This version of BIP! Finder aims to ease the exploration of COVID-19-related literature by enabling ranking articles based on various impact metrics.
Last Update: 18 - 01 - 2023 (628506 entries)
Popularity: Citation-based measure reflecting the current impact.
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*More details on these impact measures can be found here.
Exceptional score (in top 0.01%).
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CORD-19 dataset(1) (list of papers)
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| Title | Venue | Year | Impact | Source | |
|---|---|---|---|---|---|
| 2751 | Clinical Characteristics and Outcomes Among Adults Hospitalized with Laboratory-Confirmed SARS-CoV-2 Infection During Periods of B.1.617.2 (Delta) and B.1.1.529 (Omicron) Variant Predominance-One Hospital, California, July 15-September 23, 2021 and December 21, 2021-January 27, 2022 In mid-December 2021, the B.1.1.529 (Omicron) variant of SARS-CoV-2, the virus that causes COVID-19, surpassed the B.1.617.2 (Delta) variant as the predominant strain in California. Initial reports suggest that the Omicron variant is more transmissible and resistant to vaccine neutralization but causes less severe illness compared with previous variants (1-3). To describe characteristics of patients hospitalized with SARS-CoV-2 infection during periods of Delta and Omicron predominance, clinical characteristics and outcomes were retrospectively ed from the electronic health records (EHRs) of adults aged >=18 years with positive reverse transcription-polymerase chain reaction (RT-PCR) SARS-CoV-2 test results admitted to one academic hospital in Los Angeles, California, during July 15-September 23, 2021 (Delta predominant period, 339 patients) and December 21, 2021-January 27, 2022 (Omicron predominant period, 737 patients). Compared with patients during the period of Delta predominance, a higher proportion of adults admitted during Omicron predominance had received the final dose in a primary COVID-19 vaccination series (were fully vaccinated) (39.6% versus 25.1%), and fewer received COVID-19-directed therapies. Although fewer required intensive care unit (ICU) admission and invasive mechanical ventilation (IMV), and fewer died while hospitalized during Omicron predominance, there were no significant differences in ICU admission or IMV when stratified by vaccination status. Fewer fully vaccinated Omicron-period patients died while hospitalized (3.4%), compared with Delta-period patients (10.6%). Among Omicron-period patients, vaccination was associated with lower likelihood of ICU admission, and among adults aged >=65 years, lower likelihood of death while hospitalized. Likelihood of ICU admission and death were lowest among adults who had received a booster dose. Among the first 131 Omicron-period hospitalizations, 19.8% of patients were clinically assessed as admitted for non-COVID-19 conditions. Compared with adults considered likely to have been admitted because of COVID-19, these patients were younger (median age = 38 versus 67 years) and more likely to have received at least one dose of a COVID-19 vaccine (84.6% versus 61.0%). Although 20% of SARS-CoV-2-associated hospitalizations during the period of Omicron predominance might be driven by non-COVID-19 conditions, large numbers of hospitalizations place a strain on health systems. Vaccination, including a booster dose for those who are fully vaccinated, remains critical to minimizing risk for severe health outcomes among adults with SARS-CoV-2 infection. | MMWR Morb Mortal Wkly Rep | 2022 | LitCov and CORD-19 | |
| 2752 | Mental health in the pandemic: a repeated cross-sectional mixed-method study protocol to investigate the mental health impacts of the coronavirus pandemic in the UK INTRODUCTION: The WHO declared a global pandemic on 11 March 2020. Since then, the world has been firmly in the grip of the COVID-19. To date, more than 211 730 035 million confirmed cases and more than 4 430 697 million people have died. While controlling the virus and implementing vaccines are the main priorities, the population mental health impacts of the pandemic are expected to be longer term and are less obvious than the physical health ones. Lockdown restrictions, physical distancing, social isolation, as well as the loss of a loved one, working in a frontline capacity and loss of economic security may have negative effects on and increase the mental health challenges in populations around the world. There is a major demand for long-term research examining the mental health experiences and needs of people in order to design adequate policies and interventions for sustained action to respond to individual and population mental health needs both during and after the pandemic. METHODS AND ANALYSIS: This repeated cross-sectional mixed-method study conducts regular self-administered representative surveys, and targeted focus groups and semi-structured interviews with adults in the UK, as well as validation of gathered evidence through citizens’ juries for contextualisation (for the UK as a whole and for its four devolved nations) to ensure that emerging mental health problems are identified early on and are properly understood, and that appropriate policies and interventions are developed and implemented across the UK and within devolved contexts. STATA and NVIVO will be used to carry out quantitative and qualitative analysis, respectively. ETHICS AND DISSEMINATION: Ethics approval for this study has been granted by the Cambridge Psychology Research Ethics Committee of the University of Cambridge, UK (PRE 2020.050) and by the Health and Life Sciences Research Ethics Committee of De Montfort University, UK (REF 422991). While unlikely, participants completing the self-administered surveys or participating in the virtual focus groups, semi-structured interviews and citizens’ juries might experience distress triggered by questions or conversations. However, appropriate mitigating measures have been adopted and signposting to services and helplines will be available at all times. Furthermore, a dedicated member of staff will also be at hand to debrief following participation in the research and personalised thank-you notes will be sent to everyone taking part in the qualitative research. Study findings will be disseminated in scientific journals, at research conferences, local research symposia and seminars. Evidence-based open access briefings, articles and reports will be available on our study website for everyone to access. Rapid policy briefings targeting issues emerging from the data will also be disseminated to inform policy and practice. These briefings will position the findings within UK public policy and devolved nations policy and socioeconomic contexts in order to develop specific, timely policy recommendations. Additional dissemination will be done through traditional and social media. Our data will be contextualised in view of existing policies, and changes over time as-and-when policies change. | BMJ Open | 2021 | LitCov and CORD-19 | |
| 2753 | Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes. | Virus Res | 2004 | CORD-19 | |
| 2754 | The impact of COVID-19 related lockdown on ophthalmology training programs in India-Outcomes of a survey PURPOSE: In 2020, in response to the emergence and global spread of the disease COVID-19, caused by a new variant of coronavirus 2019-nCoV, the government of India ordered a nationwide lockdown for 21 days, which was then extended to a total of over 50 days. The aim of this study is to assess the effect of the lockdown on ophthalmic training programs across India. METHODS: An online survey was sent across to trainee ophthalmologists across India through various social media platforms. RESULTS: In all, 716 trainees responded; the average age was 29.1 years. Results showed that majority of the respondents were enrolled in residency programs (95.6%; 685/716) and the others were in fellowship programs. About 24.6% (176/716) of the trainees had been deployed on 'COVID-19 screening' duties. Nearly 80.7% (578/716) of the trainees felt that the COVID-19 lockdown had negatively impacted their surgical training. Furthermore, 54.8% (392/716) of the trainees perceived an increase in stress levels during the COVID-19 lockdown and 77.4% (554/716) reported that their family members had expressed an increased concern for their safety and wellbeing since the lockdown began. In all, 75.7% (542/716) of the respondents felt that online classes and webinars were useful during the lockdown period. CONCLUSION: Our survey showed that majority ophthalmology trainees across the country felt that the COVID-19 lockdown adversely affected their learning, especially surgical training. While most found online classes and webinars useful, the trainees' perceived stress levels were higher than normal during the lockdown. Training hospitals should take cognizance of this and reassure trainees; formulate guidelines to augment training to compensate for the lost time as well as mitigate the stress levels upon resumption of regular hospital services and training. Going ahead, permanent changes such as virtual classrooms and simulation-based training should be considered. | Indian J Ophthalmol | 2020 | LitCov and CORD-19 | |
| 2755 | Curricular response to COVID-19: real-time interactive telehealth experience (RITE) program Introduction. The COVID-19 pandemic placed an unprecedented strain on academic healthcare systems necessitating a pause in medical student teaching in clinical care settings, including at Weill Cornell Medicine (WCM). WCM had a preexisting telemedicine curriculum, but limited opportunities for students to apply knowledge and skills related to direct virtual patient care. The authors describe the rapid implementation of real-time interactive telehealth experience (RITE) courses for clerkship students to allow for meaningful engagement in remote patient care and continuation of academic progress during the pause. Methods of Course Development. Medical school administration disseminated a request for proposals for RITE courses conforming to the WCM electives format with rapid turnaround time of 1 week or less. Requirements included remote care activities, goals and objectives, general logistics, supervision methods and standards of achievement. RITE courses were developed in outpatient medicine, inpatient medicine, psychiatry and women’s health. A lottery process was developed to register students for the approved courses. Course Implementation and Evaluation. Using the technical platform and standard course registration process, students were assigned to 74 of 76 available RITE course slots. Students participated in supervised remote direct patient care and also provided critical support for frontline healthcare workers by performing remote clinical tasks. Online teaching and reflection sessions were incorporated into each RITE curricular offering. Student feedback was overall positive ranging from 3.33–4.57 out of 5. Discussion. The COVID-19 pandemic created a need to rapidly incorporate telehealth models in order to continue to deliver patient care and an opportunity to develop innovative remote educational experiences. We developed a framework for structured real-time interactive telehealth experiences to address COVID-19 related curricular needs that will be continued post-COVID-19. This expanded telehealth curriculum for our students will provide standardized training in telehealth logistics, communication techniques, and care delivery now essential for graduating medical students. | Med Educ Online | 2021 | LitCov and CORD-19 | |
| 2756 | Implementation of Telemedicine in a Tertiary Hospital-Based Ambulatory Practice in Detroit During the COVID-19 Pandemic: Observational Study BACKGROUND: The COVID-19 pandemic, caused by SARS-CoV-2, has forced the health care delivery structure to change rapidly. The pandemic has further widened the disparities in health care and exposed vulnerable populations. Health care services caring for such populations must not only continue to operate but create innovative methods of care delivery without compromising safety. We present our experience of incorporating telemedicine in our university hospital–based outpatient clinic in one of the worst-hit areas in the world. OBJECTIVE: Our goal is to assess the adoption of a telemedicine service in the first month of its implementation in outpatient practice during the COVID-19 pandemic. We also want to assess the need for transitioning to telemedicine, the benefits and challenges in doing so, and ongoing solutions during the initial phase of the implementation of telemedicine services for our patients. METHODS: We conducted a prospective review of clinic operations data from the first month of a telemedicine rollout in the outpatient adult ambulatory clinic from April 1, 2020, to April 30, 2020. A telemedicine visit was defined as synchronous audio-video communication between the provider and patient for clinical care longer than 5 minutes or if the video visit converted to a telephone visit after 5 minutes due to technical problems. We recorded the number of telemedicine visits scheduled, visits completed, and the time for each visit. We also noted the most frequent billing codes used based on the time spent in the patient care and the number of clinical tasks (eg, activity suggested through diagnosis or procedural code) that were addressed remotely by the physicians. RESULTS: During the study period, we had 110 telemedicine visits scheduled, of which 94 (85.4%) visits were completed. The average duration of the video visit was 35 minutes, with the most prolonged visit lasting 120 minutes. Of 94 patients, 24 (25.54%) patients were recently discharged from the hospital, and 70 (74.46%) patients were seen for urgent care needs. There was a 50% increase from the baseline in the number of clinical tasks that were addressed by the physicians during the pandemic. CONCLUSIONS: There was a high acceptance of telemedicine services by the patients, which was evident by a high show rate during the COVID-19 pandemic in Detroit. With limited staffing, restricted outpatient work hours, a shortage of providers, and increased outpatient needs, telemedicine was successfully implemented in our practice. | JMIR Public Health Surveill | 2021 | LitCov and CORD-19 | |
| 2757 | The Global Phosphorylation Landscape of SARS-CoV-2 Infection Summary The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here, we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAP kinase activation, production of diverse cytokines, and shutdown of mitotic kinases resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodia protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of p38, CK2, CDKs, AXL and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies. | Cell | 2020 | LitCov and CORD-19 | |
| 2758 | Faster... but fast enough? Responding to the epidemic of severe acute respiratory syndrome N/A | N Engl J Med | 2003 | CORD-19 | |
| 2759 | Deposition distribution of the new coronavirus in the human airways upon exposure to cough-generated droplets and aerosol particles The new coronavirus disease 2019 (COVID-19) has been emerged as a rapidly spreading pandemic. The disease is thought to spread mainly from person-to-person through respiratory droplets produced when an infected person coughs, sneezes, or talks. The pathogen of COVID-19 is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It infects the cells binding to the angiotensin-converting enzyme 2 receptor (ACE2) which is expressed by cells throughout the airways as targets for cellular entry. Although the majority of persons infected with SARS-CoV-2 experience symptoms of mild upper respiratory tract infection, in some people infections of the acinar airways result in severe, potentially fatal pneumonia. However, the induction of COVID-19 pneumonia requires that SARS-CoV-2 reaches the acinar airways. While huge efforts have been made to understand the spread of the disease as well as the pathogenesis following cellular entry, much less attention is paid to how SARS-CoV-2 from the environment reach the receptors of the target cells. The aim of the present study is to characterize the deposition distribution of SARS-CoV-2 in the airways upon exposure to cough-generated droplets and aerosol particles. For this purpose, the Stochastic Lung Deposition Model has been applied. Particle size distribution, breathing parameters supposing normal breathing through the nose, and viral loads were taken from the literature. We found that the probability of direct infection of the acinar airways due to inhalation of particles emitted by a bystander cough is very low. As the number of viruses deposited in the extrathoracic airways is about 7 times higher than in the acinar airways, we concluded that in most cases COVID-19 pneumonia must be preceded by SARS-CoV-2 infection of the upper airways. Our results suggest that without the enhancement of viral load in the upper airways, COVID-19 would be much less dangerous. The period between the onset of initial symptoms and the potential clinical deterioration could provide an opportunity for prevention of pneumonia by blocking or significantly reducing the transport of viruses towards the acinar airways. Therefore, even non-specific treatment forms like disinfection of the throat and nasal and oral mucosa may effectively keep the viral load of the upper airways low enough to avoid or prolong the progression of the disease. In addition, using a tissue or cloth in order to absorb droplets and aerosol particles emitted by own coughs of infected patients before re-inhalation is highly recommended even if they are alone in quarantine. | Sci Rep | 2020 | LitCov and CORD-19 | |
| 2760 | Transport impacts on atmosphere and climate: Aviation Aviation alters the composition of the atmosphere globally and can thus drive climate change and ozone depletion. The last major international assessment of these impacts was made by the Intergovernmental Panel on Climate Change (IPCC) in 1999. Here, a comprehensive updated assessment of aviation is provided. Scientific advances since the 1999 assessment have reduced key uncertainties, sharpening the quantitative evaluation, yet the basic conclusions remain the same. The climate impact of aviation is driven by long-term impacts from CO(2) emissions and shorter-term impacts from non-CO(2) emissions and effects, which include the emissions of water vapour, particles and nitrogen oxides (NO(x)). The present-day radiative forcing from aviation (2005) is estimated to be 55 mW m(−2) (excluding cirrus cloud enhancement), which represents some 3.5% (range 1.3–10%, 90% likelihood range) of current anthropogenic forcing, or 78 mW m(−2) including cirrus cloud enhancement, representing 4.9% of current forcing (range 2–14%, 90% likelihood range). According to two SRES-compatible scenarios, future forcings may increase by factors of 3–4 over 2000 levels, in 2050. The effects of aviation emissions of CO(2) on global mean surface temperature last for many hundreds of years (in common with other sources), whilst its non-CO(2) effects on temperature last for decades. Much progress has been made in the last ten years on characterizing emissions, although major uncertainties remain over the nature of particles. Emissions of NO(x) result in production of ozone, a climate warming gas, and the reduction of ambient methane (a cooling effect) although the overall balance is warming, based upon current understanding. These NO(x) emissions from current subsonic aviation do not appear to deplete stratospheric ozone. Despite the progress made on modelling aviation's impacts on tropospheric chemistry, there remains a significant spread in model results. The knowledge of aviation's impacts on cloudiness has also improved: a limited number of studies have demonstrated an increase in cirrus cloud attributable to aviation although the magnitude varies: however, these trend analyses may be impacted by satellite artefacts. The effect of aviation particles on clouds (with and without contrails) may give rise to either a positive forcing or a negative forcing: the modelling and the underlying processes are highly uncertain, although the overall effect of contrails and enhanced cloudiness is considered to be a positive forcing and could be substantial, compared with other effects. The debate over quantification of aviation impacts has also progressed towards studying potential mitigation and the technological and atmospheric tradeoffs. Current studies are still relatively immature and more work is required to determine optimal technological development paths, which is an aspect that atmospheric science has much to contribute. In terms of alternative fuels, liquid hydrogen represents a possibility and may reduce some of aviation's impacts on climate if the fuel is produced in a carbon-neutral way: such fuel is unlikely to be utilized until a ‘hydrogen economy’ develops. The introduction of biofuels as a means of reducing CO(2) impacts represents a future possibility. However, even over and above land-use concerns and greenhouse gas budget issues, aviation fuels require strict adherence to safety standards and thus require extra processing compared with biofuels destined for other sectors, where the uptake of such fuel may be more beneficial in the first instance. | Atmos Environ (1994) | 2009 | CORD-19 | |
| 2761 | Video consultations for covid-19 N/A | BMJ | 2020 | LitCov and CORD-19 | |
| 2762 | Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease N/A | J Proteome Res | 2020 | LitCov and CORD-19 | |
| 2763 | Longitudinal correlation of biomarkers of cardiac injury, inflammation and coagulation to outcome in hospitalized COVID-19 patients BACKGROUND: Cardiac injury, as measured by troponin elevation, has been reported among hospitalized coronavirus disease 2019 (COVID-19) patients and portends a poor prognosis. However, how the dynamics of troponin elevation interplay with inflammation and coagulation biomarkers over time is unknown. We assessed longitudinal follow-up of cardiac injury, inflammation and coagulation markers in relation to disease severity and outcome. METHODS: We retrospectively assessed 2068 patients with laboratory-confirmed COVID-19 between January 29 and April 1, 2020 at Tongji Hospital in Wuhan, China. We defined cardiac injury as an increase in high sensitivity cardiac troponin-I (hs-cTnI) above the 99th of the upper reference limit. We explored the dynamics of elevation in hs-cTnI and the relationship with inflammation (interleukin [IL]-6, IL-8, IL-10, IL-2 receptor, tumor necrosis factor-α, C-reactive protein) and coagulation (d-dimer, fibrinogen, international normalized ratio) markers in non-critically ill versus critically ill patients longitudinally and further correlated these markers to survivors and non-survivors. RESULTS: Median age was 63 years (first to third quartile 51–70 years), 51.4% of whom were women. When compared to non-critically ill patients (N = 1592, 77.0%), critically ill (defined as requiring mechanical ventilation, in shock or multiorgan failure) patients (N = 476, 23.0%), had more frequent cardiac injury on admission (30.3% vs. 2.3%, p < 0.001), with increased mortality during hospitalization (38.4% vs. 0%, p < 0.001). Among critically ill patients, non-survivors (N = 183) had a continuous increase in hs-cTnI levels during hospitalization, while survivors (N = 293) showed a decrease in hs-cTnI level between day 4 and 7 after admission. Specifically, cardiac injury is an independent marker of mortality among critically ill patients at admission, day 4–7 and 8–14. Consistent positive correlations between hs-cTnI and interleukin (IL)-6 on admission (r = 0.59), day 4–7 (r = 0.66) and day 8–14 (r = 0.61; all p < 0.001) and d-dimer (at the same timepoints r = 0.54; 0.65; 0.61, all p < 0.001) were observed. A similar behavior was observed between hs-cTnI and most of other biomarkers of inflammation and coagulation. CONCLUSIONS: Cardiac injury commonly occurs in critically ill COVID-19 patients, with increased levels of hs-cTnI beyond day 3 since admission portending a poor prognosis. A consistent positive correlation of hs-cTnI with IL-6 and d-dimer at several timepoints along hospitalization could suggest nonspecific cytokine-mediated cardiotoxicity. | J Mol Cell Cardiol | 2020 | LitCov and CORD-19 | |
| 2764 | Management of COVID-19 Respiratory Distress N/A | JAMA | 2020 | LitCov and CORD-19 | |
| 2765 | Use of medical face masks vs particulate respirators as a component of personal protective equipment for Healthcare workers in the context of the COVID-19 pandemic Currently available evidence supports that the predominant route of human-to-human transmission of the SARS-CoV-2 is through respiratory droplets and/or contact routes. The report by the World Health Organization (WHO) Joint Mission on Coronavirus Disease 2019 (COVID-19) in China supports person-to-person droplet and fomite transmission during close unprotected contact with the vast majority of the investigated infection clusters occurring within families, with a household secondary attack rate varying between 3 and 10%, a finding that is not consistent with airborne transmission. The reproduction number (R(0)) for the SARS-CoV-2 is estimated to be between 2.2–2.7, compatible with other respiratory viruses associated with a droplet/contact mode of transmission and very different than an airborne virus like measles with a R(0) widely cited to be between 12 and 18. Based on the scientific evidence accumulated to date, our view is that SARS-CoV-2 is not spread by the airborne route to any significant extent and the use of particulate respirators offers no advantage over medical masks as a component of personal protective equipment for the routine care of patients with COVID-19 in the health care setting. Moreover, prolonged use of particulate respirators may result in unintended harms. In conjunction with appropriate hand hygiene, personal protective equipment (PPE) used by health care workers caring for patients with COVID-19 must be used with attention to detail and precision of execution to prevent lapses in adherence and active failures in the donning and doffing of the PPE. | Antimicrob Resist Infect Contr | 2020 | LitCov and CORD-19 | |
| 2766 | Severe acute respiratory syndrome: identification of the etiological agent The severe acute respiratory syndrome (SARS) emerged in late 2002 in southern China and rapidly spread to countries around the globe. Three research groups within a World Health Organization (WHO)-coordinated network have independently and simultaneously shown that a novel coronavirus is linked to SARS. A fourth group has completed the Koch's postulates by infecting monkeys with the agent. Sequencing of the complete genome was achieved only weeks after the first isolate of the virus became available. | Trends Mol Med | 2003 | CORD-19 | |
| 2767 | Students' Perspective on Online Medical Education Amidst the COVID-19 Pandemic in Nepal N/A | J Nepal Health Res Counc | 2020 | LitCov and CORD-19 | |
| 2768 | Clinical Features of 69 Cases with COVID-19 in Wuhan, China BACKGROUND: From December 2019 to February 2020, 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a serious outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. Related clinical features are needed. METHODS: We reviewed 69 patients who were hospitalized in Union hospital in Wuhan between January 16 to January 29, 2020. All patients were confirmed to be infected with SARS-CoV-2 and the final date of follow-up was February 4, 2020. RESULTS: The median age of 69 enrolled patients was 42.0 years (IQR 35.0-62.0), and 32 patients (46%) were men. The most common symptoms were fever (60[87%]), cough (38[55%]), and fatigue (29[42%]). Most patients received antiviral therapy (66 [98.5%] of 67 patients) and antibiotic therapy (66 [98.5%] of 67 patients). As of February 4, 2020, 18 (26.9%) of 67 patients had been discharged, and five patients had died, with a mortality rate of 7.5%. According to the lowest SpO(2) during admission, cases were divided into the SpO(2)≥90% group (n=55) and the SpO(2)<90% group (n=14). All 5 deaths occurred in the SpO(2)<90% group. Compared with SpO(2)≥90% group, patients of the SpO(2)<90% group were older, and showed more comorbidities and higher plasma levels of IL6, IL10, lactate dehydrogenase, and c reactive protein. Arbidol treatment showed tendency to improve the discharging rate and decrease the mortality rate. CONCLUSIONS: COVID-19 appears to show frequent fever, dry cough, and increase of inflammatory cytokines, and induced a mortality rate of 7.5%. Older patients or those with underlying comorbidities are at higher risk of death. | Clin Infect Dis | 2020 | LitCov and CORD-19 | |
| 2769 | Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. | Nucleic Acids Res | 2015 | CORD-19 | |
| 2770 | Isolation and identification of SARS-coronavirus in nasal and throat swabs collected from clinically diagnosed SARS patients N/A | Zhongguo Yi Xue Ke Xue Yuan Xu | 2003 | CORD-19 | |
| 2771 | The effect of national lockdown due to COVID-19 on emergency department visits BACKGROUND: COVID-19 outbreak lead to nationwide lockdown in Finland on the March 16th, 2020. Previous data regarding to the patient load in the emergency departments during pandemics is scarce. Our aim is to describe the effect of national lockdown and social distancing on the number and reasons for emergency department (ED) visits and inpatient admissions in three large volume hospitals prior to and after the outbreak of the COVID-19 epidemic in Finland. METHODS: Data for this register-based retrospective cohort study were collected from three large ED’s in Finland, covering 1/6 of the Finnish population. All patients visiting ED’s six weeks before and six weeks after the lockdown were included. Pediatric and gynecological patients were excluded. Numbers and reasons for ED visits and inpatient admissions were collected. Corresponding time period in 2019 was used as reference. RESULTS: A total of 40,653 ED visits and 12,226 inpatient admissions were analyzed. The total number of ED visits decreased 16% after the lockdown, whereas the number of inpatient admissions decreased 15% (p < 0.001). This change in inpatient admissions was similar in all participating hospitals. Visits due to back or limb pain decreased 31% and infectious diseases 28%. The visit rate and inpatient admissions due to acute myocardial infarction and strokes remained stable throughout the study period. Interestingly, the rate of inpatient admissions due to psychiatric diagnoses remained unchanged, although the ED visit rate decreased by 19%. The number of ED visits (n = 282) and inpatient admissions (n = 55) due to COVID-19 remained low in the participating hospitals. CONCLUSIONS: Changes in ED visits and inpatient admissions prior to and during the early phase of the COVID-19 outbreak were unpredictable, and our results may help hospitals and especially ED’s focus their resources better. Surprisingly, there was a major decrease in the rate of ED visits due to back or limb pain and not so surprisingly in infectious diseases. Rates of acute myocardial infarctions and cerebral strokes remained stable. In summary, stabile resources for the treatment of patients with severe diseases will be needed in hospitals and ED’s. | Scand J Trauma Resusc Emerg Me | 2020 | LitCov and CORD-19 | |
| 2772 | Living with covid-19 N/A | Psychiatriki | 2020 | LitCov and CORD-19 | |
| 2773 | The Mark Coventry Award: diagnosis of early postoperative TKA infection using synovial fluid analysis N/A | Clin Orthop Relat Res | 2011 | CORD-19 | |
| 2774 | Increase in prevalence of current mental disorders in the context of COVID-19: analysis of repeated nationwide cross-sectional surveys AIMS: The United Nations warned of COVID-19-related mental health crisis; however, it is unknown whether there is an increase in the prevalence of mental disorders as existing studies lack a reliable baseline analysis or they did not use a diagnostic measure. We aimed to analyse trends in the prevalence of mental disorders prior to and during the COVID-19 pandemic. METHODS: We analysed data from repeated cross-sectional surveys on a representative sample of non-institutionalised Czech adults (18+ years) from both November 2017 (n = 3306; 54% females) and May 2020 (n = 3021; 52% females). We used Mini International Neuropsychiatric Interview (MINI) as the main screening instrument. We calculated descriptive statistics and compared the prevalence of current mood and anxiety disorders, suicide risk and alcohol-related disorders at baseline and right after the first peak of COVID-19 when related lockdown was still in place in CZ. In addition, using logistic regression, we assessed the association between COVID-19-related worries and the presence of mental disorders. RESULTS: The prevalence of those experiencing symptoms of at least one current mental disorder rose from a baseline of 20.02 (95% CI = 18.64; 21.39) in 2017 to 29.63 (95% CI = 27.9; 31.37) in 2020 during the COVID-19 pandemic. The prevalence of both major depressive disorder (3.96, 95% CI = 3.28; 4.62 v. 11.77, 95% CI = 10.56; 12.99); and suicide risk (3.88, 95% CI = 3.21; 4.52 v. 11.88, 95% CI = 10.64; 13.07) tripled and current anxiety disorders almost doubled (7.79, 95% CI = 6.87; 8.7 v. 12.84, 95% CI = 11.6; 14.05). The prevalence of alcohol use disorders in 2020 was approximately the same as in 2017 (10.84, 95% CI = 9.78; 11.89 v. 9.88, 95% CI = 8.74; 10.98); however, there was a significant increase in weekly binge drinking behaviours (4.07% v. 6.39%). Strong worries about both, health or economic consequences of COVID-19, were associated with an increased odds of having a mental disorder (1.63, 95% CI = 1.4; 1.89 and 1.42, 95% CI = 1.23; 1.63 respectively). CONCLUSIONS: This study provides evidence matching concerns that COVID-19-related mental health problems pose a major threat to populations, particularly considering the barriers in service provision posed during lockdown. This finding emphasises an urgent need to scale up mental health promotion and prevention globally. | Epidemiol Psychiatr Sci | 2020 | LitCov and CORD-19 | |
| 2775 | Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease N/A | Clin Microbiol Rev | 2015 | CORD-19 | |
| 2776 | Emerging viral infections in a rapidly changing world Emerging viral infections in both humans and animals have been reported with increased frequency in recent years. Recent advances have been made in our knowledge of some of these, including severe acute respiratory syndrome-associated coronavirus, influenza A virus, human metapneumovirus, West Nile virus and Ebola virus. Research efforts to mitigate their effects have concentrated on improved surveillance and diagnostic capabilities, as well as on the development of vaccines and antiviral agents. More attention needs to be given to the identification of the underlying causes for the emergence of infectious diseases, which are often related to anthropogenic social and environmental changes. Addressing these factors might help to decrease the rate of emergence of infectious diseases and allow the transition to a more sustainable society. | Curr Opin Biotechnol | 2003 | CORD-19 | |
| 2777 | A single-cell atlas of the peripheral immune response in patients with severe COVID-19 N/A | Nat Med | 2020 | LitCov and CORD-19 | |
| 2778 | The Many Mechanisms of Viral Membrane Fusion Proteins Every enveloped virus fuses its membrane with a host cell membrane, thereby releasing its genome into the cytoplasm and initiating the viral replication cycle. In each case, one or a small set of viral surface transmembrane glycoproteins mediates fusion. Viral fusion proteins vary in their mode of activation and in structural class. These features combine to yield many different fusion mechanisms. Despite their differences, common principles for how fusion proteins function are emerging: In response to an activating trigger, the metastable fusion protein converts to an extended, in some cases rodlike structure, which inserts into the target membrane via its fusion peptide. A subsequent conformational change causes the fusion protein to fold back upon itself, thereby bringing its fusion peptide and its transmembrane domain—and their attached target and viral membranes—into intimate contact. Fusion ensues as the initial lipid stalk progresses through local hemifusion, and then opening and enlargement of a fusion pore. Here we review recent advances in our understanding of how fusion proteins are activated, how fusion proteins change conformation during fusion, and what is happening to the lipids during fusion. We also briefly discuss the therapeutic potential of fusion inhibitors in treating viral infections. | Membrane Trafficking in Viral | 2005 | CORD-19 | |
| 2779 | In Silico Evaluation of the Effectivity of Approved Protease Inhibitors against the Main Protease of the Novel SARS-CoV-2 Virus The coronavirus disease, COVID-19, caused by the novel coronavirus SARS-CoV-2, which first emerged in Wuhan, China and was made known to the World in December 2019 turned into a pandemic causing more than 126,124 deaths worldwide up to April 16th, 2020. It has 79.5% sequence identity with SARS-CoV-1 and the same strategy for host cell invasion through the ACE-2 surface protein. Since the development of novel drugs is a long-lasting process, researchers look for effective substances among drugs already approved or developed for other purposes. The 3D structure of the SARS-CoV-2 main protease was compared with the 3D structures of seven proteases, which are drug targets, and docking analysis to the SARS-CoV-2 protease structure of thirty four approved and on-trial protease inhibitors was performed. Increased 3D structural similarity between the SARS-CoV-2 main protease, the HCV protease and α-thrombin was found. According to docking analysis the most promising results were found for HCV protease, DPP-4, α-thrombin and coagulation Factor Xa known inhibitors, with several of them exhibiting estimated free binding energy lower than −8.00 kcal/mol and better prediction results than reference compounds. Since some of the compounds are well-tolerated drugs, the promising in silico results may warrant further evaluation for viral anticipation. DPP-4 inhibitors with anti-viral action may be more useful for infected patients with diabetes, while anti-coagulant treatment is proposed in severe SARS-CoV-2 induced pneumonia. | Molecules | 2020 | LitCov and CORD-19 | |
| 2780 | Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons The acute respiratory illnesses are the most common type of acute illness in the United States today. The respiratory viruses—which include influenza viruses, parainfluenza viruses, respiratory syncytial virus (RSV), rhinoviruses, coronaviruses, and adenoviruses—cause the majority of these illnesses. Some of these viruses cause illness throughout the year, whereas others are most common in winter. All population groups experience these infections and illnesses. As the number of elderly persons and those with underlying disease increases, awareness is growing that these common infections can have serious consequences. This has recently been emphasized for immunocompromised persons. At the M.D. Anderson Cancer Center (MDACC), infection surveillance of mostly hospitalized adults with leukemia or a recent bone marrow transplant yielded a respiratory virus from 181 of 668 (27.1%) respiratory illness episodes. In descending order of frequency, infections with RSV, rhinoviruses, influenza viruses, parainfluenza viruses, and adenoviruses were detected in each of three surveillance years. High frequencies of nosocomial acquisition occurred, as has been noted in prior reports. Similarly, persistence of infection and high frequencies of pneumonia and death among infected patients occurred, which have also been noted earlier. At MDACC, pneumonia occurred in 58–78% of infected patients, and 22–44% died. The role of the virus infection in many cases of pneumonia is uncertain, but death from pure viral pneumonia is well documented. A number of immune deficiencies in this patient population and options for control of these infections have been described that can, respectively, account for the medical problem and provide ways to approach prevention and treatment. | Am J Med | 1998 | CORD-19 | |
| 2781 | Genetic basis for species vulnerability in the cheetah N/A | Science | 1985 | CORD-19 | |
| 2782 | Prinzipien und Aspekte der Seuchenalarmplanung am Beispiel der Influenzapandemieplanung Despite significant medical progress, recent events have shown that infectious diseases have not lost significance. Indeed, the threat of worldwide epidemics has increased. Due to their high infectious ness and rapid person-to-person transmissibility, the emergence of new influenza viruses with pandemic potential poses an especially alarming situation in this regard. The world population would be “immunologically naïve” to a new pandemic virus, permitting explosive spread of the disease. During the last century, three influenza pandemics have demonstrated that this is not merely a hypothetical risk. Currently it is feared that the possible human adaptation of avian influenza viruses that have recently become endemic in birds in Southeast Asia could result in a new pandemic strain. With the publication of the German Influenza Pandemic Preparedness Plan, preparation for this potential threat has reached an important stage in Germany. The implementation of the plan, which includes measures that go beyond the scope of public health, must now proceed swiftly. The long-term goal of pandemic preparedness planning is to be better equipped to deal with potential health threats in general, in particular those ensuing from the emergence of new infectious diseases under conditions of a growing global network. | Bundesgesundheitsblatt Gesundh | 2005 | CORD-19 | |
| 2783 | A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2 N/A | Nature | 2020 | LitCov and CORD-19 | |
| 2784 | Influence of Empathy Disposition and Risk Perception on the Psychological Impact of Lockdown During the Coronavirus Disease Pandemic Outbreak During the current COVID-19 pandemic, and especially in the absence of availability of an effective treatment or a vaccine, the main health measure is neither chemical nor biological, but behavioral. To reduce the exponential growth of infections due to the new coronavirus (SARS-CoV-2) and the resulting overburdening of the healthcare system, many European Countries, parts of the US and Switzerland gradually implemented measures of quarantine and isolation defined as lockdown. This consideration leads to the need to understand how individuals are motivated to protect themselves and others. Recent research suggested that prosocial mental dispositions, such as empathy, might promote adherence to social norms of distancing. Other research conducted during the COVID-19 outbreak indicates, however, that empathy levels might fluctuate according to anxiety linked to the risk of death, and this negatively predicted prosocial willingness. The present protocol proposes a study on whether people's empathic dispositions, interacting with the levels of risk, influence the psychological impact of lockdown. The rationale is that emphatic dispositions, encouraging the acceptance of the lockdown, determine a better psychological adaptation and less distress. One retrospective study will be developed in Switzerland and, if the pandemic conditions force a new wave of lockdown on the population, one prospective study as well. A total of 120 participants will be involved, distinguished by their level of objective risk: (1) high objective risk (COVID-19 positive patients, hospitalized in isolation in post-acute phase); (2) moderate objective risk (COVID-19 positive patients, isolated at home); (3) minimum objective risk (non-positive adults, in lockdown). Measures of perceived risk of being contagious for third parties, empathic dispositions and acceptance of lockdown will be collected. The expected results provide important answers related to the immediate impact of empathic dispositions, effective risk and risk perception on the psychological impact of lockdown during a pandemic outbreak. Data gathered from this study could inform policy makers and public health managers about the best communication strategies that will take into account the various stages of health risk and, in particular, to modulate messages to the population aimed at inducing self-isolation behaviors. | Front Public Health | 2020 | LitCov and CORD-19 | |
| 2785 | SARS-CoV-2 and RT-PCR in asymptomatic patients: Results of a cohort of workers at El Dorado International Airport in Bogotá, 2020 INTRODUCTION: The 2019 coronavirus pandemic (COVID-19) has caused around 25 million cases worldwide. Asymptomatic patients have been described as potential sources of transmission. However, there are difficulties to detect them and to establish their role in the dynamics of virus transmission, which hinders the implementation of prevention strategies. OBJECTIVE: To describe the behavior of asymptomatic SARS-CoV-2 virus infection in a cohort of workers at the El Dorado Luis Carlos Galán Sarmiento International Airport in Bogotá, Colombia. MATERIALS AND METHODS: A prospective cohort of 212 workers from the El Dorado airport was designed. The follow-up began in June, 2020. A survey was used to characterize health and work conditions. Every 21 day, a nasopharyngeal swab was taken to identify the presence of SARS-CoV-2 using RT-PCR. We analyzed the behavior of the cycle threshold (ORFlab and N genes) according to the day of follow-up. RESULTS: In the first three follow-ups of the cohort, we found an incidence of SARS-CoV-2 infection of 16.51%. The proportion of positive contacts was 14.08%. The median threshold for cycle threshold was 33.53. CONCLUSION: We characterized the asymptomatic SARS-CoV-2 infection in a cohort of workers. The identification of asymptomatic infected persons continues to be a challenge for epidemiological surveillance systems. | Biomedica | 2020 | LitCov and CORD-19 | |
| 2786 | Human Coronavirus NL63, France The human coronavirus NL63 (HCoV-NL63) was first identified in the Netherlands, and its circulation in France has not been investigated. We studied HCoV-NL63 infection in hospitalized children diagnosed with respiratory tract infections. From November 2002 to April 2003, we evaluated 300 respiratory specimens for HCoV-NL63. Of the 300 samples, 28 (9.3%) were positive for HCoV-NL63. The highest prevalence was found in February (18%). The main symptoms were fever (61%), rhinitis (39%), bronchiolitis (39%), digestive problems (33%), otitis (28%), pharyngitis (22%), and conjunctivitis (17%). A fragment of the spike protein gene was sequenced to determine the variety of circulating HCoV-NL63. Phylogenetic analysis indicated that strains with different genetic markers cocirculate in France. | Emerg Infect Dis | 2005 | CORD-19 | |
| 2787 | Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM (Jupyter notebook), https://github.com/EESI/ncov_ism (command line tool) and via an interactive website at https://covid19-ism.coe.drexel.edu/. | PLoS Comput Biol | 2020 | LitCov and CORD-19 | |
| 2788 | Acute kidney injury in patients hospitalized with COVID-19 The rate of acute kidney injury (AKI) associated with patients hospitalized with Covid-19, and associated outcomes are not well understood. This study describes the presentation, risk factors and outcomes of AKI in patients hospitalized with Covid-19. We reviewed the health records for all patients hospitalized with Covid-19 between March 1, and April 5, 2020, at 13 academic and community hospitals in metropolitan New York. Patients younger than 18 years of age, with end stage kidney disease or with a kidney transplant were excluded. AKI was defined according to KDIGO criteria. Of 5,449 patients admitted with Covid-19, AKI developed in 1,993 (36.6%). The peak stages of AKI were stage 1 in 46.5%, stage 2 in 22.4% and stage 3 in 31.1%. Of these, 14.3% required renal replacement therapy (RRT). AKI was primarily seen in Covid-19 patients with respiratory failure, with 89.7% of patients on mechanical ventilation developing AKI compared to 21.7% of non-ventilated patients. 276/285 (96.8%) of patients requiring RRT were on ventilators. Of patients who required ventilation and developed AKI, 52.2% had the onset of AKI within 24 hours of intubation. Risk factors for AKI included older age, diabetes mellitus, cardiovascular disease, black race, hypertension and need for ventilation and vasopressor medications. Among patients with AKI, 694 died (35%), 519 (26%) were discharged and 780 (39%) were still hospitalized. AKI occurs frequently among patients with Covid-19 disease. It occurs early and in temporal association with respiratory failure and is associated with a poor prognosis. | Kidney Int | 2020 | LitCov and CORD-19 | |
| 2789 | Experience with tocilizumab in severe COVID-19 pneumonia after 80 days of follow-up: A retrospective cohort study OBJECTIVES: To describe the clinical characteristics and predictors of major outcomes in patients treated with tocilizumab (TCZ) for severe COVID-19 pneumonia. PATIENTS AND METHODS: Case series of all sequential patients with severe COVID-19 pneumonia treated with TCZ at an Academic Spanish hospital (March 12 - May 2, 2020). Clinical outcomes: death, length of hospital stay. An early clinical response to TCZ (48-72 h after the administration) was assessed by variations in respiratory function markers, Brescia COVID Respiratory Severity Scale (BCRSS), inflammatory parameters, and patients' and physicians' opinion. Associations were tested by multiple logistic regression. RESULTS: From a cohort of 236 patients, 77 patients treated with TCZ were included (median age 62 years (IQR 53.0–72.0), 64.9% were males), 42.9% had Charlson index ≥3; hypertension (41.6%), obesity (34.7%), and diabetes (20.8%). Median follow-up was 83.0 days (78.0–86.5), no patient was readmitted. ICU admission was required for 42 (54.5%), invasive mechanical ventilation in 38 (49.4%) and 10 patients died (12.9% global, 23.8% at ICU admitted). After multivariate adjustment, TCZ response by BCRSS (OR 0.03 (0.01–0.68), p = 0.028), and Charlson index (OR 3.54 (1.20–10.44), p = 0.022) has been identified as independent factors associated with mortality. Median of hospital stay was 16.0 days (11.0–23.0); BCRSS, physician subjective and D-dimer response were associated with shorter hospitalization stay. CONCLUSIONS: In a Mediterranean cohort, use of tocilizumab for severe COVID-19 show 12.9% of mortality. Early TCZ-response by BCRSS and low comorbidity were associated with increased survival. Early TCZ-response was related to shorter median hospital stay. | J Autoimmun | 2020 | LitCov and CORD-19 | |
| 2790 | Detection of COVID-19: A review of the current literature and future perspectives The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) worldwide pandemic. This unprecedented situation has garnered worldwide attention. An effective strategy for controlling the COVID-19 pandemic is to develop highly accurate methods for the rapid identification and isolation of SARS-CoV-2 infected patients. Many companies and institutes are therefore striving to develop effective methods for the rapid detection of SARS-CoV-2 ribonucleic acid (RNA), antibodies, antigens, and the virus. In this review, we summarize the structure of the SARS-CoV-2 virus, its genome and gene expression characteristics, and the current progression of SARS-CoV-2 RNA, antibodies, antigens, and virus detection. Further, we discuss the reasons for the observed false-negative and false-positive RNA and antibody detection results in practical clinical applications. Finally, we provide a review of the biosensors which hold promising potential for point-of-care detection of COVID-19 patients. This review thereby provides general guidelines for both scientists in the biosensing research community and for those in the biosensor industry to develop a highly sensitive and accurate point-of-care COVID-19 detection system, which would be of enormous benefit for controlling the current COVID-19 pandemic. | Biosens Bioelectron | 2020 | LitCov and CORD-19 | |
| 2791 | Aerosols and splatter in dentistry: A brief review of the literature and infection control implications BACKGROUND: Aerosols and droplets are produced during many dental procedures. With the advent of the droplet-spread disease severe acute respiratory syndrome, or SARS, a review of the infection control procedures for aerosols is warranted. TYPES OF STUDIES REVIEWED: The authors reviewed representative medical and dental literature for studies and reports that documented the spread of disease through an airborne route. They also reviewed the dental literature for representative studies of contamination from various dental procedures and methods of reducing airborne contamination from those procedures. RESULTS: The airborne spread of measles, tuberculosis and SARS is well-documented in the medical literature. The dental literature shows that many dental procedures produce aerosols and droplets that are contaminated with bacteria and blood. These aerosols represent a potential route for disease transmission. The literature also documents that airborne contamination can be minimized easily and inexpensively by layering several infection control steps into the routine precautions used during all dental procedures. CLINICAL IMPLICATIONS: In addition to the routine use of standard barriers such as masks and gloves, the universal use of pre-procedural rinses and high-volume evacuation is recommended. | J Am Dent Assoc | 2004 | CORD-19 | |
| 2792 | Teacher Learning in Difficult Times: Examining Foreign Language Teachers' Cognitions About Online Teaching to Tide Over COVID-19 The sudden global outbreak of COVID-19 in late 2019 has led to thriving online teaching, including the teaching of languages, across the world. As the online teaching of English-as-a-foreign-language (EFL) in Chinese universities is facing new challenges, EFL teachers have been positively exploring new solutions. To understand how EFL teachers were coping with the challenges, we set up this research as part of a larger study to examine EFL teachers’ cognitions about online teaching in response to the disruption of normal teaching plans. We did so by taking a qualitative approach through analyzing in-depth interviews with three EFL teachers from a Chinese university. Through thematic analysis we found that teachers had clear cognitions about features, advantages, and constraints of online EFL teaching and that they acquired information and communication technology (ICT) literacy through understanding students’ learning needs, online teaching practice, and the necessity of integrating traditional classroom teaching methods into online delivery. We conclude this study with a discussion on its pedagogical implications for similar contexts or colleagues facing similar challenges in other parts of the world. | Front Psychol | 2020 | LitCov and CORD-19 | |
| 2793 | The moderating roles of psychological flexibility and inflexibility on the mental health impacts of COVID-19 pandemic and lockdown in Italy The Moderating Roles of Psychological Flexibility and Inflexibility on the Mental Health Impacts of COVID-19 Pandemic and Lockdown in Italy. Preliminary data suggest the COVID-19 pandemic has adverse effects on mental health in approximately a quarter of the general population. Few prior studies have identified contextual risk factors and no published study has explored factors that might moderate their adverse effects on mental health. Psychological flexibility is the cornerstone of psychological health and resiliency. This study investigated the roles of psychological flexibility and inflexibility in moderating the effects of COVID-19 risk factors on three mental health outcomes: COVID-19 peritraumatic distress, anxiety, depression. We hypothesized that psychological flexibility would mitigate and psychological inflexibility would exacerbate the adverse effects of COVID-19 risk factors on mental health. During the Italian national lockdown (M=39.29 days, SD=11.26), 1,035 adults (79% female, M=37.5 years, SD=12.3) completed an online survey. Twelve COVID-19 risk factors were identified (e.g. lockdown duration, family infected by COVID-19, increase in domestic violence and in unhealthy lifestyle behaviours) and constituted a COVID-19 Lockdown Index. As predicted, results showed that after controlling for sociodemographic variables, global psychological flexibility and four of its sub-processes (self-as context, defusion, values, committed action), mitigated the detrimental impacts of COVID-19 risk factors on mental health. In contrast and as expected, global psychological inflexibility and four of its sub-processes (lack of contact with present moment, fusion, self-as-content, lack of contact with personal values) exacerbated the detrimental impacts of COVID-19 risk factors on mental health. Findings converge with those from the broader psychological flexibility literature providing robust support for the use of ACT-based interventions to promote psychological flexibility and mental health during the COVID-19 pandemic. | J Contextual Behav Sci | 2020 | LitCov and CORD-19 | |
| 2794 | Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype An improved understanding of human T cell-mediated immunity in COVID-19 is important for optimizing therapeutic and vaccine strategies. Experience with influenza shows that infection primes CD8(+) T cell memory to peptides presented by common HLA types like HLA-A2, which enhances recovery and diminishes clinical severity upon reinfection. Stimulating peripheral blood mononuclear cells from COVID-19 convalescent patients with overlapping peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the clonal expansion of SARS-CoV-2−specific CD8(+) and CD4(+) T cells in vitro, with CD4(+) T cells being robust. We identified two HLA-A*02:01-restricted SARS-CoV-2-specfic CD8(+) T cell epitopes, A2/S(269–277) and A2/Orf1ab(3183–3191). Using peptide−HLA tetramer enrichment, direct ex vivo assessment of A2/S(269)(+)CD8(+) and A2/Orf1ab(3183)(+)CD8(+) populations indicated that A2/S(269)(+)CD8(+) T cells were detected at comparable frequencies (∼1.3 × 10(−5)) in acute and convalescent HLA-A*02:01(+) patients. These frequencies were higher than those found in uninfected HLA-A*02:01(+) donors (∼2.5 × 10(−6)), but low when compared to frequencies for influenza-specific (A2/M1(58)) and Epstein–Barr virus (EBV)-specific (A2/BMLF(1280)) (∼1.38 × 10(−4)) populations. Phenotyping A2/S(269)(+)CD8(+) T cells from COVID-19 convalescents ex vivo showed that A2/S(269)(+)CD8(+) T cells were predominantly negative for CD38, HLA-DR, PD-1, and CD71 activation markers, although the majority of total CD8(+) T cells expressed granzymes and/or perforin. Furthermore, the bias toward naïve, stem cell memory and central memory A2/S(269)(+)CD8(+) T cells rather than effector memory populations suggests that SARS-CoV-2 infection may be compromising CD8(+) T cell activation. Priming with appropriate vaccines may thus be beneficial for optimizing CD8(+) T cell immunity in COVID-19. | Proc Natl Acad Sci U S A | 2020 | LitCov and CORD-19 | |
| 2795 | Implementing Artificial Intelligence and Digital Health in Resource-Limited Settings? Top 10 Lessons We Learned in Congenital Heart Defects and Cardiology N/A | OMICS | 2020 | CORD-19 | |
| 2796 | Surviving Sepsis Campaign: Guidelines on the Management of Critically Ill Adults with COVID-19 The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, Coronavirus Disease 2019 (COVID-19), affecting thousands of people around the world. Urgent guidance for clinicians caring for the sickest of these patients is needed. METHODS: We formed a panel of 36 experts from 12 countries. All panel members completed the World Health Organization conflict of interest disclosure form. The panel proposed 53 questions that are relevant to the management of COVID-19 in the ICU. We searched the literature for direct and indirect evidence on the management of COVID-19 in critically ill patients in the ICU. We identified relevant and recent systematic reviews on most questions relating to supportive care. We assessed the certainty in the evidence using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach, then generated recommendations based on the balance between benefit and harm, resource and cost implications, equity, and feasibility. Recommendations were either strong or weak, or in the form of best practice recommendations. RESULTS: The Surviving Sepsis Campaign COVID-19 panel issued 54 statements, of which four are best practice statements, nine are strong recommendations, and 35 are weak recommendations. No recommendation was provided for six questions. The topics were: 1) infection control, 2) laboratory diagnosis and specimens, 3) hemodynamic support, 4) ventilatory support, and 5) COVID-19 therapy. CONCLUSION: The Surviving Sepsis Campaign COVID-19 panel issued several recommendations to help support healthcare workers caring for critically ill ICU patients with COVID-19. When available, we will provide new evidence in further releases of these guidelines. | Crit Care Med | 2020 | LitCov and CORD-19 | |
| 2797 | Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia BACKGROUND: A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially detected in Wuhan, a major city of China, but has subsequently been detected in other provinces of China. Travel-associated cases have also been reported in a few other countries. Outbreaks in health care workers indicate human-to-human transmission. Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients. METHODS: We developed two 1-step quantitative real-time reverse-transcription PCR assays to detect two different regions (ORF1b and N) of the viral genome. The primer and probe sets were designed to react with this novel coronavirus and its closely related viruses, such as SARS coronavirus. These assays were evaluated using a panel of positive and negative controls. In addition, respiratory specimens from two 2019-nCoV-infected patients were tested. RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays. Samples from two 2019-nCoV-infected patients were positive in the tests. CONCLUSIONS: The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients. | Clin Chem | 2020 | LitCov and CORD-19 | |
| 2798 | Physical distancing interventions and incidence of COVID-19: natural experiment in 149 countries OBJECTIVE: To evaluate the association between physical distancing interventions and incidence of coronavirus disease 2019 (covid-19) globally. DESIGN: Natural experiment using interrupted time series analysis, with results synthesised using meta-analysis. SETTING: 149 countries or regions, with data on daily reported cases of covid-19 from the European Centre for Disease Prevention and Control and data on the physical distancing policies from the Oxford covid-19 Government Response Tracker. PARTICIPANTS: Individual countries or regions that implemented one of the five physical distancing interventions (closures of schools, workplaces, and public transport, restrictions on mass gatherings and public events, and restrictions on movement (lockdowns)) between 1 January and 30 May 2020. MAIN OUTCOME MEASURE: Incidence rate ratios (IRRs) of covid-19 before and after implementation of physical distancing interventions, estimated using data to 30 May 2020 or 30 days post-intervention, whichever occurred first. IRRs were synthesised across countries using random effects meta-analysis. RESULTS: On average, implementation of any physical distancing intervention was associated with an overall reduction in covid-19 incidence of 13% (IRR 0.87, 95% confidence interval 0.85 to 0.89; n=149 countries). Closure of public transport was not associated with any additional reduction in covid-19 incidence when the other four physical distancing interventions were in place (pooled IRR with and without public transport closure was 0.85, 0.82 to 0.88; n=72, and 0.87, 0.84 to 0.91; n=32, respectively). Data from 11 countries also suggested similar overall effectiveness (pooled IRR 0.85, 0.81 to 0.89) when school closures, workplace closures, and restrictions on mass gatherings were in place. In terms of sequence of interventions, earlier implementation of lockdown was associated with a larger reduction in covid-19 incidence (pooled IRR 0.86, 0.84 to 0.89; n=105) compared with a delayed implementation of lockdown after other physical distancing interventions were in place (pooled IRR 0.90, 0.87 to 0.94; n=41). CONCLUSIONS: Physical distancing interventions were associated with reductions in the incidence of covid-19 globally. No evidence was found of an additional effect of public transport closure when the other four physical distancing measures were in place. Earlier implementation of lockdown was associated with a larger reduction in the incidence of covid-19. These findings might support policy decisions as countries prepare to impose or lift physical distancing measures in current or future epidemic waves. | BMJ | 2020 | LitCov and CORD-19 | |
| 2799 | COVID-19 Mobile Positioning Data Contact Tracing and Patient Privacy Regulations: Exploratory Search of Global Response Strategies and the Use of Digital Tools in Nigeria BACKGROUND: The coronavirus disease (COVID-19) pandemic is the biggest global economic and health challenge of the century. Its effect and impact are still evolving, with deaths estimated to reach 40 million if unchecked. One effective and complementary strategy to slow the spread and reduce the impact is to trace the primary and secondary contacts of confirmed COVID-19 cases using contact tracing technology. OBJECTIVE: The objective of this paper is to survey strategies for digital contact tracing for the COVID-19 pandemic and to present how using mobile positioning data conforms with Nigeria’s data privacy regulations. METHODS: We conducted an exploratory review of current measures for COVID-19 contact tracing implemented around the world. We then analyzed how countries are using mobile positioning data technology to reduce the spread of COVID-19. We made recommendations on how Nigeria can adopt this approach while adhering to the guidelines provided by the National Data Protection Regulation (NDPR). RESULTS: Despite the potential of digital contact tracing, it always conflicts with patient data privacy regulations. We found that Nigeria’s response complies with the NDPR, and that it is possible to leverage call detail records to complement current strategies within the NDPR. CONCLUSIONS: Our study shows that mobile position data contact tracing is important for epidemic control as long as it conforms to relevant data privacy regulations. Implementation guidelines will limit data misuse. | JMIR Mhealth Uhealth | 2020 | LitCov and CORD-19 | |
| 2800 | Lelystad Virus, the Causative Agent of Porcine Epidemic Abortion and Respiratory Syndrome (PEARS), Is Related to LDV and EAV Abstract The genome of Lelystad virus (LV), the causative agent of porcine epidemic abortion and respiratory syndrome (previously known as mystery swine disease), was shown to be a polyadenylated RNA molecule. The nucleotide sequence of the LV genome was determined from a set of overlapping cDNA clones. A consecutive sequence of 15,088 nucleotides was obtained. Eight open reading frames (ORFs) that might encode virus-specific proteins were identified. ORF1a and ORF1b are predicted to encode the vital RNA polymerase because the amino acid sequence contains sequence elements that are conserved in RNA polymerases of the torovirus Berne virus (BEV), equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), the coronaviruses, and other positive-strand RNA viruses. A heptanucleotide slippery sequence (UUUAAAC) and a putative pseudoknot structure, which are both required for efficient ribosomal frameshifting during translation of the RNA polymerase ORF 1b of BEV, EAV, and the coronaviruses, were identified in the overlapping region of ORF1a and ORF1b of LV. ORFs 2 to 6 probably encode viral membrane-associated proteins, whereas ORF7 is predicted to encode the nucleocapsid protein. Comparison of the amino acid sequences of the ORFs identified in the genome of LV, LDV, and EAV indicated that LV and LDV are more closely related than LV and EAV. A 3′ nested set of six subgenomic RNAs was detected in LV-infected cells. These subgenomic RNAs contain a common leader sequence that is derived from the 5′ end of the genomic RNA and that is joined to the 3′ terminal body sequence. Our results indicate that LV is closely related evolutionarily to LDV and EAV, both members of a recently proposed family of positive-strand RNA viruses, the Arteriviridae. | Virology | 1993 | CORD-19 |
(1) COVID-19 Open Research Dataset (CORD-19). 2020. Version 2022-06-02. Retrieved from https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/historical_releases.html. Accessed 2022-06-05. doi:10.5281/zenodo.3715506
(2) Chen Q, Allot A, & Lu Z. (2020) Keep up with the latest coronavirus research, Nature 579:193 and Chen Q, Allot A, Lu Z. LitCovid: an open database of COVID-19 literature. Nucleic Acids Research. 2020. (version 2023-01-10)
(3) Currently tweets of June 23rd to June 29th 2022 have been considered.