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COVID, Volume 1, Issue 4 (December 2021) – 10 articles

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Article
Diagnostic Performance of a Rapid Antigen Test Compared with the Reverse Transcription Polymerase Chain Reaction for SARS-CoV-2 Detection in Asymptomatic Individuals Referring to a Drive-in Testing Facility
COVID 2021, 1(4), 784-789; https://doi.org/10.3390/covid1040063 - 17 Dec 2021
Viewed by 445
Abstract
Quick and reliable identification of severe acute respiratory syndrome coronavirus SARS-CoV-2 in the population is required to manage the COVID-19 pandemic. This is a prospective observational study of diagnostic accuracy. Paired swab samples from 317 asymptomatic individuals referring to a drive-in testing facility [...] Read more.
Quick and reliable identification of severe acute respiratory syndrome coronavirus SARS-CoV-2 in the population is required to manage the COVID-19 pandemic. This is a prospective observational study of diagnostic accuracy. Paired swab samples from 317 asymptomatic individuals referring to a drive-in testing facility were tested in parallel by means of the rapid antigen test developed by Jiangsu Bioperfectus Technologies and routine nucleic acid detection. Overall specificity was 100% and sensitivity was 49% but reached 87% at higher viral loads (Ct < 25). In this study, the antigen detection test showed high specificity and good sensitivity in asymptomatic individuals carrying higher viral loads. The assay performance worsened with lower viral loads, making it useful when a rapidly deployable test is essential and to assess a potential risk of immediate transmission in the community, but not recommended for testing asymptomatic individuals. Full article
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Article
Evaluation of an Antigen Detection Rapid Diagnostic Test for Detection of SARS-CoV-2 in Clinical Samples
COVID 2021, 1(4), 775-783; https://doi.org/10.3390/covid1040062 - 17 Dec 2021
Viewed by 302
Abstract
Antigen detection rapid diagnostic tests have been developed for first-line large-scale screening given their rapidity, simplicity, and accuracy. This study evaluates the diagnostic performance of an antigen detection rapid diagnostic test (BLOK BioScience, London, UK) detecting SARS-CoV-2 nucleocapsid protein. Serially diluted SARS-CoV-2 isolate [...] Read more.
Antigen detection rapid diagnostic tests have been developed for first-line large-scale screening given their rapidity, simplicity, and accuracy. This study evaluates the diagnostic performance of an antigen detection rapid diagnostic test (BLOK BioScience, London, UK) detecting SARS-CoV-2 nucleocapsid protein. Serially diluted SARS-CoV-2 isolate and 110 NPS from COVID-19 patients were tested to determine the test’s sensitivity, and other viral isolates and 20 NPS from non-infected individuals were, for specificity, also tested. Ten clinical samples from COVID-19 patients with SARS-CoV-2 variants, including alpha, beta, gamma, delta, and eta variants, were collected to evaluate the test’s potential application in detecting emerging variants. Overall sensitivity was 92%, and stratifying into viral loads yielded 100% for Ct < 25 samples including SARS-CoV-2 variants, but 11.11% for Ct ≥ 30 samples. The analytical sensitivity of log10 TCID50/mL 2.0 was identified for SARS-CoV-2. Ninety-seven percent specificity with only SARS-CoV cross-reactivity lead to the Youden index of 0.89. The rapid diagnostic test has a high sensitivity for detecting SARS-CoV-2 in high viral load samples, possibly including emerging SARS-CoV-2 variants, but reduced sensitivity in low viral load samples suggests its optimized usage as a complementary testing method to other tests, including RT-PCR or a point-of-care test for large-scale screening, particularly for pandemic areas or airport border infection control. Full article
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Article
Computational Study of the Therapeutic Potential of Novel Heterocyclic Derivatives against SARS-CoV-2
COVID 2021, 1(4), 757-774; https://doi.org/10.3390/covid1040061 - 16 Dec 2021
Viewed by 429
Abstract
Severe Acute Respiratory Syndrome Coronavirus- 2 (SARS-CoV-2), including the recently reported severe variant B.1.617.2, has been reported to attack the respiratory tract with symptoms that may ultimately lead to death. While studies have been conducted to evaluate therapeutic interventions against the virus, this [...] Read more.
Severe Acute Respiratory Syndrome Coronavirus- 2 (SARS-CoV-2), including the recently reported severe variant B.1.617.2, has been reported to attack the respiratory tract with symptoms that may ultimately lead to death. While studies have been conducted to evaluate therapeutic interventions against the virus, this study evaluated the inhibitory potential of virtually screened novel derivatives and structurally similar compounds towards SARS-CoV-2 via a computational approach. A molecular docking simulation of the inhibitory potentials of the compounds against the SARS-CoV-2 drug targets—main protease (Mpro), spike protein (Spro), and RNA-dependent RNA polymerase (RdRp)—were evaluated and achieved utilizing AutoDock Vina in PyRx workspace. The absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of these compounds were assessed using SwissADME and ADMETLab servers. All the compounds displayed high binding affinities for the SARS-CoV-2 drug targets. However, the C13 exhibited the highest binding affinity for the drug targets, Spro and RdRp, while C15 exhibited the highest binding affinity for Mpro. The compounds interacted with the LEU A:271, LEU A:287, ASP A:289, and LEU A:272 of Mpro and the HIS A:540, PRO A:415, PHE A:486, and LEU A:370 of the Spro receptor binding motif and some active site amino acids of RdRp. The compounds also possess a favourable ADMET profile and showed no tendency towards hERG inhibition, hepatotoxicity, carcinogenicity, mutagenicity, or drug-liver injury. These novel compounds could offer therapeutic benefits against SARS-CoV-2, and wet laboratory experiments are necessary to further validate the results of this computational study. Full article
(This article belongs to the Topic Broad-Spectrum Antiviral Agents)
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Brief Report
Causes of Death during the First COVID-19 Pandemic Wave in Italy: A Comparison with Some European Countries
COVID 2021, 1(4), 751-756; https://doi.org/10.3390/covid1040060 - 16 Dec 2021
Viewed by 622
Abstract
Studies comparing cause-of-death patterns across countries during the COVID-19 outbreak are still lacking although such studies would contribute to the understanding of the direct and indirect effect of the virus on mortality. In this report, we compare the mortality pattern observed in Italy [...] Read more.
Studies comparing cause-of-death patterns across countries during the COVID-19 outbreak are still lacking although such studies would contribute to the understanding of the direct and indirect effect of the virus on mortality. In this report, we compare the mortality pattern observed in Italy during the first pandemic wave (March–April 2020) with that of some European countries. We calculated cause-specific, age-standardized mortality ratios (SMR) for Spain, England, and Sweden for the two mentioned months from 2016 to 2020, using already published data. Although Italy presented the highest crude overall mortality rate (267 per 100,000 population), age-adjusted ratios showed that all-cause and COVID-19 mortality in Italy were higher than in Sweden but lower than in the other two countries. Some causes had a similar increase in 2020 compared to previous years in all countries, i.e., endocrine diseases (especially diabetes), dementia and Alzheimer’s (in general mental disorders), and hypertensive heart diseases. Conversely, respiratory diseases, in particular pneumonia and influenza, increased to a greater extent in Italy. This latter result could be, in part, related to the underreporting of COVID-19 on death certificates during the first period of the pandemic, when Italy was the first European country severely hit by the virus. Full article
(This article belongs to the Topic Burden of COVID-19 in Different Countries)
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Article
A Descriptive Analysis of the Impact of COVID-19 on Emergency Department Attendance and Visit Characteristics in Singapore
COVID 2021, 1(4), 739-750; https://doi.org/10.3390/covid1040059 - 06 Dec 2021
Viewed by 507
Abstract
Background: The coronavirus disease 2019 (COVID-19) has impacted the utilisation of Emergency Department (ED) services worldwide. This study aims to describe the changes in attendance at a single ED and corresponding patient visit characteristics before and during the COVID-19 period. Methods: In a [...] Read more.
Background: The coronavirus disease 2019 (COVID-19) has impacted the utilisation of Emergency Department (ED) services worldwide. This study aims to describe the changes in attendance at a single ED and corresponding patient visit characteristics before and during the COVID-19 period. Methods: In a single-centre retrospective cohort study, we used descriptive statistics to compare ED attendance, patient demographics and visit characteristics during the COVID-19 period (1 January–28 June 2020) and its corresponding historical period in 2019 (2 January–30 June 2019). Results: The mean ED attendance decreased from 342 visits/day in the pre-COVID-19 period to 297 visits/day in the COVID-19 period. This was accompanied by a decline in presentations in nearly every ICD-10-CM diagnosis category except for respiratory-related diseases. Notably, we observed reductions in visits by critically ill patients and severe disease presentations during the COVID-19 period. We also noted a shift in the ED patient case-mix from ‘Non-fever’ cases to ‘Fever’ cases, likely giving rise to two distinct trough-to-peak visit patterns during the pre-Circuit Breaker and Circuit Breaker period. Conclusions: This descriptive study revealed distinct ED visit trends across different time periods. The COVID-19 pandemic caused a reduction in ED attendances amongst patients with low-acuity conditions and those with highest priority for emergency care. This raises concern about treatment-seeking delays and the possible impact on health outcomes. The downward trend in low-acuity presentations also presents learning opportunities for ED crowd management planning in a post-COVID-19 era. Full article
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Article
Combining International Survey Datasets to Identify Indicators of Stress during the COVID-19 Pandemic: A Machine Learning Approach to Improve Generalization
COVID 2021, 1(4), 728-738; https://doi.org/10.3390/covid1040058 - 01 Dec 2021
Viewed by 614
Abstract
The scale and duration of the worldwide SARS-COVID-2 virus-related quarantine measures presented the global scientific community with a unique opportunity to study the accompanying psychological stress. Since March 2020, numerous publications have reported similar findings from diverse international studies on psychological stress, depression, [...] Read more.
The scale and duration of the worldwide SARS-COVID-2 virus-related quarantine measures presented the global scientific community with a unique opportunity to study the accompanying psychological stress. Since March 2020, numerous publications have reported similar findings from diverse international studies on psychological stress, depression, and anxiety, which have increased during this pandemic. However, there remains a gap in interpreting the results from one country to another despite the global rise in mental health problems. The objective of our study was to identify global indicators of pandemic-related stress that traverse geographic and cultural boundaries. We amalgamated data from two independent global surveys across twelve countries and spanning four continents collected during the first wave of the mandated public health measures aimed at mitigating COVID-19. We applied machine learning (ML) modelling to these data, and the results revealed a significant positive correlation between PSS-10 scores and gender, relationship status, and groups. Confinement, fear of contagion, social isolation, financial hardship, etc., may be some reasons reported being the cause of the drastic increase in mental health problems worldwide. The decline of the typical protective factors (e.g., sleep, exercise, meditation) may have amplified existing vulnerabilities/co-morbidities (e.g., psychiatric history, age, gender). Our results further show that ML is an apropos tool to elucidate the underlying predictive factors in large, complex, heterogeneous datasets without invalidating the model assumptions. We believe our model provides clinicians, researchers, and decision-makers with evidence to investigate the moderators and mediators of stress and introduce novel interventions to mitigate the long-term effects of the COVID-19 pandemic. Full article
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Article
How to Implement Safe, Efficient and Cost-Effective SARS-CoV-2 Testing in Urban and Rural Schools within One Month
COVID 2021, 1(4), 717-727; https://doi.org/10.3390/covid1040057 - 30 Nov 2021
Viewed by 542
Abstract
(1) Background: With vaccination and new variants of SARS-CoV-2 on the horizon, efficient testing in schools may enable prevention of mass infection outbreaks, keeping schools safe places and buying time until decisions on feasibility and the necessity of vaccination in children and youth [...] Read more.
(1) Background: With vaccination and new variants of SARS-CoV-2 on the horizon, efficient testing in schools may enable prevention of mass infection outbreaks, keeping schools safe places and buying time until decisions on feasibility and the necessity of vaccination in children and youth are made. We established, in the course of the WICOVIR (Where Is the COrona VIRus) study, that gargle-based pool-PCR testing offers a feasible, efficient, and safe testing system for schools in Germany when applied by central university laboratories. (2) Objectives: We evaluated whether this approach can be implemented in different rural and urban settings. (3) Methods: We assessed the arrangements required for successful implementation of the WICOVIR approach in a variety of settings in terms of transport logistics, data transfer and pre-existing laboratory set-up, as well as the time required to establish the set-up. (4) Results: We found that once regulatory issues have been overcome, all challenges pertaining to logistics, data transfer, and laboratory testing on different platforms can be solved within one month. Pooling and depooling of samples down to the individual test result were achievable within one working day in all settings. Local involvement of the community and decentralized set-ups were keys for success. (5) Conclusion: The WICOVIR gargle-based pool-PCR system is so robust and simple that it can be implemented within one month in all settings now or in future pandemics. Full article
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Article
Impacts of the COVID-19 Pandemic on Children and Families from Marginalized Groups: A Qualitative Study in Kingston, Ontario
COVID 2021, 1(4), 704-716; https://doi.org/10.3390/covid1040056 - 30 Nov 2021
Viewed by 543
Abstract
The COVID-19 pandemic has been associated with unprecedented changes to societal structure. School closures, unstable employment, and inaccessible health services have caused enormous disruptions to child and family wellbeing. This study identifies major themes illustrating how child and family wellness were impacted by [...] Read more.
The COVID-19 pandemic has been associated with unprecedented changes to societal structure. School closures, unstable employment, and inaccessible health services have caused enormous disruptions to child and family wellbeing. This study identifies major themes illustrating how child and family wellness were impacted by COVID-19, including unique effects experienced by Indigenous families. In-depth interviews were conducted with key informants (n = 31) recruited from organizations providing healthcare and social services in Kingston, Ontario. Interview transcripts and written survey responses were analyzed using a phenomenological approach to explore themes related to child and family wellbeing. Three major themes identified include school closures, home safety, and outdoor spaces. School closures were generally reported as negatively impacting learning and social development; however, school closures allowed for some Indigenous children to be removed from a colonized education system, contributing to cultural and spiritual growth. Second, respondents reported increased severity and frequency of domestic violence, which negatively impacted child wellbeing. Third, the closure of public outdoor spaces created barriers to maintaining good physical health for children. This study recommends the prioritization of (1) child learning and development by avoiding school closures in pandemic settings and (2) the safety of Indigenous students by decolonizing education. To address the increased exposure to adverse childhood experiences (ACEs) during COVID-19, we recommend improved training for identifying and reporting domestic violence amongst service providers. Our study also reflects the broader need to redefine “essential services”, considering culturally specific services for Indigenous Peoples. Full article
Article
A General Computational Framework for COVID-19 Modelling with Applications to Testing Varied Interventions in Education Environments
COVID 2021, 1(4), 674-703; https://doi.org/10.3390/covid1040055 - 30 Nov 2021
Viewed by 477
Abstract
We construct a spatially-compartmental, individual-based model of the spread of SARS-CoV-2 in indoor spaces. The model can be used to predict the infection rates in a variety of locations when various non-pharmaceutical interventions (NPIs) are introduced. Tasked by the Welsh Government, we apply [...] Read more.
We construct a spatially-compartmental, individual-based model of the spread of SARS-CoV-2 in indoor spaces. The model can be used to predict the infection rates in a variety of locations when various non-pharmaceutical interventions (NPIs) are introduced. Tasked by the Welsh Government, we apply the model to secondary schools and to Further and Higher Education environments. Specifically, we consider student populations mixing in a classroom and in halls of residence. We focus on assessing the potential efficacy of Lateral Flow Devices (LFDs) when used in broad-based screens for asymptomatic infection or in ‘test-to-release’ scenarios in which individuals who have been exposed to infection are released from isolation after a negative LFD result. LFDs are also compared to other NPIs; we find that, although LFD testing can be used to mitigate the spread of SARS-CoV-2, it is more effective to invest in personal protective equipment, e.g., masks, and in increasing ventilation quality. In addition, we provide an open-access and user-friendly online applet that simulates the model, complete with user tutorials to encourage the use of the model to aid educational policy decisions as input infection data becomes available. Full article
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Communication
The Analyses of High Infectivity Mechanism of SARS-CoV-2 and Its Variants
COVID 2021, 1(4), 666-673; https://doi.org/10.3390/covid1040054 - 24 Nov 2021
Viewed by 593
Abstract
SARS-CoV-2 has high infectivity and some of its variants have higher transmissibility. To explore the high infectivity mechanism, the charge distributions of SARS-CoV, SARS-CoV-2, and variants of concern were calculated through a series of net charge calculation formulas. The results showed that the [...] Read more.
SARS-CoV-2 has high infectivity and some of its variants have higher transmissibility. To explore the high infectivity mechanism, the charge distributions of SARS-CoV, SARS-CoV-2, and variants of concern were calculated through a series of net charge calculation formulas. The results showed that the SARS-CoV-2 spike protein had more positive charges than that of SARS-CoV. Further results showed that the variants had similar but higher positive charges than preexisting SARS-CoV-2. In particular, the Delta variant had the greatest increase in positive charges in S1 resulting in the highest infectivity. In particular, the S1 positive charge increased greatly in the Delta variant. The S1 positive charge increased, and due to the large negative charge of angiotensin-converting enzyme-2 (ACE2), this resulted in a large increase in Coulomb’s force between S1 and ACE2. This finding agrees with the expectation that the positive charges in the spike protein result in more negative charges on SARS-CoV-2 antibodies than that of SARS-CoV. Thus, the infectivity of a novel SARS-CoV-2 variant may be evaluated preliminarily by calculating the charge distribution. Full article
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