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1.
Mymensingh Med J ; 29(3): 589-595, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-746324

ABSTRACT

The coronavirus disease (COVID-19) is highly pathogenic viral infection caused by SARS-CoV-2. Currently, COVID-19 has caused global health concern. WHO has declared COVID-19 as a pandemic disease on March 11, 2020 and characterized by fever, dry cough, fatigue, myalgia and chest pain with pneumonia in severe cases. The virus has spread to at least 213 countries and more than 9093827 confirmed cases and 471490 deaths have been recorded. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. There are some newly developed and promising methods for detection of SARS-CoV-2, in order to facilitate the development of novel approaches for early diagnosis. Nucleic acid based tests currently offer the most sensitive and early detection and confirmation for SARS-CoV-2 infection. Among them Real-time reverse transcription polymerase chain reaction (rRT-PCR) is the most popular and the "gold standard" testing method for the detection of SARS-CoV-2. The present study was carried out to detect 2019-Novel Coronavirus (2019-nCoV) by rRT-PCR method at Mymensingh Medical College, Mymensingh, Bangladesh from 1st April, 2020 to 31st May, 2020. A total of 14356 samples were tested from four districts of Mymensingh division namely, Mymensingh, Jamalpur, Sherpur, Netrokona and some parts of Sunamganj for rRT-PCR. Among them 1086 (7.5%) patients were positive for SARS-CoV-2. Out of 1086 positive cases 716(65.9%) were male and 370(34.1%) were female with a Mean±SD age 34.1±12 years. Maximum positivity was found in Mymensingh district followed by Netrokona, Jamalpur, Sherpur and Sunamganj respectively. This is the first base line study for genetic detection of 2019-nCoV in Mymensingh division which may reflect the total scenario of Bangladesh situation. We hope this paper will help the researcher to increase the availability, accuracy, and speed of widespread COVID-19 testing throughout the world in this crisis moment.


Subject(s)
Coronavirus Infections/diagnosis , Coronavirus/genetics , Coronavirus/isolation & purification , Pandemics , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Bangladesh , Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections/epidemiology , Humans , Pneumonia, Viral/epidemiology
2.
Zhonghua Liu Xing Bing Xue Za Zhi ; 41(8): 1204-1209, 2020 Aug 10.
Article in Chinese | MEDLINE | ID: covidwho-737781

ABSTRACT

Objective: By analyzed the transmission patterns of 4 out of the 51 COVID-19 cluster cases in Shaanxi province to provide evidences for the COVID-19 control and prevention. Methods: The epidemiological data of RT-PCR test-confirmed COVID-19 cases were collected. Transmission chain was drawn and the transmission process was analyzed. Results: Cluster case 1 contained 13 cases and was caused by a family of 5 who traveled by car to Wuhan and returned to Shaanxi. Cluster case 2 had 5cases and caused by initial patient who participated family get-together right after back from Wuhan while under incubation period. Cluster case 3 contained 10 cases and could be defined as nosocomial infection. Cluster case 4 contained 4 cases and occurred in work place. Conclusion: Higher contact frequency and smaller places were more likely to cause a small-scale COVID-19 cluster outbreak, with potential longer incubation period. COVID-19 control strategies should turn the attention to infection prevention and control in crowded places, management of enterprise resumption and prevention of nosocomial infection.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Pandemics , Pneumonia, Viral/epidemiology , Reverse Transcriptase Polymerase Chain Reaction/methods , Betacoronavirus/genetics , China/epidemiology , Coronavirus Infections/transmission , Disease Outbreaks , Humans , Pneumonia, Viral/transmission
3.
J Korean Med Sci ; 35(34): e314, 2020 Aug 31.
Article in English | MEDLINE | ID: covidwho-736660

ABSTRACT

A 14-day quarantine is implemented in many countries in response to the coronavirus disease pandemic. Korea implemented a mandatory quarantine for those who had close contact with infected patients and those returning from abroad. The present study explored the implications of mandatory coronavirus disease 2019 testing before releasing individuals from the 14-day quarantine in Incheon, Korea. From February 11 to July 5, 2020, 19,296 people were self-quarantined, and 56 (0.3%) of them were confirmed cases of COVID-19. Twenty (35.7%) were identified through the reporting of symptoms during quarantine, and 32 (57.1%) were identified using mandatory pre-release RT-PCR tests. Among the 32, 14 (25%) individuals reported mild symptoms and 18 (32.1%) were asymptomatic. It is suggested that mandatory diagnostic testing prior to release and the symptom-based surveillance after the 14-day quarantine may help control delayed or asymptomatic COVID-19 cases.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Infection Control/legislation & jurisprudence , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Public Health/legislation & jurisprudence , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus/isolation & purification , Contact Tracing , Female , Humans , Infection Control/methods , Male , Middle Aged , Pandemics , Quarantine , Republic of Korea/epidemiology , Reverse Transcriptase Polymerase Chain Reaction/methods , Young Adult
4.
Radiology ; 296(2): E72-E78, 2020 08.
Article in English | MEDLINE | ID: covidwho-736233

ABSTRACT

Background Current coronavirus disease 2019 (COVID-19) radiologic literature is dominated by CT, and a detailed description of chest radiography appearances in relation to the disease time course is lacking. Purpose To describe the time course and severity of findings of COVID-19 at chest radiography and correlate these with real-time reverse transcription polymerase chain reaction (RT-PCR) testing for severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2, nucleic acid. Materials and Methods This is a retrospective study of patients with COVID-19 confirmed by using RT-PCR and chest radiographic examinations who were admitted across four hospitals and evaluated between January and March 2020. Baseline and serial chest radiographs (n = 255) were reviewed with RT-PCR. Correlation with concurrent CT examinations (n = 28) was performed when available. Two radiologists scored each chest radiograph in consensus for consolidation, ground-glass opacity, location, and pleural fluid. A severity index was determined for each lung. The lung scores were summed to produce the final severity score. Results The study was composed of 64 patients (26 men; mean age, 56 years ± 19 [standard deviation]). Of these, 58 patients had initial positive findings with RT-PCR (91%; 95% confidence interval: 81%, 96%), 44 patients had abnormal findings at baseline chest radiography (69%; 95% confidence interval: 56%, 80%), and 38 patients had initial positive findings with RT-PCR testing and abnormal findings at baseline chest radiography (59%; 95% confidence interval: 46%, 71%). Six patients (9%) showed abnormalities at chest radiography before eventually testing positive for COVID-19 with RT-PCR. Sensitivity of initial RT-PCR (91%; 95% confidence interval: 83%, 97%) was higher than that of baseline chest radiography (69%; 95% confidence interval: 56%, 80%) (P = .009). Radiographic recovery (mean, 6 days ± 5) and virologic recovery (mean, 8 days ± 6) were not significantly different (P = .33). Consolidation was the most common finding (30 of 64; 47%) followed by ground-glass opacities (21 of 64; 33%). Abnormalities at chest radiography had a peripheral distribution (26 of 64; 41%) and lower zone distribution (32 of 64; 50%) with bilateral involvement (32 of 64; 50%). Pleural effusion was uncommon (two of 64; 3%). The severity of findings at chest radiography peaked at 10-12 days from the date of symptom onset. Conclusion Findings at chest radiography in patients with coronavirus disease 2019 frequently showed bilateral lower zone consolidation, which peaked at 10-12 days from symptom onset. © RSNA, 2020.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnostic imaging , Pneumonia, Viral/diagnostic imaging , Adolescent , Adult , Aged , Aged, 80 and over , Clinical Laboratory Techniques/methods , Coronavirus Infections/complications , Coronavirus Infections/diagnosis , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , Pneumonia, Viral/virology , Radiographic Image Interpretation, Computer-Assisted/methods , Reproducibility of Results , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction/methods , Severity of Illness Index , Tomography, X-Ray Computed/methods , Young Adult
5.
PLoS Pathog ; 16(8): e1008705, 2020 08.
Article in English | MEDLINE | ID: covidwho-732988

ABSTRACT

The recent outbreak of human infections caused by SARS-CoV-2, the third zoonotic coronavirus has raised great public health concern globally. Rapid and accurate diagnosis of this novel pathogen posts great challenges not only clinically but also technologically. Metagenomic next-generation sequencing (mNGS) and reverse-transcription PCR (RT-PCR) have been the most commonly used molecular methodologies. However, each has their own limitations. In this study, we developed an isothermal, CRISPR-based diagnostic for COVID-19 with near single-copy sensitivity. The diagnostic performances of all three technology platforms were also compared. Our study aimed to provide more insights into the molecular detection of SARS-CoV-2, and also to present a novel diagnostic option for this new emerging virus.


Subject(s)
Betacoronavirus/genetics , CRISPR-Cas Systems/genetics , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/genetics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/genetics , Bacteria/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Genes, Viral/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Molecular Diagnostic Techniques/economics , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/economics , Nucleic Acid Amplification Techniques/methods , Pandemics , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity
6.
mSphere ; 5(4)2020 08 26.
Article in English | MEDLINE | ID: covidwho-730989

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak urgently necessitates sensitive and convenient COVID-19 diagnostics for the containment and timely treatment of patients. We aimed to develop and validate a novel reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay to detect SARS-CoV-2. Patients with suspected COVID-19 and close contacts were recruited from two hospitals between 26 January and 8 April 2020. Respiratory samples were collected and tested using RT-LAMP, and the results were compared with those obtained by reverse transcription-quantitative PCR (RT-qPCR). Samples yielding inconsistent results between these two methods were subjected to next-generation sequencing for confirmation. RT-LAMP was also applied to an asymptomatic COVID-19 carrier and patients with other respiratory viral infections. Samples were collected from a cohort of 129 cases (329 nasopharyngeal swabs) and an independent cohort of 76 patients (152 nasopharyngeal swabs and sputum samples). The RT-LAMP assay was validated to be accurate (overall sensitivity and specificity of 88.89% and 99.00%, respectively) and diagnostically useful (positive and negative likelihood ratios of 88.89 and 0.11, respectively). RT-LAMP showed increased sensitivity (88.89% versus 81.48%) and high consistency (kappa, 0.92) compared to those of RT-qPCR for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection. The time required for RT-LAMP was less than 1 h from sample preparation to the result. In addition, RT-LAMP was feasible for use with asymptomatic patients and did not cross-react with other respiratory pathogens. The developed RT-LAMP assay offers rapid, sensitive, and straightforward detection of SARS-CoV-2 infection and may aid the expansion of COVID-19 testing in the public domain and hospitals.IMPORTANCE We developed a visual and rapid reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the S gene for SARS-CoV-2 infection. The strength of our study was that we validated the RT-LAMP assay using 481 clinical respiratory samples from two prospective cohorts of suspected COVID-19 patients and on the serial samples from an asymptomatic carrier. The developed RT-LAMP approach showed an increased sensitivity (88.89%) and high consistency (kappa, 0.92) compared with those of reverse transcription-quantitative PCR (RT-qPCR) for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection, facilitating SARS-CoV-2 screening in well-equipped labs as well as in the field. The time required for RT-LAMP was less than 1 h from sample preparation to the result (more than 2 h for RT-qPCR). This study showed that the RT-LAMP assay was a simple, rapid, and sensitive approach for SARS-CoV-2 infection and can facilitate COVID-19 diagnosis, especially in resource-poor settings.


Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , Adult , Asymptomatic Diseases , Female , Humans , Male , Middle Aged , Pandemics , Prospective Studies , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity
7.
J Infect Dev Ctries ; 14(7): 691-695, 2020 07 31.
Article in English | MEDLINE | ID: covidwho-721537

ABSTRACT

As the incidence of Coronavirus Disease 19 (COVID-19) continues to rise, many countries have been seeking for medical assistance such as donation or procurement of laboratory test kits and strips. These consumables are largely intended for use in the laboratory investigations of COVID-19 cases, suspected contacts, asymptomatic persons and in discharging cured persons. Thus, this article was instigated to update and remind healthcare providers and policymakers (especially those in developing countries) on the principles of sample collections, storage, transportation, laboratory protocols and networks needed for appropriate public health response against COVID-19 pandemic in Africa and other developing countries. In addition, this article presents challenges that hinder adequate COVID-19 laboratory response and discuss some possible solutions that could ameliorate these constrains.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Laboratories , Pneumonia, Viral/diagnosis , Specimen Handling , Africa/epidemiology , Betacoronavirus/chemistry , Betacoronavirus/genetics , Betacoronavirus/immunology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Epidemiological Monitoring , Humans , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Public Health , Reverse Transcriptase Polymerase Chain Reaction/methods , Serologic Tests
8.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-711711

ABSTRACT

The global coronavirus (CoV) disease 2019 (COVID-19) pandemic has resulted in a worldwide shortage of viral transport media and raised questions about specimen stability. The objective of this study was to determine the stability of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) RNA in specimen transport media under various storage conditions. Transport media tested included UTM, UTM-RT, ESwab, M4, and saline (0.9% NaCl). Specimen types tested included nasopharyngeal/oropharyngeal swabs in the above-named transport media, bronchoalveolar lavage (BAL) fluid, and sputum. A high-titer SARS-CoV-2 remnant patient specimen was spiked into pooled SARS-CoV-2 RNA-negative specimen remnants for the various medium types. Aliquots of samples were stored at 18°C to 26°C, 2°C to 8°C, and -10°C to -30°C and then tested at time points up to 14 days. Specimens consistently yielded amplifiable RNA with mean cycle threshold differences of <3 over the various conditions assayed, thus supporting the use and transport of alternative collection media and specimen types under a variety of temperature storage conditions.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Laboratory Chemicals/chemistry , Pneumonia, Viral/diagnosis , Specimen Handling/methods , Humans , Pandemics , Reverse Transcriptase Polymerase Chain Reaction/methods , Temperature
9.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-711698

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as the cause of a worldwide pandemic. Many commercial SARS-CoV-2 reverse transcription-PCR (RT-PCR) assays have received Emergency Use Authorization from the U.S. Food and Drug Administration. However, there are limited data describing their performance, in particular the performance of high-throughput SARS-CoV-2 RT-PCR systems. We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. The overall agreement between the platforms was 96.4% (375/389). Cohen's kappa analysis rated the strength of agreement between the two platforms as "almost perfect" (κ = 0.922; standard error, 0.051). Furthermore, there was no significant difference between corresponding cycle threshold values generated on the two systems (P value = 0.88; Student's t test). Taken together, these data imply that the two platforms can be considered comparable in terms of their clinical performance. We believe that this information will be useful for those who have already adopted these platforms or are seeking to implement high-throughput RT-PCR testing to stem the SARS-CoV-2 pandemic.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , High-Throughput Screening Assays , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Betacoronavirus/genetics , Coronavirus Infections/virology , Humans , Nasopharynx/virology , Pandemics , Pneumonia, Viral/virology , United States
10.
Biochem Med (Zagreb) ; 30(3): 030402, 2020 Oct 15.
Article in English | MEDLINE | ID: covidwho-709641

ABSTRACT

After December 2019 outbreak in China, the novel Coronavirus infection (COVID-19) has very quickly overflowed worldwide. Infection causes a clinical syndrome encompassing a wide range of clinical features, from asymptomatic or oligosymptomatic course to acute respiratory distress and death. In a very recent work we preliminarily observed that several laboratory tests have been shown as characteristically altered in COVID-19. We aimed to use the Corona score, a validated point-based algorithm to predict the likelihood of COVID-19 infection in patients presenting at the Emergency rooms. This approach combines chest images-relative score and several laboratory parameters to classify emergency room patients. Corona score accuracy was satisfactory, increasing the detection of positive patients' rate.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Emergency Service, Hospital , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Biomarkers/metabolism , Cohort Studies , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/metabolism , Emergency Service, Hospital/standards , False Negative Reactions , Humans , Negative Results , Pandemics , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/metabolism , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/standards , Tomography, X-Ray Computed/methods , Tomography, X-Ray Computed/standards
11.
PLoS One ; 15(7): e0236859, 2020.
Article in English | MEDLINE | ID: covidwho-690540

ABSTRACT

BACKGROUND: Corona virus disease 2019 (COVID-19) which initially started as a cluster of pneumonia cases in the Wuhan city of China has now become a full-blown pandemic. Timely diagnosis of COVID-19 is the key in containing the pandemic and breaking the chain of transmission. In low- and middle-income countries availability of testing kits has become the major bottleneck in testing. Novel methods like pooling of samples are the need of the hour. OBJECTIVE: We undertook this study to evaluate a novel protocol of pooling of RNA samples/elutes in performance of PCR for SARS CoV-2 virus. STUDY DESIGN: Extracted RNA samples were randomly placed in pools of 8 on a 96 well plate. Both individual RNA (ID) and pooled RNA RT-qPCR for the screening E gene were done in the same plate and the positivity for the E gene was seen. RESULTS: The present study demonstrated that pool testing with RNA samples can easily detect even up to a single positive sample with Ct value as high as 38. The present study also showed that the results of pool testing is not affected by number of positive samples in a pool. CONCLUSION: Pooling of RNA samples can reduce the time and expense, and can help expand diagnostic capabilities, especially during constrained supply of reagents and PCR kits for the diagnosis of SARS-CoV-2 infection.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Coronavirus Infections/virology , Diagnostic Tests, Routine/economics , Diagnostic Tests, Routine/methods , Humans , India/epidemiology , Mass Screening/economics , Mass Screening/methods , Pandemics , Pneumonia, Viral/virology , Prospective Studies , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction/economics , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/economics , Viral Envelope Proteins/genetics
12.
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
13.
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
14.
BMC Med Res Methodol ; 20(1): 196, 2020 07 23.
Article in English | MEDLINE | ID: covidwho-685422

ABSTRACT

BACKGROUND: The number of confirmed COVID-19 cases divided by population size is used as a coarse measurement for the burden of disease in a population. However, this fraction depends heavily on the sampling intensity and the various test criteria used in different jurisdictions, and many sources indicate that a large fraction of cases tend to go undetected. METHODS: Estimates of the true prevalence of COVID-19 in a population can be made by random sampling and pooling of RT-PCR tests. Here I use simulations to explore how experiment sample size and degrees of sample pooling impact precision of prevalence estimates and potential for minimizing the total number of tests required to get individual-level diagnostic results. RESULTS: Sample pooling can greatly reduce the total number of tests required for prevalence estimation. In low-prevalence populations, it is theoretically possible to pool hundreds of samples with only marginal loss of precision. Even when the true prevalence is as high as 10% it can be appropriate to pool up to 15 samples. Sample pooling can be particularly beneficial when the test has imperfect specificity by providing more accurate estimates of the prevalence than an equal number of individual-level tests. CONCLUSION: Sample pooling should be considered in COVID-19 prevalence estimation efforts.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Diagnostic Tests, Routine/methods , Pneumonia, Viral/diagnosis , Population Surveillance/methods , Specimen Handling/methods , Algorithms , Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Humans , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Prevalence , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/methods , Sample Size , Sensitivity and Specificity
16.
mSphere ; 5(4)2020 07 29.
Article in English | MEDLINE | ID: covidwho-684544

ABSTRACT

Coronavirus disease 2019 (COVID-19) has wreaked havoc across the globe; although the number of cases in Africa remains lower than in other regions, it is on a gradual upward trajectory. To date, COVID-19 cases have been reported in 54 out of 55 African countries. However, due to limited severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacity and scarcity of testing reagents, it is probable that the total number of cases could far exceed published statistics. In this viewpoint, using Ghana, Malawi, South Africa, and Zimbabwe as examples of countries that have implemented different testing strategies, we argue that the implementation of sample pooling for rRT-PCR over antibody rapid diagnostic testing could have a greater impact in assessing disease burden. Sample pooling offers huge advantages compared to single test rRT-PCR, as it reduces diagnostic costs, personnel time, burnout, and analytical run times. Africa is already strained in terms of testing resources for COVID-19; hence, cheaper alternative ways need to be implemented to conserve resources, maximize mass testing, and reduce transmission in the wider population.


Subject(s)
Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Immunoassay/methods , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Serologic Tests/methods , Africa , Developing Countries , Health Care Costs , Humans , Pandemics , Specimen Handling/methods , Time Factors
17.
Radiology ; 296(2): E97-E104, 2020 08.
Article in English | MEDLINE | ID: covidwho-683271

ABSTRACT

Background A categorical CT assessment scheme for suspicion of pulmonary involvement of coronavirus disease 2019 (COVID-19 provides a basis for gathering scientific evidence and improved communication with referring physicians. Purpose To introduce the COVID-19 Reporting and Data System (CO-RADS) for use in the standardized assessment of pulmonary involvement of COVID-19 on unenhanced chest CT images and to report its initial interobserver agreement and performance. Materials and Methods The Dutch Radiological Society developed CO-RADS based on other efforts for standardization, such as the Lung Imaging Reporting and Data System or Breast Imaging Reporting and Data System. CO-RADS assesses the suspicion for pulmonary involvement of COVID-19 on a scale from 1 (very low) to 5 (very high). The system is meant to be used in patients with moderate to severe symptoms of COVID-19. The system was evaluated by using 105 chest CT scans of patients admitted to the hospital with clinical suspicion of COVID-19 and in whom reverse transcription-polymerase chain reaction (RT-PCR) was performed (mean, 62 years ± 16 [standard deviation]; 61 men, 53 with positive RT-PCR results). Eight observers used CO-RADS to assess the scans. Fleiss κ value was calculated, and scores of individual observers were compared with the median of the remaining seven observers. The resulting area under the receiver operating characteristics curve (AUC) was compared with results from RT-PCR and clinical diagnosis of COVID-19. Results There was absolute agreement among observers in 573 (68.2%) of 840 observations. Fleiss κ value was 0.47 (95% confidence interval [CI]: 0.45, 0.47), with the highest κ value for CO-RADS categories 1 (0.58, 95% CI: 0.54, 0.62) and 5 (0.68, 95% CI: 0.65, 0.72). The average AUC was 0.91 (95% CI: 0.85, 0.97) for predicting RT-PCR outcome and 0.95 (95% CI: 0.91, 0.99) for clinical diagnosis. The false-negative rate for CO-RADS 1 was nine of 161 cases (5.6%; 95% CI: 1.0%, 10%), and the false-positive rate for CO-RADS category 5 was one of 286 (0.3%; 95% CI: 0%, 1.0%). Conclusion The coronavirus disease 2019 (COVID-19) Reporting and Data System (CO-RADS) is a categorical assessment scheme for pulmonary involvement of COVID-19 at unenhanced chest CT that performs very well in predicting COVID-19 in patients with moderate to severe symptoms and has substantial interobserver agreement, especially for categories 1 and 5. © RSNA, 2020 Online supplemental material is available for this article.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnostic imaging , Pneumonia, Viral/diagnostic imaging , Tomography, X-Ray Computed/standards , Adult , Aged , Communication , Female , Humans , Lung/diagnostic imaging , Male , Middle Aged , Netherlands , Observer Variation , Pandemics , Radiology Information Systems , Reverse Transcriptase Polymerase Chain Reaction/methods , Tomography, X-Ray Computed/methods
18.
Jpn J Infect Dis ; 73(4): 304-307, 2020 07 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
19.
Int J Mol Med ; 46(3): 957-964, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-676117

ABSTRACT

Reverse transcription­quantitative polymerase chain reaction (RT­qPCR) is the gold standard method for the diagnosis of COVID­19 infection. Due to pre­analytical and technical limitations, samples with low viral load are often misdiagnosed as false­negative samples. Therefore, it is important to evaluate other strategies able to overcome the limits of RT­qPCR. Blinded swab samples from two individuals diagnosed positive and negative for COVID­19 were analyzed by droplet digital PCR (ddPCR) and RT­qPCR in order to assess the sensitivity of both methods. Intercalation chemistries and a World Health Organization (WHO)/Center for Disease Control and Prevention (CDC)­approved probe for the SARS­CoV­2 N gene were used. SYBR­Green RT­qPCR is not able to diagnose as positive samples with low viral load, while, TaqMan Probe RT­qPCR gave positive signals at very late Ct values. On the contrary, ddPCR showed higher sensitivity rate compared to RT­qPCR and both EvaGreen and probe ddPCR were able to recognize the sample with low viral load as positive even at 10­fold diluted concentration. In conclusion, ddPCR shows higher sensitivity and specificity compared to RT­qPCR for the diagnosis of COVID­19 infection in false­negative samples with low viral load. Therefore, ddPCR is strongly recommended in clinical practice for the diagnosis of COVID­19 and the follow­up of positive patients until complete remission.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Humans , Nucleocapsid Proteins/genetics , Pandemics , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
20.
Eur J Radiol ; 130: 109192, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-670315

ABSTRACT

OBJECTIVES: The goal of this study was to assess chest computed tomography (CT) diagnostic accuracy in clinical practice using RT-PCR as standard of reference. METHODS: From March 4th to April 9th 2020, during the peak of the Italian COVID-19 epidemic, we enrolled a series of 773 patients that performed both non-contrast chest CT and RT-PCR with a time interval no longer than a week due to suspected SARS-CoV-2 infection. The diagnostic performance of CT was evaluated according to sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic accuracy, considering RT-PCR as the reference standard. An analysis on the patients with discrepant CT scan and RT-PCR result and on the patient with both negative tests was performed. RESULTS: RT-PCR testing showed an overall positive rate of 59.8 %. CT sensitivity, specificity, PPV, NPV, and accuracy for SARS-CoV-2 infection were 90.7 % [95 % IC, 87.7%-93.2%], 78.8 % [95 % IC, 73.8-83.2%], 86.4 % [95 % IC, 76.1 %-88.9 %], 85.1 % [95 % IC, 81.0 %-88.4] and 85.9 % [95 % IC 83.2-88.3%], respectively. Twenty-five/66 (37.6 %) patients with positive CT and negative RT-PCR results and 12/245 (4.9 %) patients with both negative tests were nevertheless judged as positive cases by the clinicians based on clinical and epidemiological criteria and consequently treated. CONCLUSIONS: In our experience, in a context of high pre-test probability, CT scan shows good sensitivity and a consistently higher specificity for the diagnosis of COVID-19 pneumonia than what reported by previous studies, especially when clinical and epidemiological features are taken into account.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Tomography, X-Ray Computed/methods , Adult , Coronavirus Infections/diagnostic imaging , Female , Humans , Italy , Lung/diagnostic imaging , Male , Middle Aged , Pandemics , Pneumonia, Viral/diagnostic imaging , Reproducibility of Results , Retrospective Studies , Sensitivity and Specificity
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