Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (82)

Fever (61)

Cough (57)

Falls (23)

Respiratory distress (17)


    displaying 1 - 10 records in total 1127
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    Repurposing of Approved Drugs with Potential to Interact with SARS-CoV-2 Receptor

    Authors: Abu Sajib

    id:202004.0369/v2 Date: 2020-08-02 Source:

    Respiratory transmission TRANS is the primary route of Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) infection MESHD. Angiotensin I converting enzyme 2 (ACE2) is the known receptor of SARS-CoV-2 surface spike glycoprotein for entry into human cells. A recent study reported absent to low expression of ACE2 in a variety of human lung epithelial cell samples. Three bioprojects (PRJEB4337, PRJNA270632 and PRJNA280600) invariably found abundant expression of ACE1 (a homolog of ACE2 and also known as ACE) in human lungs compared to very low expression of ACE2. In fact, ACE1 has a wider and more abundant tissue distribution compared to ACE2. Although it is not obvious from the primary sequence alignment of ACE1 and ACE2, comparison of X-ray crystallographic structures show striking similarities in the regions of the peptidase domains (PD) of these proteins, which is known (for ACE2) to interact with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Critical amino acids in ACE2 that mediate interaction with the viral spike protein are present and organized in the same order in the PD of ACE1. In silico analysis predicts comparable interaction of SARS-CoV-2 spike protein with ACE1 and ACE2. In addition, this study predicts from a list of 1263 already approved drugs that may interact with ACE2 and/or ACE1, potentially interfere with the entry of SARS-CoV-2 inside the host cells and alleviate the symptoms of Coronavirus disease MESHD (COVID-19).

    Modeling latent infection MESHD transmissions TRANS through biosocial stochastic dynamics

    Authors: Bosiljka Tadic; Roderick Melnik

    doi:10.1101/2020.07.30.20164491 Date: 2020-08-01 Source: medRxiv

    The events of the recent SARS-CoV-02 epidemics have shown the importance of social factors, especially given the large number of asymptomatic TRANS cases that effectively spread the virus, which can cause a medical emergency MESHD to very susceptible individuals. Besides, the SARS-CoV-02 virus survives for several hours on different surfaces, where a new host can contract it with a delay. These passive modes of infection MESHD transmission TRANS remain an unexplored area for traditional mean-field epidemic models. Here, we design an agent-based model for simulations of infection MESHD transmission TRANS in an open system driven by the dynamics of social activity; the model takes into account the personal characteristics of individuals, as well as the survival time of the virus and its potential mutations. A growing bipartite graph embodies this biosocial process, consisting of active carriers TRANS (host) nodes that produce viral nodes during their infectious period TRANS. With its directed edges passing through viral nodes between two successive hosts, this graph contains complete information about the routes leading to each infected individual. We determine temporal fluctuations of the number of exposed and the number of infected individuals, the number of active carriers TRANS and active viruses at hourly resolution. The simulated processes underpin the latent infection MESHD transmissions TRANS, contributing significantly to the spread of the virus within a large time window. More precisely, being brought by social dynamics and exposed to the currently existing infection MESHD, an individual passes through the infectious state until eventually spontaneously recovers or otherwise is moves to a controlled hospital environment. Our results reveal complex feedback mechanisms that shape the dependence of the infection MESHD curve on the intensity of social dynamics and other sociobiological factors. In particular, the results show how the lockdown effectively reduces the spread of infection MESHD and how it increases again after the lockdown is removed. Furthermore, a reduced level of social activity but prolonged exposure of susceptible individuals have adverse effects. On the other hand, virus mutations that can gradually reduce the transmission TRANS rate by hopping to each new host along the infection MESHD path can significantly reduce the extent of the infection MESHD, but can not stop the spreading without additional social strategies. Our stochastic processes, based on graphs at the interface of biology and social dynamics, provide a new mathematical framework for simulations of various epidemic control strategies with high temporal resolution and virus traceability.

    Household transmission TRANS of SARS-CoV-2: a systematic review and meta-analysis of secondary attack rate TRANS

    Authors: Zachary J. Madewell; Yang Yang; Ira M. Longini Jr.; M. Elizabeth Halloran; Natalie E. Dean

    doi:10.1101/2020.07.29.20164590 Date: 2020-08-01 Source: medRxiv

    Background: Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is spread by direct, indirect, or close contact TRANS with infected people via infected respiratory droplets or saliva. Crowded indoor environments with sustained close contact TRANS and conversations are a particularly high-risk setting. Methods: We performed a meta-analysis through July 29, 2020 of SARS-CoV-2 household secondary attack rate TRANS ( SAR TRANS), disaggregating by several covariates (contact type, symptom status, adult TRANS/ child TRANS contacts, contact sex, relationship to index case, index case sex, number of contacts in household TRANS, coronavirus). Findings: We identified 40 relevant published studies that report household secondary transmission TRANS. The estimated overall household SAR TRANS was 18.8% (95% confidence interval [CI]: 15.4%-22.2%), which is higher than previously observed SARs for SARS-CoV and MERS-CoV. We observed that household SARs were significantly higher from symptomatic index cases than asymptomatic TRANS index cases, to adult TRANS contacts than children TRANS contacts, to spouses than other family contacts, and in households TRANS with one contact than households TRANS with three or more contacts. Interpretation: To prevent the spread of SARS-CoV-2, people are being asked to stay at home worldwide. With suspected or confirmed infections TRANS infections MESHD referred to isolate at home, household transmission TRANS will continue to be a significant source of transmission TRANS.

    Rapid real-time tracking of non-pharmaceutical interventions and their association SARS-CoV-2 positivity: The COVID-19 Pandemic Pulse Study

    Authors: Steven J. Clipman; Amy P. Wesolowski; Dustin G. Gibson; Smisha Agarwal; Anastasia S. Lambrou; Gregory D. Kirk; Alain B. Labrique; Shruti H. Mehta; Sunil S. Solomon

    doi:10.1101/2020.07.29.20164665 Date: 2020-08-01 Source: medRxiv

    Background: Current mitigation strategies for severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Collecting demographically and geographically resolved data on NPIs and their association with SARS-CoV-2 infection MESHD history can provide critical information related to reopening geographies. Methods: We sampled 1,030 individuals in Maryland from June 17 - June 28, 2020 to capture socio-demographically and geographically resolved information about NPI adoption, access to SARS-CoV-2 testing, and examine associations with self-reported SARS-CoV-2 positivity. Results: Median age TRANS of the sample was 43 years and 45% were men; Whites and Blacks/African Americans represented 60% and 23%, respectively. Overall, 96% of the sample reported traveling TRANS outside their home for non-employment related services: most commonly cited reasons were essential services (92%) and visiting friends TRANS/family (66%). Use of public transport was reported by 18% of respondents. 68% reported always social distancing indoors and 53% always wearing masks indoors; indoor social distancing was significantly less common among younger vs. older individuals, and race/ethnicity and income were significantly associated with mask use (p<0.05 for all). 55 participants (5.3%) self-reported ever testing positive for SARS-CoV-2 with strong dose-response relationships between movement frequency and SARS-CoV-2 positivity that were significantly attenuated by social distancing. In multivariable analysis, history of SARS-CoV-2 infection MESHD was negatively associated with the practice of social distancing (adjusted Odd Ratio [aOR]: 0.10; 95% Confidence Interval: 0.03 - 0.33); the only travel TRANS associated with higher likelihood of SARS-CoV-2 infection MESHD was use of public transport (aOR for 7 or more times vs. never: 4.29) and visiting a place of worship (aOR for 3 or more times vs. never: 16.0) after adjusting for social distancing. Conclusions: Using a rapid cost-efficient approach, we highlight the role of movement and social distancing on SARS-CoV-2 transmission risk TRANS. Continued monitoring of NPI uptake, access to testing, and the subsequent impact on SARS-CoV-2 transmission TRANS will be critical for pandemic control and decisions about reopening geographies.

    Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19.

    Authors: Giselle Ibette Silva Lopez-Lopes; Cintia Mayumi Ahagon; Margarete Aparecida Bonega; Fabiana Pereira dos Santos; Katia Correa de Oliveira Santos; Audrey Cilli; Lincoln Spinazola do Prado; Daniela Bernardes Borges da Silva; Nuria Borges da Luz; Claudia Patara Saraceni; Ana Maria Sardinha Afonso; Maria do Carmo Timenetsky; Luis Fernando de Macedo Brigido

    doi:10.1101/2020.07.29.20163998 Date: 2020-08-01 Source: medRxiv

    Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection MESHD. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance SERO of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute. Methods: Consecutive volunteer testing of LWH and external household and close contacts TRANS were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea). Results: Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection MESHD observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease MESHD. Over a third (38%) of asymptomatic TRANS cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic TRANS and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease TRANS disease MESHD.

    Regional now- and forecasting for data reported with delay: A case study in COVID-19 infections MESHD

    Authors: Giacomo De Nicola; Marc Schneble; Göran Kauermann; Ursula Berger

    id:2007.16058v1 Date: 2020-07-31 Source: arXiv

    Governments around the world continue to act to contain and mitigate the spread of COVID-19. The rapidly evolving situation compels officials and executives to continuously adapt policies and social distancing measures depending on the current state of the spread of the disease TRANS disease MESHD. In this context, it is crucial for policymakers to have a firm grasp on what the current state of the pandemic is as well as to have an idea of how the infective situation is going to unfold in the next days. However, as in many other situations of compulsorily-notifiable diseases MESHD and beyond, cases are reported with delay to a central register, with this delay deferring an up-to-date view of the state of things. We provide a stable tool for monitoring current infection MESHD levels as well as predicting infection MESHD numbers in the immediate future at the regional level. We accomplish this through nowcasting of cases that have not yet been reported as well as through forecasting of future infections MESHD. The two steps are also combined in forenowcasting. We apply our model to German data, for which our focus lies in explaining and predicting infectious behaviour by district, age group TRANS and gender TRANS.

    Dynamics of epidemic diseases MESHD without guaranteed immunity

    Authors: Kurt Langfeld

    id:2007.15971v1 Date: 2020-07-31 Source: arXiv

    The global SARS-CoV-2 pandemic suggests a novel type of disease MESHD disease spread TRANS spread dynamics. WHO states that there is currently no evidence that people who have recovered from COVID-19 and have antibodies SERO are immune from a second infection MESHD [WHO]. Conventional mathematical models consider cases for which a recovered individual either becomes susceptible again or develops an immunity. Here, we study the case where infected agents recover and only develop immunity if they are continuously infected for some time. Otherwise, they become susceptible again. We show that field theory bounds the peak of the infectious rate. Consequently, the theory's phases characterise the disease MESHD dynamics: (i) a pandemic phase and (ii) a response regime. The model excellently describes the epidemic spread of the SARS-CoV-2 outbreak in the city of Wuhan, China. We find that only 30% of the recovered agents have developed an immunity. We anticipate our paper to influence the decision making upon balancing the economic impact and the pandemic impact on society. As long as disease MESHD controlling measures keep the disease MESHD dynamics in the "response regime", a pandemic escalation ('second wave') is ruled out.

    Stochastic modelling of the effects of human-mobility restriction and viral infection MESHD characteristics on the spread of COVID-19

    Authors: Shiho Ando; Yuki Matsuzawa; Hiromichi Tsurui; Tetsuya Mizutani; Damien Hall; Yutaka Kuroda

    doi:10.1101/2020.07.28.20163980 Date: 2020-07-30 Source: medRxiv

    After several weeks of "lockdown" as the sole answer to the COVID-19 pandemic, many countries are restarting their economic and social activities. However, balancing the re-opening of society against the implementation of non-pharmaceutical measures needed for minimizing interpersonal contacts requires a careful assessment of the risks of infection TRANS risks of infection TRANS infection MESHD as a function of the confinement relaxation strategies. Here, we present a stochastic coarse grained model that examines this problem. In our model, people are allowed to move between discrete positions on a one-dimensional grid with viral infection MESHD possible when two people are collocated at the same site. Our model features three sets of adjustable parameters, which characterize (i) viral transmission TRANS, (ii) viral detection, and (iii) degree of personal mobility, and as such, it is able to provide a qualitative assessment of the potential for second-wave infection MESHD outbreaks based on the timing, extent, and pattern of the lockdown relaxation strategy. In line with general expectations, our model predicts that a full lockdown yields the best results, namely, the lowest number of total infections MESHD. A less anticipated result was that when personal mobility is increased beyond a critical level, the risk of infection TRANS risk of infection TRANS infection MESHD rapidly reaches a constant value, which depends solely on the population density. Furthermore, according to our model, confinement alone is not effective if it is not accompanied by a detection capacity (coupled with quarantine) that surpasses 40% of the patients during their symptomatic phase. The results of our simulation also showed that keeping the virus transmission TRANS probability to less than 0.4, which can be achieved in real life by respecting social distancing or wearing masks, is as effective as imposing a mild lockdown. Finally, we note that detection and quarantine of pre-symptomatic patients, even with a probability as low as 0.2, would reduce the final numbers of infections MESHD by a factor of ten or more.

    Incidence and outcomes of healthcare-associated COVID-19 infections MESHD: significance of delayed diagnosis and correlation with staff absence

    Authors: Kirstin Khonyongwa; Surabhi K Taori; Ana Soares; Nergish Desai; Malur Sudhanva; William Bernal; Silke Schelenz; Lisa A Curran

    doi:10.1101/2020.07.24.20148262 Date: 2020-07-30 Source: medRxiv

    Background: The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 has led to onward transmissions TRANS among vulnerable inpatients. Aims: This study was performed to evaluate the prevalence SERO and clinical outcomes of Healthcare-associated COVID-19 infections MESHD (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission TRANS in a London Teaching Hospital Trust. Methods: Electronic laboratory, patient and staff self-reported sickness records were interrogated for the period 1st March to 18th April 2020. HA-COVID-19 was defined as symptom onset TRANS >14d of admission. Test performance SERO of a single combined throat and nose swab (CTNS) for patient placement and the effect of delayed RNA positivity (DRP, defined as >48h delay) on patient outcomes was evaluated. The incidence of staff self-reported COVID-19 sickness absence, hospital bed occupancy, community incidence and DRP was compared HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections MESHD (OHAI) was compared to previous years. Results: 58 HA-COVID-19 (7.1%) cases were identified. As compared to community-acquired cases, significant differences were observed in age TRANS (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30d mortality. CTNS negative predictive value SERO was 60.3%. DRP was associated with greater mortality (p=0.034) and 34.5% HA-COVID-19 cases could be traced TRANS to delayed diagnosis in CA-COVID-19. Incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). OHAI rates were similar to previous 2 years. Conclusion: Early diagnosis and isolation of COVID-19 would help reduce transmission TRANS. A single CTNS has limited value in segregating patients into positive and negative pathways.

    Mechanistic modelling of coronavirus infections MESHD and the impact of confined neighbourhoods on a short time scale

    Authors: Danish A Ahmed; Ali R Ansari; Mudassar Imran; Kamaludin Dingle; Naveed Ahmed; Michael A Bonsall

    doi:10.1101/2020.07.28.20163634 Date: 2020-07-30 Source: medRxiv

    Background: To mitigate the spread of the COVID-19 coronavirus, some countries have adopted more stringent non-pharmaceutical interventions in contrast to those widely used (for e.g. the state of Kuwait). In addition to standard practices such as enforcing curfews, social distancing, and closure of non-essential service industries, other non-conventional policies such as the total confinement of highly populated areas has also been implemented. Methods: In this paper, we model the movement of a host population using a mechanistic approach based on random walks, which are either diffusive or super-diffusive. Infections MESHD are realised through a contact process, whereby a susceptible host may be infected if in close spatial proximity of the infectious host. Our focus is only on the short-time scale prior to the infectious period TRANS, so that no further transmission TRANS is assumed. Results: We find that the level of infection MESHD depends heavily on the population dynamics, and increases in the case of slow population diffusion, but remains stable for a high or super-diffusive population. Also, we find that the confinement of homogeneous or overcrowded sub-populations has minimal impact in the short term. Conclusions: Our results indicate that on a short time scale, confinement restrictions or complete lock down of whole residential areas may not be effective. Finally, we discuss the possible implications of our findings for total confinement in the context of the current situation in Kuwait.

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MeSH Disease
Human Phenotype

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