (virus cultured in Vero E6 cell lines) were tested; (3) viral presence in different fractions of seminal fluid (whole sample, seminal plasma and post-centrifugation pellet) was evaluated. Semen samples from mild and recovered COVID-19 subjects were collected by patients referring to the Infectious Disease Department of the Policlinico Umberto I Hospital - "Sapienza" University of Rome. Control subjects were recruited at the Laboratory of Seminology-Sperm Bank "Loredana Gandini'' of the same hospital. RESULTS: The control panel using viral preparations diluted in saline and seminal fluid showed the capability to detect viral RNA presence with Ct values depending on the initial viral concentration. All tested semen samples were negative for SARS-CoV-2, regardless of the nasopharyngeal swab result or seminal fluid fraction. CONCLUSION: These preliminary data show that RT-PCR for SARS-CoV-2 RNA testing appears to be a feasible method for the molecular diagnosis of SARS-CoV-2 in seminal fluid, supported by results of the control panel. The ability to detect SARS-CoV-2 in semen is extremely important for reproductive medicine, especially in assisted reproductive technology and sperm cryopreservation.


Subject(s)
COVID-19/diagnosis , Pathology, Molecular/methods , Semen/virology , Adult , Animals , Chlorocebus aethiops , Feasibility Studies , Humans , Male , RNA, Messenger/chemistry , RNA, Viral/chemistry , Real-Time Polymerase Chain Reaction , Reproductive Techniques , Vero Cells
4.
Rev Esp Quimioter ; 33(6): 444-447, 2020 Dec.
Article in Spanish | MEDLINE | ID: covidwho-1390020

ABSTRACT

OBJECTIVE: Co-circulation of the two Influenza B lineages hinders forecast of strain to include in trivalent vaccine. Autonomous Communities such as Cantabria continue without supplying tetravalent vaccine. The aim of this study was to analyse epidemiological characteristics of influenza type B in Cantabria (2019-2020 season) as well as to establish the predominant lineage and its relation to the recommended vaccine. METHODS: Retrospective study whereby flu diagnosis and lineage analysis were determined by RT-PCR. RESULTS: All samples belonged to the Victoria lineage. Most prevalent viral co-infection was due to SARS-CoV-2. The population affected by influenza B was mainly paediatric and non-vaccinated patients more frequently required hospital admittance. CONCLUSIONS: Influenza type B has a higher incidence in the paediatric population and type A affects more the adult population. Only 28.8% of patients with Influenza B that presented with some underlying condition or risk factor were vaccinated. This shows the need to increase coverage with tetravalent vaccines in order to reduce the burden of disease associated with the Influenza B virus.


Subject(s)
COVID-19/epidemiology , Influenza B virus , Influenza, Human/epidemiology , Pandemics , SARS-CoV-2 , Adult , COVID-19/virology , Chi-Square Distribution , Child , Coinfection/epidemiology , Coinfection/virology , Epidemics , Female , Hospitalization/statistics & numerical data , Humans , Influenza Vaccines/administration & dosage , Influenza, Human/prevention & control , Influenza, Human/virology , Male , Retrospective Studies , Seasons , Spain/epidemiology , Statistics, Nonparametric
5.
J AOAC Int ; 104(4): 872-888, 2021 Aug 20.
Article in English | MEDLINE | ID: covidwho-1387921

ABSTRACT

BACKGROUND: The Eurofins GeneScan Technologies' VIRSeek SARS-CoV-2 Mplex kit is a RT (reverse transcription) real-time polymerase chain reaction (RT-qPCR) assay for the detection of two targets on the N-gene (nucleocapsid) of SARS-CoV-2. An extraction control, that allows monitoring of the extraction procedure and PCR inhibition, is included. OBJECTIVE: In silico analysis and wet testing showed inclusivity and exclusivity of the assay. The complete workflow starting from surface swabbing (VIRSeek PATHOSwab kit), RNA extraction (VIRSeek RNAExtractor), RT-PCR (VIRSeek SARS-CoV-2 Mplex), and evaluation with FastFinder was validated in comparison to the CDC method for detection of SARS-CoV-2 on stainless steel. METHOD: In silico analysis was performed by using the MFOLD online program. The matrix study was performed for stainless steel inoculated with SARS-CoV-2 isolated from the first documented US case of a traveler from Wuhan, China. RESULTS: For inclusivity, 15 764 sequences were analyzed and all mismatches (0.37% of the sequences had single mismatches) were considered non-critical. Cross reactivity for closely related viruses and background organisms was performed, resulting in correct exclusion of all. No significant differences were observed for the probability of detection (POD) study when comparing to the CDC method. CONCLUSIONS: Results of the inclusivity and exclusivity study show that the assay is specific for detection of SARS-CoV-2. The POD study showed no statistically significant difference compared to the CDC reference method, results were identical for the uninoculated and the high level. For the fractional recovery level, the candidate method detected 9/17 samples leading to a POD of 0.47, the reference method detected 11/20 samples leading to a POD of 0.55. HIGHLIGHT: The complete workflow starting from swabbing of the surface (VIRSeek PATHOSwab kit), RNA extraction (VIRSeek RNAExtractor), RT-PCR (VIRSeek SARS CoV-2 Mplex) and evaluation with FastFinder was validated in comparison to the US Centers for Disease Control and Prevention method for detection of SARS-CoV-2 on Stainless Steel.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Stainless Steel
6.
J Med Virol ; 93(9): 5538-5543, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1363694

ABSTRACT

In the current coronavirus disease 2019 (COVID-19) pandemic there is a mass screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) happening around the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite the identification of cases and to facilitate early isolation and control spread. Hence this study evaluates six different rapid nucleic acid detection assays that are commercially available for SARS-CoV-2 virus detection. Nasopharyngeal samples were collected from 4981 participants and were tested for the SARS-CoV-2 virus by the gold standard real-time reverse-transcription polymerase chain reaction (RT-PCR) method and with one of these six rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT-qPCR results for SARS-COV-2 detection. AQ-TOP had the highest sensitivity (98%) and a strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT-PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ-TOP with 6% and POCKIT with 3.7% of invalid reports. Genechecker system, Abbott ID NOW, and Cobas Liat were found to have the best performance and agreement when compared with the standard RT-PCR for COVID-19 detection. With further research, these rapid tests have the potential to be employed in large-scale screening of COVID-19.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , COVID-19 Nucleic Acid Testing/instrumentation , COVID-19 Nucleic Acid Testing/standards , Humans , Nasopharynx/virology , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity , United Arab Emirates
7.
J Glaucoma ; 30(8): 711-717, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-1358502

ABSTRACT

PRECIS: Vascular diseases have been linked to alterations in optic nerve head perfusion. PURPOSE: The main objective was to investigate the changes in peripapillary vessel density (VD) in post coronavirus disease (COVID-19) patients. METHODS: In this prospective pilot exploratory study, patients with COVID-19 that were attended in the Emergency Department of Hospital Clinico San Carlos (Madrid) were included. All patients underwent optic nerve head optical coherence tomography angiography using the Cirrus HD-OCT 500 with AngioPlex OCTA (Zeiss, Dublin, CA) 4 and 12 weeks after diagnosis by positive reverse transcriptase-polymerase chain reaction test from nasopharyngeal swab at the Emergency Department. Sociodemographic data, medical history, disease severity, and laboratory work-up were collected. RESULTS: One hundred and eighty eyes of 90 patients with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection were included. None of the patients reported visual changes. Severe patients were older, more frequently hispanic, dyslipidemic, and presented lower lymphocytes counts, as well as increased ferritin, D-dimer, fibrinogen, and international normalized ratio levels. No changes in optic nerve head vascularization were observed when both visits were compared. No correlation was found between VD and clinical parameters, disease severity and laboratory work-up. CONCLUSIONS: Changes to peripapillary VD were not observed in patients with COVID-19 in the early months following diagnosis.


Subject(s)
COVID-19 , Optic Disk , Fluorescein Angiography , Humans , Intraocular Pressure , Prospective Studies , Retinal Vessels , SARS-CoV-2 , Tomography, Optical Coherence
8.
Clin Infect Dis ; 73(3): 545-548, 2021 08 02.
Article in English | MEDLINE | ID: covidwho-1338666

ABSTRACT

We characterized serology following a nursing home outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) where residents were serially tested by reverse-transcription polymerase chain reaction (RT-PCR) and positive residents were cohorted. When tested 46-76 days later, 24 of 26 RT-PCR-positive residents were seropositive; none of the 124 RT-PCR-negative residents had confirmed seropositivity, supporting serial SARS-CoV-2 RT-PCR testing and cohorting in nursing homes.


Subject(s)
COVID-19 , SARS-CoV-2 , Disease Outbreaks , Humans , Polymerase Chain Reaction , Skilled Nursing Facilities
9.
Ultrasound Med Biol ; 47(8): 1997-2005, 2021 08.
Article in English | MEDLINE | ID: covidwho-1286382

ABSTRACT

The goal of this review was to systematize the evidence on pulmonary ultrasound (PU) use in diagnosis, monitorization or hospital discharge criteria for patients with coronavirus disease 2019 (COVID-19). Evidence on the use of PU for diagnosis and monitorization of or as hospital discharge criteria for COVID-19 patients confirmed to have COVID-19 by reverse transcription polymerase chain reaction (RT-PCR) between December 1, 2019 and July 5, 2020 was compared with evidence obtained with thoracic radiography (TR), chest computed tomography (CT) and RT-PCR. The type of study, motives for use of PU, population, type of transducer and protocol, results of PU and quantitative or qualitative correlation with TR and/or chest CT and/or RT-PCR were evaluated. A total of 28 articles comprising 418 patients were involved. The average age was 50 y (standard deviation: 25.1 y), and there were 395 adults and 23 children. One hundred forty-three were women, 13 of whom were pregnant. The most frequent result was diffuse, coalescent and confluent B-lines. The plural line was irregular, interrupted or thickened. The presence of subpleural consolidation was noduliform, lobar or multilobar. There was good qualitative correlation between TR and chest CT and a quantitative correlation with chest CT of r = 0.65 (p < 0.001). Forty-four patients were evaluated only with PU. PU is a useful tool for diagnosis and monitorization and as criteria for hospital discharge for patients with COVID-19.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Lung/diagnostic imaging , Ultrasonography/methods , Humans , SARS-CoV-2
10.
Clin Chem Lab Med ; 59(7): 1315-1322, 2021 Jun 25.
Article in English | MEDLINE | ID: covidwho-1278216

ABSTRACT

OBJECTIVES: Severe forms of coronavirus disease 2019 (COVID-19) are characterized by an excessive production of inflammatory cytokines. Activated monocytes secrete high levels of cytokines. Human monocytes are divided into three major populations: conventional (CD14posCD16neg), non-classical (CD14dimCD16pos), and intermediate (CD14posCD16pos) monocytes. The aim of this study was to analyze whether the distribution of conventional (CD16neg) and CD16pos monocytes is different in patients with COVID-19 and whether the variations could be predictive of the outcome of the disease. METHODS: We performed a prospective study on 390 consecutive patients referred to the Emergency Unit, with a proven diagnosis of SARS-CoV 2 infection by RT-PCR. Using the CytoDiff™ reagent, an automated routine leukocyte differential, we quantified CD16neg and CD16pos monocytes. RESULTS: In the entire population, median CD16neg and CD16pos monocyte levels (0.398 and 0.054×109/L, respectively) were in the normal range [(0.3-0.7×109/L) and (0.015-0.065×109/L), respectively], but the 35 patients in the intensive care unit (ICU) had a significantly (p<0.001) lower CD16pos monocyte count (0.018 × 109/L) in comparison to the 70 patients who were discharged (0.064 × 109/L) or were hospitalized in conventional units (0.058 × 109/L). By ROC curve analysis, the ratio [absolute neutrophil count/CD16pos monocyte count] was highly discriminant to identify patients requiring ICU hospitalization: with a cut-off 193.1, the sensitivity and the specificity were 74.3 and 81.8%, respectively (area under the curve=0.817). CONCLUSIONS: Quantification of CD16pos monocytes and the ratio [absolute neutrophil count/CD16pos monocyte count] could constitute a marker of the severity of disease in COVID-19 patients.


Subject(s)
COVID-19/diagnosis , Monocytes/cytology , Adult , Aged , Aged, 80 and over , Area Under Curve , Biomarkers/blood , COVID-19/blood , Female , Humans , Intensive Care Units/statistics & numerical data , Leukocyte Count/statistics & numerical data , Male , Middle Aged , Monocytes/classification , Prognosis , Prospective Studies , ROC Curve , SARS-CoV-2 , Young Adult
11.
Clin J Am Soc Nephrol ; 16(11): 1755-1765, 2021 11.
Article in English | MEDLINE | ID: covidwho-1269953

ABSTRACT

Despite evidence of multiorgan tropism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with coronavirus disease 2019 (COVID-19), direct viral kidney invasion has been difficult to demonstrate. The question of whether SARS-CoV2 can directly infect the kidney is relevant to the understanding of pathogenesis of AKI and collapsing glomerulopathy in patients with COVID-19. Methodologies to document SARS-CoV-2 infection that have been used include immunohistochemistry, immunofluorescence, RT-PCR, in situ hybridization, and electron microscopy. In our review of studies to date, we found that SARS-CoV-2 in the kidneys of patients with COVID-19 was detected in 18 of 94 (19%) by immunohistochemistry, 71 of 144 (49%) by RT-PCR, and 11 of 84 (13%) by in situ hybridization. In a smaller number of patients with COVID-19 examined by immunofluorescence, SARS-CoV-2 was detected in 10 of 13 (77%). In total, in kidneys from 102 of 235 patients (43%), the presence of SARS-CoV-2 was suggested by at least one of the methods used. Despite these positive findings, caution is needed because many other studies have been negative for SARS-CoV-2 and it should be noted that when detected, it was only in kidneys obtained at autopsy. There is a clear need for studies from kidney biopsies, including those performed at early stages of the COVID-19-associated kidney disease. Development of tests to detect kidney viral infection in urine samples would be more practical as a noninvasive way to evaluate SARS-CoV-2 infection during the evolution of COVID-19-associated kidney disease.


Subject(s)
COVID-19/virology , Kidney Diseases/virology , Kidney/virology , SARS-CoV-2/pathogenicity , Animals , Biopsy , COVID-19/complications , COVID-19/diagnosis , COVID-19/mortality , COVID-19 Testing , Host-Pathogen Interactions , Humans , Kidney Diseases/diagnosis , Kidney Diseases/mortality , Predictive Value of Tests , Prognosis , Risk Assessment , Risk Factors
12.
JAMA Pediatr ; 175(10): e212025, 2021 10 01.
Article in English | MEDLINE | ID: covidwho-1265361

ABSTRACT

Importance: The association between COVID-19 symptoms and SARS-CoV-2 viral levels in children living in the community is not well understood. Objective: To characterize symptoms of pediatric COVID-19 in the community and analyze the association between symptoms and SARS-CoV-2 RNA levels, as approximated by cycle threshold (Ct) values, in children and adults. Design, Setting, and Participants: This cross-sectional study used a respiratory virus surveillance platform in persons of all ages to detect community COVID-19 cases from March 23 to November 9, 2020. A population-based convenience sample of children younger than 18 years and adults in King County, Washington, who enrolled online for home self-collection of upper respiratory samples for SARS-CoV-2 testing were included. Exposures: Detection of SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) from participant-collected samples. Main Outcomes and Measures: RT-PCR-confirmed SARS-CoV-2 infection, with Ct values stratified by age and symptoms. Results: Among 555 SARS-CoV-2-positive participants (mean [SD] age, 33.7 [20.1] years; 320 were female [57.7%]), 47 of 123 children (38.2%) were asymptomatic compared with 31 of 432 adults (7.2%). When symptomatic, fewer symptoms were reported in children compared with adults (mean [SD], 1.6 [2.0] vs 4.5 [3.1]). Symptomatic individuals had lower Ct values (which corresponded to higher viral RNA levels) than asymptomatic individuals (adjusted estimate for children, -3.0; 95% CI, -5.5 to -0.6; P = .02; adjusted estimate for adults, -2.9; 95% CI, -5.2 to -0.6; P = .01). The difference in mean Ct values was neither statistically significant between symptomatic children and symptomatic adults (adjusted estimate, -0.7; 95% CI, -2.2 to 0.9; P = .41) nor between asymptomatic children and asymptomatic adults (adjusted estimate, -0.6; 95% CI, -4.0 to 2.8; P = .74). Conclusions and Relevance: In this community-based cross-sectional study, SARS-CoV-2 RNA levels, as determined by Ct values, were significantly higher in symptomatic individuals than in asymptomatic individuals and no significant age-related differences were found. Further research is needed to understand the role of SARS-CoV-2 RNA levels and viral transmission.


Subject(s)
COVID-19/complications , COVID-19/diagnosis , RNA, Viral/metabolism , SARS-CoV-2/isolation & purification , Viral Load , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Infant , Male , Middle Aged , Reverse Transcriptase Polymerase Chain Reaction , Symptom Assessment , Washington , Young Adult
13.
PLoS One ; 16(6): e0252440, 2021.
Article in English | MEDLINE | ID: covidwho-1259242

ABSTRACT

Chest X-rays (CXRs) can help triage for Coronavirus disease (COVID-19) patients in resource-constrained environments, and a computer-aided detection system (CAD) that can identify pneumonia on CXR may help the triage of patients in those environment where expert radiologists are not available. However, the performance of existing CAD for identifying COVID-19 and associated pneumonia on CXRs has been scarcely investigated. In this study, CXRs of patients with and without COVID-19 confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) were retrospectively collected from four and one institution, respectively, and a commercialized, regulatory-approved CAD that can identify various abnormalities including pneumonia was used to analyze each CXR. Performance of the CAD was evaluated using area under the receiver operating characteristic curves (AUCs), with reference standards of the RT-PCR results and the presence of findings of pneumonia on chest CTs obtained within 24 hours from the CXR. For comparison, 5 thoracic radiologists and 5 non-radiologist physicians independently interpreted the CXRs. Afterward, they re-interpreted the CXRs with corresponding CAD results. The performance of CAD (AUCs, 0.714 and 0.790 against RT-PCR and chest CT, respectively hereinafter) were similar with those of thoracic radiologists (AUCs, 0.701 and 0.784), and higher than those of non-radiologist physicians (AUCs, 0.584 and 0.650). Non-radiologist physicians showed significantly improved performance when assisted with the CAD (AUCs, 0.584 to 0.664 and 0.650 to 0.738). In addition, inter-reader agreement among physicians was also improved in the CAD-assisted interpretation (Fleiss' kappa coefficient, 0.209 to 0.322). In conclusion, radiologist-level performance of the CAD in identifying COVID-19 and associated pneumonia on CXR and enhanced performance of non-radiologist physicians with the CAD assistance suggest that the CAD can support physicians in interpreting CXRs and helping image-based triage of COVID-19 patients in resource-constrained environment.


Subject(s)
COVID-19/diagnostic imaging , Deep Learning , Lung , Radiographic Image Interpretation, Computer-Assisted , Aged , Female , Humans , Lung/diagnostic imaging , Lung/pathology , Male , Middle Aged , Radiography, Thoracic , Republic of Korea/epidemiology , Retrospective Studies , Tomography, X-Ray Computed
14.
Open Biol ; 11(6): 200288, 2021 06.
Article in English | MEDLINE | ID: covidwho-1249358

ABSTRACT

We describe the epidemiological characteristics and associated risk factors of those presenting at a large testing centre for SARS-CoV-2 infection. This is a retrospective record review of individuals who underwent SARS-CoV-2 testing by reverse transcription-polymerase chain reaction (RT-PCR) at a high-throughput national-level government facility located in the north of India. Samples collected from 6 April to 31 December 2020 are included in this work and represent four highly populous regions. Additionally, there was a prospective follow-up of 1729 cases through telephone interviews from 25 May 2020 to 20 June 2020. Descriptive analysis has been performed for profiling clinic-epidemiological aspects of suspect cases. Multivariable logistic regression analysis was undertaken to determine risk factors that are associated with SARS-CoV-2 test positivity and symptom status. A total of 125 600 participants' details have been included in this report. The mean (s.d.) age of the participants was 33.1 (±15.3) years and 66% were male. Among these tested, 9515 (7.6%) were positive for COVID-19. A large proportion of positive cases were asymptomatic. In symptomatic positive cases, the commonest symptoms were cough and fever. Increasing age (groups 20-59 and ≥60 years compared to age group less than 5 years), male sex, history of international travel, symptoms for SARS-CoV-2, and participants from Delhi and Madhya Pradesh were positively associated with SARS-CoV-2 test positivity. Having co-morbidity, risk behaviours and intra-familial positivity were associated with a positive odds ratio for exhibiting SARS-CoV-2 symptoms. Intensified testing and isolation of cases, identification of both asymptomatic and symptomatic individuals and additional care of those with co-morbidities and risk behaviours will all be collectively important for disease containment in India. Reasons for differentials in testing between men and women remain an important area for in-depth study. The increased deployment of vaccines is likely to impact the trajectory of COVID-19 in the coming time, and therefore our data will serve as a comparative resource as India experiences the second wave of infection in light of newer variants that are likely to accelerate disease spread.


Subject(s)
COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19/epidemiology , Adolescent , Adult , Age Factors , Aged , Comorbidity , Female , Humans , India , Male , Middle Aged , Risk Factors , Sex Factors , Travel/statistics & numerical data
15.
Clin Epidemiol ; 13: 317-324, 2021.
Article in English | MEDLINE | ID: covidwho-1244938

ABSTRACT

INTRODUCTION: Madrid has been the epicenter of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Spain. We analyzed our experience with SARS-CoV-2 infected and cancer patients. PATIENTS AND METHODS: We included patients from March 1 to April 30 2020 at Hospital Universitario Puerta de Hierro, Majadahonda, Madrid (Spain). The inclusion criteria were diagnosis of SARS-CoV-2 infection made by reverse transcription polymerase chain reaction (RT-PCR) of nasopharyngeal specimens in cancer patients who were admitted to the hospital due to the need for respiratory support. The exclusion criteria were suspected cases not confirmed. The primary objective was to analyze the mortality rates of patients with cancer, especially those with lung cancer and COVID-19. RESULTS: Overall in-hospital mortality of cancer patients with coronavirus disease 2019 (COVID-19) was 15.2% similar to 12.7% of the global COVID-19 hospitalized population (p=0.615) and greater than that of patients admitted without SARS-CoV-2 infection during the same period 4.3% (p<0.001). Among 653 patients receiving active cancer therapy during the study period, 24 (3.7%) developed COVID-19 and required admission, 4.2% of those receiving chemotherapy, 9.5% immunotherapy and 2.1% targeted therapies. Lung and breast cancer were the most frequent cancer types (26.1%), followed by colorectal cancer (19.6%). Mortality in patients with lung cancer was 25%. The univariate analysis comparing patients who developed a serious event to those who did not showed that the higher Brescia index, CURB-65 scale, lactate dehydrogenase (LDH) or C-reactive protein (CRP) were the risk factors of developing severe complications. CONCLUSION: Patients with cancer, especially lung cancer, and SARS-CoV-2 infection have a worse overall prognosis than the general population.

16.
Anal Chem ; 93(22): 7825-7832, 2021 06 08.
Article in English | MEDLINE | ID: covidwho-1243271

ABSTRACT

COVID-19 first appeared in December of 2019 in Wuhan, China. Since then, it has become a global pandemic. A robust and scalable diagnostics strategy is crucial for containing and monitoring the pandemic. RT-PCR is a known, reliable method for COVID-19 diagnostics, which can differentiate between SARS-CoV-2 and other viruses. However, PCR is location-dependent, time-consuming, and relatively expensive. Thus, there is a need for a more flexible method, which may be produced in an off-the-shelf format and distributed more widely. Paper-based immunoassays can fulfill this function. Here, we present the first steps toward a paper-based test, which can differentiate between different spike proteins of various coronaviruses, SARS-CoV-1, SARS-CoV-2, and CoV-HKU1, with negligible cross-reactivity for HCoV-OC43 and HCoV-229E in a single assay, which takes less than 30 min. Furthermore, our test can distinguish between fractions of the same spike protein. This is done by an altered assay design with four test line locations where each antigen builds a unique, identifiable binding pattern. The effect of several factors, such as running media, immunoprobe concentration, and antigen interference, is considered. We find that running media has a significant effect on the final binding pattern where human saliva provides results while human serum leads to the lowest signal quality.


Subject(s)
COVID-19 , Coronavirus OC43, Human , China , Humans , SARS-CoV-2 , Spike Glycoprotein, Coronavirus
17.
Trials ; 22(1): 349, 2021 May 19.
Article in English | MEDLINE | ID: covidwho-1236569

ABSTRACT

OBJECTIVES: In this study, we will investigate the effect of hydroxychloroquine on the prevention of novel coronavirus disease (COVID-19) in cancer patients being treated. TRIAL DESIGN: This is a two-arm, parallel-group, triple-blind, phase 2-3 randomized controlled trial. PARTICIPANTS: All patients over the age of 15 years from 5 types of cancer will be included in the study. Patients with acute lymphoid and myeloid leukemias in the first line treated with curative intent, patients with high-grade non-Hodgkin's lymphoma treated with leukemia regimens, and patients with non-metastatic breast and colon cancer in the first line of treatment will enter the study. INTERVENTION AND COMPARATOR: Patients are randomly assigned to two groups: one being given hydroxychloroquine and the other is given placebo. During 2 months of treatment, the two groups will be treated with hydroxychloroquine every other day with a single 200-mg tablet (Amin® Pharmaceutical Company, Isfahan, Iran) or placebo (identical in terms of shape, color, and smell). Patients will be monitored for COVID-19 symptoms during follow-up period. If any COVID-19-related signs or symptoms occur, they will be examined, thoroughly, investigated with a high resolution computerize tomography (CT) scan of the lungs and nasopharyngeal swab assessed by RT-PCR for SARS-CoV-2 virus. This study will be performed in five centers affiliated to Mashhad University of Medical Sciences, Mashhad, Iran. MAIN OUTCOMES: The primary end point of this study is to investigate the incidence of COVID-19 in patients being treated for their cancer and receiving prophylactic Hydroxychloroquine. RANDOMIZATION: Randomization will be performed using random permuted blocks. By using online website ( www.randomization.com ), the randomization sequence will be produced by quadruple blocks. The allocation ratio in intervention and control groups is 1:1. BLINDING (MASKING): Participants and caregivers do not know whether the patient is in the intervention or the control group. Those assessing the outcomes and data analyzer are also blinded to group assignment. SAMPLE SIZE: The calculated total sample size is 60 patients, with 30 patients in each group.


Subject(s)
COVID-19 , Neoplasms , Adolescent , COVID-19/drug therapy , Humans , Hydroxychloroquine/adverse effects , Iran , Neoplasms/diagnosis , Neoplasms/drug therapy , Randomized Controlled Trials as Topic , SARS-CoV-2 , Treatment Outcome
18.
BMJ Open Gastroenterol ; 8(1)2021 05.
Article in English | MEDLINE | ID: covidwho-1236440

ABSTRACT

OBJECTIVE: This study will test the performance of the anal swab PCR test when compared with the nasopharyngeal swab PCR test as a diagnostic tool for COVID-19. DESIGN: An observational descriptive study which included hospitalised suspected, or probable cases of hopitalised COVID-19 patients, conducted in Dr. Cipto Mangunkusumo National Hospital, Ciputra Hospital, Mitra Keluarga Depok Hospital and Mitra Keluarga Kelapa Gading Hospital, Indonesia. Epidemiological, clinical, laboratory and radiology data were obtained. Nasopharyngeal and anal swabs specimens were collected for SARS-CoV-2 RNA detection. RESULTS: We analysed 136 subjects as part of this study. The clinical spectrum of COVID-19 manifesation in this study was typical of hospitalised patients, with 25% classified as mild cases, 14.7% in severe condition and 12.5% of subjects classified as having acute respiratory distress syndrome. When compared with nasopharyngeal swab as the standard specimen for reverse transcription polymerase chain reaction (RT-PCR) detection of SARS-CoV-2 antigen, the sensitivity and specificity of the anal swab was 36.7% and 93.8%, respectively. The positive and negative predictive value were 97.8% and 16.5 %, respectively. The performance of the anal swab remained similar when only the subgroup of patients with gastrointestinal symptoms (n=92, 67.6%) was analysed (sensitivity 40% and specificity 91.7%). Out of all the subjects included in analysis, 67.6% had gastrointestinal symptoms. Similarly, 73.3% of patients in the anal swab-positive group had gastrointestinal symptoms. The two most common gastrointestinal symptoms in the subjects' population were nausea and anorexia. CONCLUSION: Anal swab specimen has low sensitivity (36.7%) but high specificity (93.8%) for detecting SARS-CoV-2 antigen by RT-PCR. Only one additional positive result was found by anal swab among the nasopharyngeal swab-negative group. Anal swab may not be needed as an additional test at the beginning of a patient's diagnostic investigation and nasopharyngeal swab RT-PCR remains as the standard diagnostic test for COVID-19.


Subject(s)
Anal Canal/virology , COVID-19/diagnosis , Gastrointestinal Diseases/virology , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Adult , COVID-19/epidemiology , COVID-19/virology , COVID-19 Testing/methods , Diagnostic Tests, Routine/standards , Diagnostic Tests, Routine/statistics & numerical data , Female , Gastrointestinal Diseases/diagnosis , Hospitalization , Humans , Indonesia/epidemiology , Male , Middle Aged , Nasopharynx/virology , Predictive Value of Tests , Reverse Transcriptase Polymerase Chain Reaction/statistics & numerical data , Sensitivity and Specificity
19.
Pathologe ; 42(2): 208-215, 2021 Mar.
Article in German | MEDLINE | ID: covidwho-1235730

ABSTRACT

BACKGROUND: Analyses for the presence of SARS-CoV­2 in the tissues of COVID-19 patients is important in order to improve our understanding of the disease pathophysiology for interpretation of diagnostic histopathological findings in autopsies, biopsies, or surgical specimens and to assess the potential for occupational infectious hazard. MATERIAL AND METHODS: In this review we identified 136 published studies in PubMed's curated literature database LitCovid on SARS-CoV­2 detection methods in tissues and evaluated them regarding sources of error, specificity, and sensitivity of the methods, taking into account our own experience. RESULTS: Currently, no sufficiently specific histomorphological alterations or diagnostic features for COVID-19 are known. Therefore, three approaches for SARS-CoV­2 detection are used: RNA, proteins/antigens, or morphological detection by electron microscopy. In the preanalytical phase, the dominant source of error is tissue quality, especially the different intervals between sample collection and processing or fixation (and its duration) and specifically the interval between death and sample collection in autopsies. However, this information is found in less than half of the studies (e.g., in only 42% of autopsy studies). Our own experience and first studies prove the significantly higher sensitivity and specificity of RNA-based detection methods compared to antigen or protein detection by immunohistochemistry or immunofluorescence. Detection by electron microscopy is time consuming and difficult to interpret. CONCLUSIONS: Different methods are available for the detection of SARS-CoV­2 in tissue. Currently, RNA detection by RT-PCR is the method of choice. However, extensive validation studies and method harmonization are not available and are absolutely necessary.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral , Sensitivity and Specificity
20.
Elife ; 102021 04 20.
Article in English | MEDLINE | ID: covidwho-1234904

ABSTRACT

Diagnosis of SARS-CoV-2 (COVID-19) requires confirmation by reverse transcription-polymerase chain reaction (RT-PCR). Abbott ID NOW provides fast results but has been criticized for low sensitivity. Here we determine the sensitivity of ID NOW in an ambulatory population presented for testing. The study enrolled 785 symptomatic patients, of whom 21 were positive by both ID NOW and RT-PCR, and 2 only by RT-PCR. All 189 asymptomatic patients tested negative. The positive percent agreement between the ID NOW assay and the RT-PCR assay was 91.3%, and negative percent agreement was 100%. The results from the current study were included into a larger systematic review of literature where at least 20 subjects were simultaneously tested using ID NOW and RT-PCR. The overall sensitivity for ID NOW assay was calculated at 84% (95% confidence interval 55-96%) and had the highest correlation to RT-PCR at viral loads most likely to be associated with transmissible infections.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Adult , Female , Genome, Viral , Humans , Male , Middle Aged , Nose/virology , Nucleic Acid Amplification Techniques/methods , Point-of-Care Systems , SARS-CoV-2/genetics , Sensitivity and Specificity , Specimen Handling , Viral Load
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