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1.
Lancet Respir Med ; 8(7): e63-e64, 2020 07.
Article in English | MEDLINE | ID: covidwho-689472
2.
Indian J Med Microbiol ; 38(1): 9-17, 2020.
Article in English | MEDLINE | ID: covidwho-688963

ABSTRACT

High-throughput, accurate, cost-effective and rapid testing for severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is the need of the hour in face of the global coronavirus disease pandemic. This target is achievable, within a relatively short time through capacity building of reverse transcription polymerase chain reaction (RT-PCR) tests by utilising the strengths of intra and inter institutional networks. These networks act as force multiplier for vital resources which are required for capacity building, namely, leadership, expertise, equipment, space, infection control inputs and human resources. In this article, we report the experience of capacity building for delivery of RT-PCR tests for SARS CoV-2 from a cancer hospital in Eastern India. The relevance, mode of operation and value addition of this essential public health service are discussed in the context of inter departmental collaboration and interaction with other institutes through the existing diagnostic, surveillance and infection control networks. This networking model for service development and delivery could be used by other centres.


Subject(s)
Betacoronavirus/isolation & purification , Capacity Building/organization & administration , Clinical Laboratory Techniques/methods , Community Networks/organization & administration , Coronavirus Infections/diagnosis , Diagnostic Services/organization & administration , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Betacoronavirus/genetics , Humans , India , Pandemics
3.
Indian J Med Microbiol ; 38(1): 87-93, 2020.
Article in English | MEDLINE | ID: covidwho-688925

ABSTRACT

Objective: This study aims to provide scientific basis for rapid screening and early diagnosis of the coronavirus disease 2019 (COVID-19) through analysing the clinical characteristics and early imaging/laboratory findings of the inpatients. Methods: Three hundred and three patients with laboratory-confirmed COVID-19 from the East Hospital of People's Hospital of Wuhan University (Wuhan, China) were selected and divided into four groups: youth (20-40 years, n = 64), middle-aged (41-60 years, n = 89), older (61-80 years, n = 118) and elderly (81-100 years, n = 32). The clinical characteristics and imaging/laboratory findings including chest computed tomography (CT), initial blood count, C-reactive protein [CRP]), procalcitonin (PCT) and serum total IgE were captured and analysed. Results: (1) The first symptoms of all age groups were primarily fever (76%), followed by cough (12%) and dyspnoea (5%). Beside fever, the most common initial symptom of elderly patients was fatigue (13%). (2) Fever was the most common clinical manifestation (80%), with moderate fever being the most common (40%), followed by low fever in patients above 40 years old and high fever in those under 40 years (35%). Cough was the second most common clinical manifestation and was most common (80%) in the middle-aged. Diarrhoea was more common in the middle-aged (21%) and the older (19%). Muscle ache was more common in the middle-aged (15%). Chest pain was more common in the youth (13%), and 13% of the youth had no symptoms. (3) The proportion of patients with comorbidities increased with age. (4) Seventy-one per cent of the patients had positive reverse transcription-polymerase chain reaction results and 29% had positive chest CT scans before admission to the hospital. (5) Lesions in all lobes of the lung were observed as the main chest CT findings (76%). (6) Decrease in lymphocytes and increase in monocytes were common in the patients over 40 years old but rare in the youth. Eosinophils (50%), red blood cells (39%) and haemoglobin (40%) decreased in all age groups. (7) The proportion of patients with CRP and PCT elevation increased with age. (8) Thirty-nine per cent of the patients had elevated IgE, with the highest proportion in the old (49%). Conclusion: The clinical characteristics and imaging/laboratory findings of COVID-19 patients vary in different age groups. Personalised criteria should be formulated according to different age groups in the early screening and diagnosis stage.


Subject(s)
Betacoronavirus/growth & development , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/pathology , Diagnostic Tests, Routine/methods , Pneumonia, Viral/diagnosis , Pneumonia, Viral/pathology , Tomography, X-Ray Computed/methods , Adult , Age Factors , Aged , Aged, 80 and over , China , Coronavirus Infections/diagnostic imaging , Early Diagnosis , Female , Hospitals, University , Humans , Male , Mass Screening/methods , Middle Aged , Pandemics , Pneumonia, Viral/diagnostic imaging , Young Adult
4.
Indian J Med Microbiol ; 38(1): 18-23, 2020.
Article in English | MEDLINE | ID: covidwho-688890

ABSTRACT

Background and Objectives: Timely diagnosis is essential for the containment of the disease and breaks in the chain of transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The present situation demands the countries to scale up their testing and design innovative strategies to conserve diagnostic kits and reagents. The pooling of samples saves time, workforce and most importantly diagnostic kits and reagents. In the present study, we tried to define the pool size that could be applied with acceptable confidence for testing. Materials and Methods: We used repeatedly tested positive clinical sample elutes having different levels of SARS CoV 2 RNA and negative sample elutes to prepare seven series of 11 pools each, having pool sizes ranging from 2 to 48 samples to estimate the optimal pool size. Each pool had one positive sample elute in different compositions. All the pools were tested by SARS CoV 2 reverse transcriptase quantitative polymerase chain reaction. Results: Out of the 77 pools, only 53 (68.8%) were found positive. The sensitivity of pools of 2-48 samples was decreased from 100% (95% confidence interval [CL]; 98.4-100) to 41.41% (95% CL; 34.9-48.1). The maximum size of the pool with acceptable sensitivity (>95%) was found to be of six samples. For the pool size of six samples, the sensitivity was 97.8% and the efficiency of pooling was 0.38. Conclusions: The pooling of samples is a practical way for scaling up testing and ultimately containing the further spread of the CoV disease 2019 pandemic.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Specimen Handling/methods , Betacoronavirus/genetics , Humans , Pandemics , Sensitivity and Specificity
6.
JCI Insight ; 5(10)2020 05 21.
Article in English | MEDLINE | ID: covidwho-687860

ABSTRACT

BACKGROUNDThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a novel viral pneumonia (COVID-19), which is rapidly spreading throughout the world. The positive result of nucleic acid test is a golden criterion to confirm SARS-CoV-2 infection, but the detection features remain unclear.METHODSWe performed a retrospective analysis in 5630 high-risk individuals receiving SARS-CoV-2 nucleic acid tests in Wuhan, China, and investigated their characteristics and diagnosis rates.RESULTSThe overall diagnosis rate was 34.7% (1952/5630). Male (P = 0.025) and older populations (P = 2.525 × 10-39) were at significantly higher risk of SARS-CoV-2 infection. People were generally susceptible, and most cases concentrated in people of 30-79 years. Furthermore, we investigated the association between diagnosis rate and the amount of testing in 501 subjects. Results revealed a 1.27-fold improvement (from 27.9% to 35.5%) of diagnosis rate from testing once to twice (P = 5.847 × 10-9) and a 1.43-fold improvement (from 27.9% to 39.9%) from testing once to 3 times (P = 7.797 × 10-14). More than 3 testing administrations was not helpful for further improvement. However, this improvement was not observed in subjects with pneumonia (P = 0.097).CONCLUSIONAll populations are susceptible to SARS-CoV-2 infection, and male and older-aged populations are at significantly higher risk. Increasing the amount of testing could significantly improve diagnosis rates, except for subjects with pneumonia. It is recommended to test twice in those high-risk individuals whose results are negative the first time, and performing 3 tests is better, if possible.FUNDINGThis work was supported by National Mega Project on Major Infectious Disease Prevention (no. 2017ZX10103005-007) and National Key Research and Development Program of China (no. 2018YFE0204500).


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Child , Child, Preschool , China/epidemiology , Clinical Laboratory Techniques/methods , Coronavirus Infections/epidemiology , Female , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , Molecular Diagnostic Techniques , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Retrospective Studies , Sex Factors , Young Adult
7.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-684555

ABSTRACT

An outbreak of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) began in Wuhan, Hubei, China, in December 2019 and spread rapidly worldwide. The response by the Alberta Precision Laboratories, Public Health Laboratory (ProvLab), AB, Canada, included the development and implementation of nucleic acid detection-based assays and dynamic changes in testing protocols for the identification of cases as the epidemic curve increased exponentially. This rapid response was essential to slow down and contain transmission and provide valuable time to the local health authorities to prepare appropriate response strategies. As of May 24, 2020, 236,077 specimens were tested, with 6,475 (2.74%) positives detected in the province of Alberta, Canada. Several commercial assays are now available; however, the response from commercial vendors to develop and market validated tests is a time-consuming process. In addition, the massive global demand made it difficult to secure a reliable commercial supply of testing kits and reagents. A public health laboratory serves a unique and important role in the delivery of health care. One of its functions is to anticipate and prepare for novel emerging pathogens with a plan for pandemic preparedness. Here, we outline the response that involved the development and deployment of testing methodologies that evolved as SARS-CoV-2 spread worldwide, the challenges encountered, and mitigation strategies. We also provide insight into the organizational structure of how a public health response is coordinated in Alberta, Canada, and its benefits.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Diagnostic Services/organization & administration , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Public Health Administration/methods , Alberta , Humans , Pandemics
9.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-684350

ABSTRACT

Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the clinical performance of these tests is still poorly understood, particularly with regard to disease course, patient-specific factors, and viral shedding. From 10 March to 1 May 2020, NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed for 3,432 patients, of which 2,413 had initial negative and 802 had initial positive results. Repeat-tested patients were more likely to have severe disease and low viral loads. The negative predictive value of the first-day result among repeat-tested patients was 81.3% The clinical sensitivity of SARS-CoV-2 molecular assays was estimated between 58% and 96%, depending on the unknown number of false-negative results in single-tested patients. Conversion to negative was unlikely to occur before 15 to 20 days after initial testing or 20 to 30 days after the onset of symptoms, with 50% conversion occurring at 28 days after initial testing. Conversion from first-day negative to positive results increased linearly with each day of testing, reaching 25% probability in 20 days. Sixty patients fluctuated between positive and negative results over several weeks, suggesting that caution is needed when single-test results are acted upon. In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely, 15 to 20 days after a positive test and the same day or next 2 days after a negative test for patients with high suspicion for COVID-19.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Diagnostic Tests, Routine/methods , Pneumonia, Viral/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus/genetics , Child , Child, Preschool , Coronavirus Infections/pathology , Coronavirus Infections/virology , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , New York , Pandemics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Predictive Value of Tests , Sensitivity and Specificity , Viral Load , Young Adult
10.
J Breath Res ; 14(4): 041001, 2020 07 21.
Article in English | MEDLINE | ID: covidwho-682126

ABSTRACT

The COVID-19 pandemic has highlighted the importance of rapid, cost effective, accurate, and non-invasive testing for viral infections. Volatile compounds (VCs) have been suggested for several decades as fulfilling these criteria. However currently very little work has been done in trying to diagnose viral infections using VCs. Much of the work carried out to date involves the differentiation of bacterial and viral sources of infection and often the detection of bacterial and viral co-infection. However, this has usually been done in vitro and very little work has involved the use of human participants. Viruses hijack the host cell metabolism and do not produce their own metabolites so identifying virus specific VCs is at best a challenging task. However, there are proteins and lipids that are potential candidates as markers of viral infection. The current understanding is that host cell glycolysis is upregulated under viral infection to increase the available energy for viral replication. There is some evidence that viral infection leads to the increase of production of fatty acids, alkanes, and alkanes related products. For instance, 2,3-butandione, aldehydes, 2,8-dimethyl-undecane and n-propyl acetate have all been correlated with viral infection. Currently, the literature points to markers of oxidative stress (e.g. nitric oxide, aldehydes etc) being the most useful in the determination of viral infection. The issue, however, is that there are also many other conditions that can lead to oxidative stress markers being produced. In this review a range of (mainly mass spectrometric) methods are discussed for viral detection in breath, including breath condensate. Currently MALDI-ToF-MS is likely to be the preferred method for the identification of viral strains and variants of those strains, however it is limited by its need for the viral strains to have been sequenced and logged in a database.


Subject(s)
Breath Tests/methods , Virus Diseases/diagnosis , Aldehydes/metabolism , Animals , Betacoronavirus , Biomarkers/metabolism , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/metabolism , Gas Chromatography-Mass Spectrometry , Hepatitis B/diagnosis , Hepatitis B/metabolism , Humans , Influenza, Human/diagnosis , Influenza, Human/metabolism , Mass Spectrometry , Nitric Oxide/metabolism , Orthomyxoviridae Infections/diagnosis , Orthomyxoviridae Infections/metabolism , Oxidative Stress , Pandemics , Picornaviridae Infections/diagnosis , Picornaviridae Infections/metabolism , Pneumonia, Viral/diagnosis , Pneumonia, Viral/metabolism , Rotavirus Infections/diagnosis , Rotavirus Infections/metabolism , Spectrometry, Mass, Electrospray Ionization , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Swine , Virus Diseases/metabolism , Viruses
11.
Lima; Perú. Ministerio de salud; 20200400. 11 p. tab.
Monography in Spanish | LILACS (Americas) | ID: covidwho-677356

ABSTRACT

El documento estable los procedimientos para el control y vigilancia del ingreso, distribución, comercialización, uso, registro de resultados y control de calidad de los dispositivos de diagnóstico IN VITRO: Pruebas rápidas y moleculares para el COVID-19.


Subject(s)
Serologic Tests , Communicable Disease Control , Coronavirus , Clinical Laboratory Techniques
12.
Neurologia ; 35(6): 357-362, 2020.
Article in English, Spanish | MEDLINE | ID: covidwho-680554

ABSTRACT

INTRODUCTION: The COVID-19 pandemic is changing approaches to diagnosis, treatment, and care provision in multiple sclerosis (MS). During both the initial and peak phases of the epidemic, the administration of disease-modifying drugs, typically immunosuppressants administered in pulses, was suspended due to the uncertainty about their impact on SARS-CoV-2 infection, mainly in contagious asymptomatic/presymptomatic patients. The purpose of this study is to present a safety algorithm enabling patients to resume pulse immunosuppressive therapy (PIT) during the easing of lockdown measures. METHODS: We developed a safety algorithm based on our clinical experience with MS and the available published evidence; the algorithm assists in the detection of contagious asymptomatic/presymptomatic cases and of patients with mild symptoms of SARS-CoV-2 infection with a view to withdrawing PIT in these patients and preventing new infections at day hospitals. RESULTS: We developed a clinical/microbiological screening algorithm consisting of a symptom checklist, applied during a teleconsultation 48hours before the scheduled session of PIT, and PCR testing for SARS-CoV-2 in nasopharyngeal exudate 24hours before the procedure. CONCLUSION: The application of our safety algorithm presents a favourable risk-benefit ratio despite the fact that the actual proportion of asymptomatic and presymptomatic individuals is unknown. Systematic PCR testing, which provides the highest sensitivity for detecting presymptomatic cases, combined with early detection of symptoms of SARS-CoV-2 infection may reduce infections and improve detection of high-risk patients before they receive PIT.


Subject(s)
Algorithms , Betacoronavirus/isolation & purification , Coronavirus Infections/prevention & control , Immunosuppressive Agents/administration & dosage , Multiple Sclerosis/drug therapy , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Ambulatory Care , Asymptomatic Diseases , Checklist , Clinical Laboratory Techniques , Contraindications, Drug , Coronavirus Infections/diagnosis , Disease Susceptibility , Humans , Immunocompromised Host , Immunosuppressive Agents/adverse effects , Immunosuppressive Agents/therapeutic use , Mass Screening/methods , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Polymerase Chain Reaction , Pulse Therapy, Drug , Quarantine , Risk Assessment , Symptom Assessment , Telemedicine
13.
Korean J Radiol ; 21(5): 541-544, 2020 05.
Article in English | MEDLINE | ID: covidwho-678713

ABSTRACT

The coronavirus disease 2019 (COVID-19) pneumonia is a recent outbreak in mainland China and has rapidly spread to multiple countries worldwide. Pulmonary parenchymal opacities are often observed during chest radiography. Currently, few cases have reported the complications of severe COVID-19 pneumonia. We report a case where serial follow-up chest computed tomography revealed progression of pulmonary lesions into confluent bilateral consolidation with lower lung predominance, thereby confirming COVID-19 pneumonia. Furthermore, complications such as mediastinal emphysema, giant bulla, and pneumothorax were also observed during the course of the disease.


Subject(s)
Coronavirus Infections/complications , Mediastinal Emphysema/etiology , Pneumonia, Viral/complications , Pneumothorax/etiology , Adult , Betacoronavirus , Blister , China , Clinical Laboratory Techniques , Coronavirus , Coronavirus Infections/diagnosis , Coronavirus Infections/diagnostic imaging , Disease Progression , Humans , Lung/pathology , Male , Pandemics , Pneumonia, Viral/diagnostic imaging , Tomography, X-Ray Computed
14.
Jpn J Infect Dis ; 73(4)2020 Jul 22.
Article in English | MEDLINE | ID: covidwho-678395

ABSTRACT

During the emergence of novel coronavirus 2019 (nCoV) outbreak in Wuhan city, China at the end of 2019, there was movement of many airline travelers between Wuhan and Japan, suggesting that the Japanese population was at high risk of infection by the virus. Hence, we urgently developed diagnostic systems for detection of 2019 nCoV. Two nested RT-PCR and two real-time RT-PCR assays were adapted for use in Japan. As of February 8, 2020, these assays have successfully detected 25 positive cases of infection in Japan.


Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Humans , Japan , Pandemics , Reverse Transcriptase Polymerase Chain Reaction/methods , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
15.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-676653

ABSTRACT

In this commentary, we provide a broad overview of how the rapidly evolving coronavirus disease 2019 (COVID-19) diagnostic landscape has impacted clinical care during the COVID-19 pandemic. We review aspects of both molecular and serologic testing and discuss the logistical challenges faced with each. We also highlight the progress that has been made in the development and implementation of these assays as well as the need for ongoing improvement in diagnostic testing capabilities.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Betacoronavirus/genetics , Betacoronavirus/immunology , Clinical Laboratory Techniques/trends , Diagnostic Tests, Routine/methods , Diagnostic Tests, Routine/trends , Humans , Pandemics
19.
PLoS One ; 15(7): e0236564, 2020.
Article in English | MEDLINE | ID: covidwho-676213

ABSTRACT

To circumvent the limited availability of RNA extraction reagents, we aimed to develop a protocol for direct RT-qPCR to detect SARS-CoV-2 in nasopharyngeal swabs without RNA extraction. Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. The results were compared to that of standard approach that involves RNA extraction. Incubation of specimens at 65°C for 10 minutes along with the use of TaqPath™ 1-Step RT-qPCR Master Mix provides higher analytical sensitivity for detection of SARS-CoV-2 RNA than many other conditions tested. The optimized direct RT-qPCR approach demonstrated a limit of detection of 6.6x103 copy/ml and high reproducibility (co-efficient of variation = 1.2%). In 132 nasopharyngeal specimens submitted for SARS-CoV-2 testing, the sensitivity, specificity and accuracy of our optimized approach were 95%, 99% and 98.5%, respectively, with reference to the standard approach. Also, the RT-qPCR CT values obtained by the two methods were positively correlated (Pearson correlation coefficient r = 0.6971, p = 0.0013). The rate of PCR inhibition by the direct approach was 8% compared to 9% by the standard approach. Our simple approach to detect SARS-CoV-2 RNA by direct RT-qPCR may help laboratories continue testing for the virus despite reagent shortages or expand their testing capacity in resource limited settings.


Subject(s)
Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , Specimen Handling/methods , Betacoronavirus , Humans , Nasopharynx/virology , Pandemics , Reproducibility of Results , Sensitivity and Specificity
20.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-676018

ABSTRACT

Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) got off to a slow start in the United States. In this commentary, I describe my experience with CoV disease 2019 (COVID-19), with a focus on being tested at the University of North Carolina-Chapel Hill Respiratory Diagnostic Center on its inaugural day.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Academic Medical Centers , Coronavirus Infections/virology , Diagnostic Services/organization & administration , Hospitals, University , Humans , North Carolina , Pandemics , Pneumonia, Viral/virology
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