scholarly journals Pooling of samples to optimize SARS-CoV-2 diagnosis by RT-qPCR: comparative analysis of two protocols.

2020 ◽  
Author(s):  
Fabiana Volpato ◽  
Daiana Lima-Morales ◽  
Priscila Lamb Wink ◽  
Julia Willig ◽  
Fernanda de-Paris ◽  
...  
Keyword(s):  
Large Scale ◽  
Diagnostic Yield ◽  
Rna Extraction ◽  
Clinical Samples ◽  
The Novel ◽  
Positive Individual ◽  
Sample Pooling ◽  
Novel Coronavirus ◽  
The Individual ◽  
Pooled Samples

RT-qPCR for SARS-CoV-2 is the main diagnostic test used to identify the novel coronavirus. Several countries have used large scale SARS-CoV-2 RT-qPCR testing as one of the important strategies for combating the pandemic. In order to process the massive needs for coronavirus testing, the usual throughput of routine clinical laboratories has reached and often surpassed its limits and new approaches to cope with this challenge must be developed. This study has aimed to evaluate the use pool of samples as a strategy to optimize the diagnostic of SARS-CoV-2 by RT-qPCR in a general population. A total of 220 naso/orofaryngeal swab samples were collected and tested using two different protocols of sample pooling. In the first protocol (Protocol A); 10 clinical samples were pooled before RNA extraction. The second protocol (Protocol B) consisted of pooling the already extracted RNAs from 10 individual samples. Results from Protocol A were identical (100% agreement) with the individual results. However, for results from Protocol B, reduced agreement (91%) was observed in relation to results obtained by individual testing. Inconsistencies observed were related to RT-qPCR results with higher Cycle Thresholds (Ct > 32.73). Furthermore, in pools containing more than one positive individual, the Ct of the pool was equivalent to the lowest Ct among the individual results. These results provide additional evidence in favor of the clinical use of pooled samples for SARS-CoV-2 diagnosis by RT-qPCR and suggest that pooling of samples before RNA extraction is preferrable in terms of diagnostic yield.

scholarly journals Swab pooling for large-scale RT-qPCR screening of SARS-CoV-2

2020 ◽  
Author(s):  
Ana Paula Christoff ◽  
Giuliano Netto Flores Cruz ◽  
Aline Fernanda Rodrigues Sereia ◽  
Dellyana Rodrigues Boberg ◽  
Daniela Carolina de Bastiani ◽  
...  
Keyword(s):  
Large Scale ◽  
Sample Collection ◽  
Laboratory Capacity ◽  
Positive Individual ◽  
Sample Pooling ◽  
Pooling Strategies ◽  
Low Prevalence ◽  
Pooled Samples ◽  
Sample Dilution ◽  
Large Scale Screening

Pool testing has been proposed as an alternative for large-scale SARS-CoV-2 screening. However, dilution factors proportional to the number of pooled samples have been a source of major concern regarding its diagnostic performance. Further, sample pooling can lead to increased laboratory workload and operational complexity. Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. Here, we describe a pooling procedure in which nasopharyngeal swabs are pooled together at the time of sample collection (swab pooling), decreasing laboratory manipulation and minimizing dilution of the viral RNA present in the samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individual tests. Having individual testing as a reference, no false-positives or false-negatives were observed for swab pooling. A Bayesian model estimated a sensitivity of 99% (Cr.I. 96.9% to 100%) and a specificity of 99.8% (Cr.I. 99.4% to 100%) for the swab pooling procedure. Data from additional 18,922 patients screened with swab pooling were included for further quantitative analysis. Mean Cq differences between individual and corresponding pool samples ranged from 0.1 Cq (Cr.I. -0.98 to 1.17) to 2.09 Cq (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic and presymptomatic patients were screened using 4,400 RT-qPCR assays, resulting in 246 positive patients (positivity rate 1.26%). This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Finally, these data demonstrate that swab pooling can significantly minimize sample dilution and sensitivity issues commonly seen in its traditional counterpart. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.

scholarly journals High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads

2020 ◽  
Author(s):  
Mahesh K. R. Kalikiri ◽  
Mohammad Rubayet Hasan ◽  
Faheem Mirza ◽  
Thabisile Xaba ◽  
Patrick Tang ◽  
...  
Keyword(s):  
Large Scale ◽  
Solid Phase ◽  
Rna Extraction ◽  
Viral Rna ◽  
The Novel ◽  
Care Workers ◽  
Large Scale Testing ◽  
Viral Transport Medium ◽  
Accredited Laboratory ◽  
Novel Coronavirus

ABSTRACTThe ongoing pandemic of the novel coronavirus, SARS-CoV-2, has led to a global surge in laboratory testing for the virus. The gold standard approach to detecting an active viral infection is the use of RT-qPCR. This approach requires the isolation of viral RNA from respiratory specimens, such as nasopharyngeal swabs.We developed a method using a widely available lysis buffer coupled with solid-phase reverse immobilization (SPRI) beads to extract viral RNA from swabs collected in viral transport medium (VTM) which can be performed manually or on a Hamilton STAR liquid-handling robot. Using a WHO recommended, laboratory-developed RT-qPCR for SARS-CoV-2, we validated this method in a CAP-accredited laboratory, against the IVD-labelled bioMérieux NucliSENS easyMAG automated extraction platform.Our method demonstrates a comparable sensitivity and specificity, making it suitable for large-scale testing and monitoring of suspected COVID-19 cases and health care workers. This is especially important as the world faces critical shortages of viral RNA extraction reagents for the existing commercial extraction systems.

scholarly journals Multi-Objective Optimization of Integrated Civilian-Military Scheduling of Medical Supplies for Epidemic Prevention and Control

Healthcare ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 126
Author(s):  
Hai-Feng Ling ◽  
Zheng-Lian Su ◽  
Xun-Lin Jiang ◽  
Yu-Jun Zheng
Keyword(s):  
Prevention And Control ◽  
Large Scale ◽  
Medical Services ◽  
The Novel ◽  
Multi Objective ◽  
Medical Supplies ◽  
Problem Instances ◽  
Novel Coronavirus ◽  
And Control ◽  
Minimum Ratio

In a large-scale epidemic, such as the novel coronavirus pneumonia (COVID-19), there is huge demand for a variety of medical supplies, such as medical masks, ventilators, and sickbeds. Resources from civilian medical services are often not sufficient for fully satisfying all of these demands. Resources from military medical services, which are normally reserved for military use, can be an effective supplement to these demands. In this paper, we formulate a problem of integrated civilian-military scheduling of medical supplies for epidemic prevention and control, the aim of which is to simultaneously maximize the overall satisfaction rate of the medical supplies and minimize the total scheduling cost, while keeping a minimum ratio of medical supplies reservation for military use. We propose a multi-objective water wave optimization (WWO) algorithm in order to efficiently solve this problem. Computational results on a set of problem instances constructed based on real COVID-19 data demonstrate the effectiveness of the proposed method.

scholarly journals Understanding the Anticontagion Process and Reopening of China during COVID-19 via Coevolution Network of Epidemic and Awareness

Complexity ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Lingbo Li ◽  
Ying Fan ◽  
An Zeng ◽  
Zengru Di
Keyword(s):  
Large Scale ◽  
The Novel ◽  
Large Scale Data ◽  
Effective Interventions ◽  
Human Movements ◽  
Simulation Based ◽  
The World ◽  
Novel Coronavirus ◽  
Prevention Methods ◽  
The Impact

The novel coronavirus (COVID-19) pandemic is intensifying all over the world, but some countries, including China, have developed extensive and successful experience in controlling this pandemic. In this context, some questions arise naturally: What can countries caught up in the epidemic learn from China’s experience? In regions where the outbreak is under control, what would lead to a resurgence of the epidemic? To address these issues, we investigate China’s experience in anticontagion interventions and reopening process, focusing on the coevolution of epidemic and awareness during COVID-19 outbreak. Through an empirical analysis based on large-scale data and simulation based on a metapopulation and multilayer network model, we ascertain the impact of human movements and awareness diffusion on the epidemic, elucidate the inherent patterns and effective interventions of different epidemic prevention methods, and highlight the crunch time of each measure. The results are also employed to analyze COVID-19 evolution in other countries so as to find unified rules in complex situations around the world and provide advice on anticontagion and reopening policies. Our findings explain some key mechanisms of epidemic prevention and may help the epidemic analysis and decision-making in various countries suffering from COVID-19.

scholarly journals Who Should Get Vaccinated First? An effective Network Information-driven Priority Vaccination Strategy

2021 ◽  
Author(s):  
Dong Liu ◽  
Chi Kong Tse ◽  
Rosa H. M. Chan ◽  
Choujun Zhan
Keyword(s):  
Large Scale ◽  
Early Stage ◽  
Vaccination Strategy ◽  
Cumulative Number ◽  
The Novel ◽  
Vaccination Programs ◽  
Network Information ◽  
Network Properties ◽  
Effective Network ◽  
Novel Coronavirus

Abstract Approval of emergency use of the Novel Coronavirus Disease 2019 (COVID-19) vaccines in many countries has brought hope to ending the COVID-19 pandemic sooner. Considering the limited vaccine supply in the early stage of COVID-19 vaccination programs in most countries, a highly relevant question to ask is: who should get vaccinated first? In this article we propose a network information- driven vaccination strategy where a small number of people in a network (population) are categorized, according to a few key network properties, into priority groups. Using a network-based SEIR model for simulating the pandemic progression, the network information-driven vaccination strategy is compared with a random vaccination strategy. Results for both large-scale synthesized networks and real social networks have demonstrated that the network information-driven vaccination strategy can significantly reduce the cumulative number of infected individuals and lead to a more rapid containment of the pandemic. The results provide insight for policymakers in designing an effective early-stage vaccination plan.

scholarly journals Pharmacotherapy for COVID-19: A Ray of Hope

2021 ◽  
Author(s):  
Mayank Kapoor ◽  
Prasan Kumar Panda ◽  
Vivek Mohanty
Keyword(s):  
Large Scale ◽  
Kinase Inhibitors ◽  
Viral Infections ◽  
Treatment Options ◽  
Interferon Alfa ◽  
The Novel ◽  
Plasma Therapy ◽  
Therapeutic Drugs ◽  
Novel Coronavirus ◽  
Multiple Drugs

Most viral infections have limited treatment options available and the same holds for COVID-19, its causative agent being the SARS-CoV-2 virus. Drugs used in the past against Severe Acute Respiratory Syndrome (SARS) or Middle East Respiratory Syndrome (MERS) viruses, which belong to the same family of viruses as the novel Coronavirus included ribavirin, interferon (alfa and beta), lopinavir-ritonavir combination, and corticosteroids. There remains controversy regarding their efficacy to date, except for the last one. Hence, large-scale multicentric trials are being conducted involving multiple drugs. Chloroquine and hydroxy-chloroquine were initially taking the race ahead but have now been rejected. Remdesivir was a promising candidate, for which the FDA had issued an emergency use authorization, but now is not recommended by the WHO. Convalescent plasma therapy had promising results in the early severe viremia phase, but the PLACID trial made an obscure end. Only corticosteroids have shown demonstrable benefits in improving mortality rates among severe COVID-19 cases. Many new modalities like monoclonal antibodies and tyrosine kinase inhibitors are discussed. In this chapter, we review the therapeutic drugs under investigation for the COVID-19 treatment, their mode of action, degree of effectiveness, and recommendations by different centers regarding their use in current settings.

scholarly journals A Study on Effectiveness of Online Learning System during COVID-19 in Sargodha

2020 ◽  
Vol 2 (4) ◽  
pp. 122-137
Author(s):  
Ijaz Hussain Ijaz Hussain ◽  
Rana Muhammad Basharat Saeed ◽  
Ali Furqan Syed
Keyword(s):  
Online Learning ◽  
Statistical Design ◽  
Learning System ◽  
Educational Institutions ◽  
The Novel ◽  
Efficient System ◽  
Individual Perception ◽  
The World ◽  
Novel Coronavirus ◽  
The Individual

The novel coronavirus (COVID-19) is known to be the worst pandemic on the planet which has not only affected humankind very severely but also frozen all areas of life on the sphere. The pandemic caused the largest turmoil in the field of education across the world. The conventional system of education has been disrupted resulting in the closure of all educational institutions around the globe. The exams were postponed which made the students more concerned about their academic achievements. The educationists around the world started thinking about some good alternatives for this problem and subsequently considered online learning as the best substitute for conventional learning at educational institutes. The current study was carried out to accentuate the effectiveness of online learning system during the wave of COVID-19. To achieve the objective of the study, two educational institutes, one government and one private institute, were selected in Sargodha through convenient sampling and the individual perception of the participant teachers was documented using questionnaire as the data collection tool. The descriptive and inferential statistical design was followed for the analysis of the data. The overall findings revealed that the online learning was an effective and efficient system of learning to fulfill the educational needs of learners at distant locations. On the whole, the inferences supported the effectiveness of the online learning system during COVID-19.

Neurological symptoms in patients after the novel coronavirus infection COVID-19, determining further rehabilitation strategy

2021 ◽  
pp. 5-12
Author(s):  
Albina Ayratovna Zvegintseva ◽  
Maksim Leonidovich Maksimov
Keyword(s):  
Large Scale ◽  
Neuronal Damage ◽  
Severe Form ◽  
Neurological Symptoms ◽  
The Novel ◽  
Cellular Mechanisms ◽  
Spanish Flu ◽  
Cerebral Reorganization ◽  
Coronavirus Infection ◽  
Novel Coronavirus

Since the Spanish flu in 1918, there has not been such a large-scale pandemic, causing significant damage to the economy of Russia and other countries, as the novel coronavirus infection COVID-19, which began in December 2019. The SARS-CoV-2 virus is highly infectious and can proceed both asymptomatic and in an extremely severe form, especially in the presence of comorbidity. Despite the fact that the clinical picture is associated with respiratory syndrome, long-term neurological symptoms are increasingly observed. In this study, we tried to find out the most pronounced and long-lasting neurological symptoms in the first 6 months after the novel coronavirus infection COVID-19. An important role in the rehabilitation process of this group of patients is played by the strategy of neurocytoprotection, which is aimed at preventing and reducing neuronal damage by affecting the cellular mechanisms of neuroregeneration and cerebral reorganization, which leads not only to structural and metabolic, but also to functional recovery.

scholarly journals Characterizing altruistic motivation in potential volunteers for SARS-CoV-2 challenge trials

2021 ◽  
Author(s):  
Sophie M Rose ◽  
Virginia L Schmit ◽  
Thomas C Darton ◽  
Nir Eyal ◽  
Monica Magalhaes ◽  
...  
Keyword(s):  
Large Scale ◽  
Vaccine Development ◽  
The Novel ◽  
Ethical Concerns ◽  
Risk Seeking ◽  
Economic Vulnerability ◽  
Large Scale Survey ◽  
Novel Coronavirus ◽  
Scientific Questions ◽  
Special Indication

AbstractIn human challenge trials, volunteers are deliberately infected with a pathogen to accelerate vaccine development and answer key scientific questions. In the U.S., preparations for challenge trials with the novel coronavirus are complete, and in the U.K., challenge trials have recently begun. However, ethical concerns have been raised about the potential for invalid consent or exploitation. These concerns largely reflect worries that challenge trial volunteers may be unusually risk-seeking or too economically vulnerable to refuse the payments these trials provide, rather than being motivated primarily by altruistic goals. We conducted the first large-scale survey of intended human challenge trial volunteers and found that SARS-CoV-2 challenge trial volunteers exhibit high levels of altruistic motivations without any special indication of poor risk perception or economic vulnerability. Findings indicate that challenge trials with the novel coronavirus can attract volunteers with background conditions, attitudes, and motivations that should allay key ethical concerns.

scholarly journals Preparation for Quarantine on the Cruise Ship Diamond Princess in Japan due to COVID-19 (Preprint)

2020 ◽  
Author(s):  
Yoshihiro Yamahata ◽  
Ayako Shibata
Keyword(s):  
Large Scale ◽  
Emerging Infectious Diseases ◽  
The Novel ◽  
Cruise Ship ◽  
Rt Pcr ◽  
Ventilator Support ◽  
Cruise Ships ◽  
Asymptomatic Patients ◽  
The Future ◽  
Novel Coronavirus

BACKGROUND Japan implemented a large-scale quarantine on the Diamond Princess cruise ship in an attempt to control the spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in February 2020. OBJECTIVE We aim to describe the medical activities initiated and difficulties in implementing quarantine on a cruise ship. METHODS Reverse transcription–polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 were performed for all 3711 people (2666 passengers and 1045 crew) on board. RESULTS Of those tested, 696 (18.8%) tested positive for coronavirus disease (COVID-19), of which 410 (58.9%) were asymptomatic. We also confirmed that 54% of the asymptomatic patients with a positive RT-PCR result had lung opacities on chest computed tomography. There were many difficulties in implementing quarantine, such as creating a dividing traffic line between infectious and noninfectious passengers, finding hospitals and transportation providers willing to accept these patients, transporting individuals, language barriers, and supporting daily life. As of March 8, 2020, 31 patients (4.5% of patients with positive RT-PCR results) were hospitalized and required ventilator support or intensive care, and 7 patients (1.0% of patients with positive RT-PCR results) had died. CONCLUSIONS There were several difficulties in implementing large-scale quarantine and obtaining medical support on the cruise ship. In the future, we need to prepare for patients’ transfer and the admitting hospitals when disembarking the passengers. We recommend treating the crew the same way as the passengers to control the infection. We must also draw a plan for the future, to protect travelers and passengers from emerging infectious diseases on cruise ships.

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