Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (183)

Cough (152)

Fever (139)

Falls (68)

Anxiety (34)


    displaying 1 - 10 records in total 3409
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    COVID-19's unfortunate events in schools: mitigating classroom clusters in the context of variable transmission TRANS

    Authors: Paul Tupper; Caroline Colijn; Andressa Barreto Glaeser Jr.; Janini Cristina Paiz Jr.; Gabriel Dickin Caldana Jr.; Carem Luana Machado Lessa Jr.; Amanda de Menezes Mayer Jr.; Julia Goncalves Kuchle Jr.; Paulo Ricardo Gazzola Zen Sr.; Alvaro Vigo Sr.; Ana Trindade Winck Sr.; Liane Nanci Rotta Sr.; Claudia Elizabeth Thompson Sr.; Andres F. Henao-Martinez; Leland Shapiro

    doi:10.1101/2020.10.20.20216267 Date: 2020-10-22 Source: medRxiv

    Widespread school closures occurred during the COVID-19 pandemic. Because closures are costly and damaging, many jurisdictions have since reopened schools with control measures in place. Early evidence indicated that schools were low risk and children TRANS were unlikely to be very infectious, but it is becoming clear that children TRANS and youth can acquire and transmit COVID-19 in school settings and that transmission TRANS clusters and outbreaks can be large. We describe the contrasting literature on school transmission TRANS, and argue that the apparent discrepancy can be reconciled by heterogeneity, or ``overdispersion'' in transmission TRANS, with many exposures yielding little to no risk of onward transmission TRANS, but some unfortunate exposures causing sizeable onward transmission TRANS. In addition, respiratory viral loads are as high in children TRANS and youth as in adults TRANS, pre- and asymptomatic TRANS transmission TRANS occur, and the possibility of aerosol transmission TRANS has been established. We use a stochastic individual-based model to find the implications of these combined observations for cluster sizes and control measures. We consider both individual and environment/activity contributions to the transmission TRANS rate, as both are known to contribute to variability in transmission TRANS. We find that even small heterogeneities in these contributions result in highly variable transmission TRANS cluster sizes in the classroom setting, with clusters ranging from 1 to 20 individuals in a class of 25. None of the mitigation protocols we modeled, initiated by a positive test in a symptomatic individual, are able to prevent large transmission TRANS clusters unless the transmission TRANS rate is low (in which case large clusters do not occur in any case). Among the measures we modeled, only rapid universal monitoring (for example by regular, onsite, pooled testing) accomplished this prevention. We suggest approaches and the rationale for mitigating these ``unfortunate events'', even if they are expected to be rare.

    Review of Infective Dose, Routes of Transmission TRANS, and Outcome of COVID-19 Caused by the SARS-CoV-2 Virus MESHD: Comparison with Other Respiratory Viruses MESHD

    Authors: Sedighe Karimzadeh; Raj Bhopal; Huy Nguyen Tien

    id:202007.0613/v2 Date: 2020-10-22 Source:

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pandemic. Prevention and control strategies require an improved understanding of SARS-CoV-2 dynamics. We did a rapid review of the literature on SARS-CoV-2 viral dynamics with a focus on infective dose. We sought comparisons of SARS-CoV-2 with other respiratory viruses including SARS-CoV-1 and MERS-CoV. We examined laboratory animal, and human studies. The literature on infective dose, transmission TRANS, and routes of exposure was limited specially in humans, and varying endpoints were used for measurement of infection MESHD. We propose the minimum infective dose of COVID-19 in humans, is higher than 100 particles, possibly slightly lower than the 700 particles estimated for H1N1 influenza. Despite variability in animal studies, there was some evidence that increased dose at exposure correlated with higher viral load clinically, and severer symptoms. Higher viral load measures did not reflect COVID-19 severity. Aerosol transmission TRANS seemed to raise the risk of more severe respiratory complications in animals. An accurate quantitative estimate of the infective dose of SARS-CoV-2 in humans is not currently feasible and needs further research. Further work is also required on the relationship between routes of transmission TRANS, infective dose, co-infection MESHD, and outcomes.

    Population-based prevalence SERO surveys during the COVID-19 pandemic: a systematic review

    Authors: Vinicius Bonetti Franceschi Jr.; Andressa Schneiders Santos Jr.; Andressa Barreto Glaeser Jr.; Janini Cristina Paiz Jr.; Gabriel Dickin Caldana Jr.; Carem Luana Machado Lessa Jr.; Amanda de Menezes Mayer Jr.; Julia Goncalves Kuchle Jr.; Paulo Ricardo Gazzola Zen Sr.; Alvaro Vigo Sr.; Ana Trindade Winck Sr.; Liane Nanci Rotta Sr.; Claudia Elizabeth Thompson Sr.; Andres F. Henao-Martinez; Leland Shapiro

    doi:10.1101/2020.10.20.20216259 Date: 2020-10-22 Source: medRxiv

    Population-based prevalence SERO surveys of COVID-19 contribute to establish the burden and epidemiology of infection MESHD, the role of asymptomatic TRANS and mild infections MESHD in transmission TRANS, and allow more precise decisions about reopen policies. We performed a systematic review to evaluate qualitative aspects of these studies, their reliability, and biases. The available data described 37 surveys from 19 countries, mostly from Europe and America and using antibody testing SERO. They reached highly heterogeneous sample sizes and prevalence SERO estimates. Disproportional prevalence SERO was observed in minority communities. Important risk of bias was detected in four domains: sample size, data analysis with sufficient coverage, measurements in standard way, and response rate. The correspondence analysis showed few consistent patterns for high risk of bias. Intermediate risk of bias was related to American and European studies, blood SERO samples and prevalence SERO >1%. Low risk of bias was related to Asian studies, RT-PCR tests and prevalence SERO <1%.

    Distinct Phenotypes of SARS-CoV-2 Isolates Reveal Viral Traits Critical for Replication in Primary Human Respiratory Cells

    Authors: Marie O Pohl; Idoia Busnadiego; Verena Kufner; Stefan Schmutz; Maryam Zaheri; Irene Abela; Alexandra Trkola; Michael Huber; Silke Stertz; Benjamin G Hale; Federica Barra; Adriano Leuzzi; Eleonora Lilli; Giuseppina Miselli; Alessia Noto; Maria Ferraiuolo; Francesco Talotta; Theocharis Tsoleridis; Silvia Meschi; Marco Soriani; Antonella Folgori; Jonathan K Ball; Stefano Colloca

    doi:10.1101/2020.10.22.350207 Date: 2020-10-22 Source: bioRxiv

    Since entering the human population, SARS-CoV-2 (the causative agent of COVID-19) has spread across the world, causing >40 million infections and >1 million deaths. While large-scale sequencing efforts have identified numerous genetic mutations in SARS-CoV-2 during its circulation, it remains largely unclear whether these changes impact adaptation, replication or transmission TRANS of the virus in its new host. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all the major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, viral stocks and passaging experiments, with kinetic virus replication data from non-human Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 sequence features that associate with distinct phenotypes. Notably, naturally-occurring substitutions in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G substitution generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E, and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin-cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human respiratory cells. Overall, our study uncovers natural sequence features in the SARS-CoV-2 genome that determine efficient virus replication and tropism for the human respiratory epithelium.

    Broad transcriptional dysregulation of brain and choroid plexus cell types with COVID-19

    Authors: Andrew Chris Yang; Fabian Kern; Patricia M Losada; Christina A Maat; Georges Schmartz; Tobias Fehlmann; Nicholas Schaum; Davis P Lee; Kruti Calcuttawala; Ryan T Vest; David Gate; Daniela Berdnik; M. Windy McNerney; Divya Channappa; Inma Cobos; Nicole Ludwig; Walter J. Schulz-Schaeffer; Andreas Keller; Tony Wyss-Coray; Marco Soriani; Antonella Folgori; Jonathan K Ball; Stefano Colloca

    doi:10.1101/2020.10.22.349415 Date: 2020-10-22 Source: bioRxiv

    Though SARS-CoV-2 primarily targets the respiratory system, it is increasingly appreciated that patients may suffer neurological symptoms of varied severity. However, an unbiased understanding of the molecular processes across brain cell types that could contribute to these symptoms in COVID-19 patients is still missing. Here, we profile 47,678 droplet-based single-nucleus transcriptomes from the frontal cortex and choroid plexus across 10 non-viral, 4 COVID-19, and 1 influenza patient. We complement transcriptomic data with immunohistochemical staining for the presence of SARS-CoV-2. We find that all major cortex parenchymal and choroid plexus cell types are affected transcriptionally with COVID-19. This arises, in part, from SARS-CoV-2 infection MESHD of the cortical brain vasculature, meninges, and choroid plexus MESHD, stimulating increased inflammatory signaling into the brain. In parallel, peripheral immune cells infiltrate the brain, microglia activate programs mediating the phagocytosis of live neurons, and astrocytes dysregulate genes involved in neurotransmitter homeostasis. Among neurons, layer 2/3 excitatory neurons--evolutionarily expanded in humans--show a specific downregulation of genes encoding major SNARE and synaptic vesicle components, predicting compromised synaptic transmission TRANS. These perturbations are not observed in terminal influenza. Many COVID-19 gene expression changes are shared with those in chronic brain disorders MESHD and reside in genetic variants associated with cognitive function, schizophrenia HP schizophrenia MESHD, and depression MESHD. Our findings and public dataset provide a molecular framework and new opportunities to understand COVID-19 related neurological disease MESHD.

    Effect of park use and landscape structure on COVID-19 transmission TRANS rates

    Authors: Thomas Frederick Johnson; Lisbeth A Hordley; Matthew P Greenwell; Luke C Evans; Monique van Straaten; Hedda Wardemann; Erec Stebbins; Hans-Georg Kraeusslich; Ralf Bartenschlager; Hermann Brenner; Vibor Laketa; Ben Schoettker; Barbara Mueller; Uta Merle; Tim Waterboer; James Watmough; Jude Dzevela Kong; Iain Moyles; Huaiping Zhu

    doi:10.1101/2020.10.20.20215731 Date: 2020-10-21 Source: medRxiv

    The COVID-19 pandemic has had severe impacts on global public health. In the UK, social distancing measures and a nationwide lockdown were introduced to reduce the spread of the virus. Green space accessibility may have been particularly important during this lockdown, as it could have provided benefits for physical and mental wellbeing, while also limiting the risk of transmission TRANS. However, the effects of public green space use on the rate of COVID-19 transmission TRANS are yet to be quantified, and as the size and accessibility of green spaces vary within local authorities, the risks and benefits to the public of using green space may well be context-dependent. To evaluate how green space affected COVID-19 transmission TRANS across 98 local authorities in England, we first split case rates into two periods, the pre-peak rise and the post-peak decline in cases, and assessed how baseline health and mobility variables influenced these rates. Next, looking at the residual case rates, we investigated how landscape structure (e.g. area and patchiness of green space) and park use influenced transmission TRANS. We first show that pre- and post-peak case rates were significantly reduced when overall mobility was low, especially in areas with high population clustering, and high population density during the post-peak period only. After accounting for known mechanisms behind transmission TRANS rates, we found that park use (showing a preference for park mobility) decreased residual pre-peak case rates, especially when green space was low and contiguous (not patchy). Whilst in the post-peak period, park use and green landscape structure had no effect on residual case rates. Our results show that utilising green spaces rather than other activities (e.g. visiting shops and workplaces) can reduce the transmission TRANS rate of COVID-19, especially during an exponential phase of transmission TRANS.

    On nonlinear incidence rate of Covid-19

    Authors: Swarna Kamal Paul; Saikat Jana; Parama Bhaumik; Victoria Indenbaum; Merav Weil; Michal Elul; Oran Erster; Alin Sela Brown; Ella Mendelson; Batya Mannasse; Rachel Shirazi; Satish Lakkakula; Oren Miron; Ehud Rinott; Ricardo Gilead Baibich; Iris Bigler; Matan Malul; Rotem Rishti; Asher Brenner; Yair E. Lewis; Eran Friedler; Yael Gilboa; Sara Sabach; Yuval Alfiya; Uta Cheruti; Nadav Davidovitch; Natalya Bilenko; Jacob Moran-Gilad; Yakir Berchenko; Itay Bar-Or; Ariel Kushmaro; Timothy Spector; Claire J Steves

    doi:10.1101/2020.10.19.20215665 Date: 2020-10-21 Source: medRxiv

    Classical Susceptible-Infected-Removed model with constant transmission TRANS rate and removal rate may not capture real world dynamics of epidemic due to complex influence of multiple external factors on the spread. On top of that transmission TRANS rate may vary widely in a large region due to non-stationarity of spatial features which poses difficulty in creating a global model. We modified discrete global Susceptible-Infected-Removed model by using time varying transmission TRANS rate, recovery rate and multiple spatially local models. No specific functional form of transmission TRANS rate has been assumed. We have derived the criteria for disease-free equilibrium within a specific time period. A single Convolutional LSTM model is created and trained to map multiple spatiotemporal features to transmission TRANS rate. The model achieved 8.39% mean absolute percent error in terms of cumulative infection MESHD cases in each locality in a 10-day prediction period. Local interpretations of the model using perturbation method reveals local influence of different features on transmission TRANS rate which in turn is used to generate a set of generalized global interpretations. A what-if scenario with modified recovery rate illustrates rapid dampening of the spread when forecasted with the trained model. A comparative study with current normal scenario reveals key necessary steps to reach baseline.

    Prevalence SERO of SARS-CoV-2 antibodies SERO in France: results from nationwide serological surveillance

    Authors: Stephane Le Vu; Gabrielle Jones; Francois Anna; Thierry Rose; Jean-Baptiste Richard; Sibylle Bernard-Stoecklin; Sophie Goyard; Caroline Demeret; Olivier Helynck; Corinne Robin; Virgile Monnet; Louise Perrin de Facci; Marie-Noelle Ungeheuer; Lucie Leon; Yvonnick Guillois; Laurent Filleul; Pierre Charneau; Daniel Levy-Bruhl; Sylvie van der Werf; Harold Noel; Eran Friedler; Yael Gilboa; Sara Sabach; Yuval Alfiya; Uta Cheruti; Nadav Davidovitch; Natalya Bilenko; Jacob Moran-Gilad; Yakir Berchenko; Itay Bar-Or; Ariel Kushmaro; Timothy Spector; Claire J Steves

    doi:10.1101/2020.10.20.20213116 Date: 2020-10-21 Source: medRxiv

    Background Assessment of cumulative incidence of SARS-CoV-2 infections MESHD is critical for monitoring the course and the extent of the epidemic. As asymptomatic TRANS or mild cases were typically not captured by surveillance data in France, we implemented nationwide serological surveillance. We present estimates for prevalence SERO of anti- SARS-CoV-2 antibodies SERO in the French population and the proportion of infected individuals who developed potentially protective neutralizing antibodies SERO throughout the first epidemic wave. Methods We performed serial cross-sectional sampling of residual sera over three periods: prior to (9-15 March), during (6-12 April) and following (11-17 May) a nationwide lockdown. Each sample was tested for anti-SARS-CoV-2 SERO IgG antibodies SERO targeting the Nucleoprotein and Spike using two Luciferase-Linked ImmunoSorbent Assays, and for neutralising antibodies SERO using a pseudo-neutralisation assay. We fitted a general linear mixed model of seropositivity in a Bayesian framework to derive prevalence SERO estimates stratified by age TRANS, sex and region. Findings In total, sera from 11 021 individuals were analysed. Nationwide seroprevalence SERO of SARS-CoV-2 antibodies SERO was estimated at 0.41% [0.05;0.88] mid-March, 4.14% [3.31;4.99] mid-April and 4.93% [4.02;5.89] mid-May. Approximately 70% of seropositive individuals had detectable neutralising antibodies SERO. Seroprevalence SERO was higher in regions where circulation occurred earlier and was more intense. Seroprevalence SERO was lowest in children TRANS under 10 years of age TRANS (2.72% [1.10;4.87]). Interpretation Seroprevalence SERO estimates confirm that the nationwide lockdown substantially curbed transmission TRANS and that the vast majority of the French population remains susceptible to SARS-CoV-2. Low seroprevalence SERO in school age TRANS children TRANS suggests limited susceptibility and/or transmissibility TRANS in this age group TRANS. Our results show a clear picture of the progression of the first epidemic wave and provide a framework to inform the ongoing public health response as viral transmission TRANS is picking up again in France and globally.

    The Causal Effect of Air Pollution on COVID-19 Transmission TRANS: Evidence from China

    Authors: Guojun He; Yuhang PAN; Takanao Tanaka; Tejal Vaghela; Matthew Knight; Rahul Moghal; Jaswinder Singh; Lisa G Spencer; Erica Thwaite; Harry Mitchell; Sam Calmonson; Noor Mahdi; Shershah Assadullah; Matthew Leung; Aisling O'Neill; Chhaya Popat; Radhika Kumar; Thomas J Humphries; Rebecca Talbutt; Sarika Raghunath; Philip L Molyneaux; Miriam Schechter; Jeremy Lowe; Andrew Barlow

    doi:10.1101/2020.10.19.20215236 Date: 2020-10-21 Source: medRxiv

    There is increasing concern that ambient air pollution could exacerbate COVID-19 transmission TRANS. However, estimating the relationship is challenging because it requires one to account for epidemiological characteristics, to isolate the impact of air pollution from potential confounders, and to capture the dynamic impact. We propose a new econometric framework to address these challenges: we rely on the epidemiological Susceptible-Infectious-Recovered-Deceased ( SIRD MESHD) model to construct the outcome of interest, the Instrument Variable (IV) model to estimate the causal relationship, and the Flexible-Distributed-Lag (FDL) model to understand the dynamics. Using data covering all prefectural Chinese cities, we find that a 10-point (14.3%) increase in the Air Quality Index would lead to a 2.80 percentage point increase in the daily COVID-19 growth rate with 2 to 13 days of delay (0.14 ~ 0.22 increase in the reproduction number TRANS: R0 TRANS). These results imply that improving air quality can be a powerful tool to contain the spread of COVID-19.

    Efficacy of stay-at-home policy and transmission TRANS of COVID-19 in Toronto, Canada: a mathematical modeling study

    Authors: Pei Yuan; Juan Li; Elena Aruffo; Qi Li; Tingting Zheng; Nicholas Ogden; Beate Sander; Jane Heffernan; Evgenia Gatov; Effie Gournis; Sarah Collier; Yi Tan; Jun Li; Julien Arino; Jacques Belair; James Watmough; Jude Dzevela Kong; Iain Moyles; Huaiping Zhu

    doi:10.1101/2020.10.19.20181057 Date: 2020-10-21 Source: medRxiv

    Background In many parts of the world, restrictive non-pharmaceutical interventions (NPI) that aim to reduce contact rates, including stay-at-home orders, limitations on gatherings, and closure of public places, are being lifted, with the possibility that the epidemic resurges if alternative measures are not strong enough. Here we aim to capture the combination of use of NPIs and reopening measures which will prevent an infection rebound. Methods We employ a SEAIR model with a household structure able to capture the stay-at-home policy (SAHP). To reflect the changes in the SAHP over the course of the epidemic, we vary the SAHP compliance rate, assuming that the time to compliance of all the people requested to stay-at-home follows a Gamma distribution. Using confirmed case TRANS data for the City of Toronto, we evaluate basic and instantaneous reproduction numbers TRANS and simulate how the average household size, the stay-at-home rate, the efficiency and duration of SAHP implementation, affect the outbreak trajectory. Findings The estimated basic reproduction number TRANS R_0 TRANS was 2.36 (95% CI: 2.28, 2.45) in Toronto. After the implementation of the SAHP, the contact rate outside the household fell HP by 39%. When people properly respect the SAHP, the outbreak can be quickly controlled, but extending its duration beyond two months (65 days) had little effect. Our findings also suggest that to avoid a large rebound of the epidemic, the average number of contacts per person per day should be kept below nine. This study suggests that fully reopening schools, offices, and other activities, is possible if the use of other NPIs is strictly adhered to. Interpretation Our model confirmed that the SAHP implemented in Toronto had a great impact in controlling the spread of COVID-19. Given the lifting of restrictive NPIs, we estimated the thresholds values of the maximum number of contacts, probability of transmission TRANS and testing needed to ensure that the reopening will be safe, i.e. maintaining an R_t<1.

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MeSH Disease
Human Phenotype

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