Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (156)

Fever (106)

Cough (106)

Falls (51)

Fatigue (26)


    displaying 1381 - 1390 records in total 2531
    records per page

    A sub-national analysis of the rate of transmission TRANS of COVID-19 in Italy

    Authors: Michaela A. C. Vollmer; Swapnil Mishra; H Juliette T Unwin; Axel Gandy; Thomas A Mellan; Valerie Bradley; Harrison Zhu; Helen Coupland; Iwona Hawryluk; Michael Hutchinson; Oliver Ratmann; Melodie Monod; Patrick Walker; Charlie Whittaker; Lorenzo Cattarino; Constance Ciavarella; Lucia Cilloni; Kylie Ainslie; Marc Baguelin; Sangeeta Bhatia; Adhiratha Boonyasiri; Nicholas Brazeau; Giovanni Charles; Laura V Cooper; Zulma Cucunuba; Gina Cuomo-Dannenburg; Amy Dighe; Bimandra Djaafara; Jeff Eaton; Sabine L van Elsland; Richard FitzJohn; Keith Fraser; Katy Gaythorpe; Will Green; Sarah Hayes; Natsuko Imai; Ben Jeffrey; Edward Knock; Daniel Laydon; John Lees; Tara Mangal; Andria Mousa; Gemma Nedjati-Gilani; Pierre Nouvellet; Daniela Olivera; Kris V Parag; Michael Pickles; Hayley A Thompson; Robert Verity; Caroline Walters; Haowei Wang; Yuanrong Wang; Oliver J Watson; Lilith Whittles; Xiaoyue Xi; Azra A M Ghani; Steven Riley; Lucy C Okell; Christl A Donnelly; Neil M Ferguson; Ilaria Dorigatti; Seth Flaxman; Samir Bhatt

    doi:10.1101/2020.05.05.20089359 Date: 2020-05-09 Source: medRxiv

    Italy was the first European country to experience sustained local transmission TRANS of COVID-19. As of 1st May 2020, the Italian health authorities reported 28,238 deaths MESHD nationally. To control the epidemic, the Italian government implemented a suite of non-pharmaceutical interventions (NPIs), including school and university closures, social distancing and full lockdown involving banning of public gatherings and non essential movement. In this report, we model the effect of NPIs on transmission TRANS using data on average mobility. We estimate that the average reproduction number TRANS (a measure of transmission TRANS intensity) is currently below one for all Italian regions, and significantly so for the majority of the regions. Despite the large number of deaths MESHD, the proportion of population that has been infected by SARS-CoV-2 (the attack rate TRANS) is far from the herd immunity threshold in all Italian regions, with the highest attack rate TRANS observed in Lombardy (13.18% [10.66%-16.70%]). Italy is set to relax the currently implemented NPIs from 4th May 2020. Given the control achieved by NPIs, we consider three scenarios for the next 8 weeks: a scenario in which mobility remains the same as during the lockdown, a scenario in which mobility returns to pre-lockdown levels by 20%, and a scenario in which mobility returns to pre-lockdown levels by 40%. The scenarios explored assume that mobility is scaled evenly across all dimensions, that behaviour stays the same as before NPIs were implemented, that no pharmaceutical interventions are introduced, and it does not include transmission TRANS reduction from contact tracing TRANS, testing and the isolation of confirmed or suspected cases. New interventions, such as enhanced testing and contact tracing TRANS are going to be introduced and will likely contribute to reductions in transmission TRANS; therefore our estimates should be viewed as pessimistic projections. We find that, in the absence of additional interventions, even a 20% return to pre-lockdown mobility could lead to a resurgence in the number of deaths MESHD far greater than experienced in the current wave in several regions. Future increases in the number of deaths MESHD will lag behind the increase in transmission TRANS intensity and so a second wave will not be immediately apparent from just monitoring of the daily number of deaths MESHD. Our results suggest that SARS-CoV-2 transmission TRANS as well as mobility should be closely monitored in the next weeks and months. To compensate for the increase in mobility that will occur due to the relaxation of the currently implemented NPIs, adherence to the recommended social distancing measures alongside enhanced community surveillance including swab testing, contact tracing TRANS and the early isolation of infections MESHD are of paramount importance to reduce the risk of resurgence in transmission TRANS.

    Containing Covid-19 outbreaks with spatiallytargeted short-term lockdowns and mass-testing

    Authors: Justin Alsing; Nairi Usher; Philip JD Crowley

    doi:10.1101/2020.05.05.20092221 Date: 2020-05-09 Source: medRxiv

    We assess the efficacy of spatially targeted lockdown or mass-testing and case-isolation in individual communities, as a complement to contact-tracing TRANS and social-distancing, for containing SARS-CoV-2 outbreaks. Using the UK as a case study, we construct a stochastic branching process model for the virus transmission TRANS, embedded on a network interaction model encoding mobility patterns in the UK. The network model is based on commuter data from the 2011 census, a catchment area model for schools, and a phenomenological model for mobility and interactions outside of work, school, and the home. We show that for outbreak scenarios where contact-tracing TRANS and moderate social distancing alone provide suppression but do not contain the spread, targeted lockdowns or mass-testing interventions at the level of individual communities (with just a few thousand inhabitants) can be effective at containing outbreaks. For spatially targeted mass-testing, a moderate increase in testing capacity would be required (typically < 40000 additional tests per day), while for local lockdowns we find that only a small fraction (typically < 0.1%) of the population needs to be locked down at any one time (assuming that one third of transmission TRANS occurs in the home, at work or school, and out in the wider community respectively). The efficacy of spatially targeted interventions is contingent on an appreciable fraction of transmission TRANS events occurring within (relative to across) communities. Confirming the efficacy of community-level interventions therefore calls for detailed investigation of spatial transmission TRANS patterns for SARS-CoV-2, accounting for sub-community-scale transmission TRANS dynamics, and changes in mobility patterns due to the presence of other containment measures (such as social distancing and travel TRANS restrictions).

    Impact of small-area lockdowns for the control of the COVID-19 pandemic

    Authors: Cristóbal Cuadrado; María José Monsalves; Jean Gajardo; María Paz Bertoglia; Manuel Najera; Tania Alfaro; Mauricio Canals; Jay Kaufmann; Sebastián Peña

    doi:10.1101/2020.05.05.20092106 Date: 2020-05-09 Source: medRxiv

    Background Countries confronting the COVID-19 pandemic are implementing different social distancing strategies. We evaluated the impact of small-area lockdowns in Chile, aimed to reduce viral transmission TRANS while minimizing the population disrupted. The effectiveness of this intervention on the outbreak control is unknown. Methods A natural experiment assessing the impact of small-area lockdowns between February 15th and April 25th, 2020. We used mobility data and official governmental reports to compare regions with small-area lockdowns versus regions without. The primary outcome was the mean difference in the effective reproductive number TRANS (Re) of COVID-19. Secondary outcomes were changes in mobility indicators. We used quasi-experimental methods for the analysis and examined the impact of other concurrent public health interventions to disentangle their effects. Results Small-area lockdown produced a sizable reduction in human mobility, equivalent to an 11.4% reduction (95%CI -14.4% to -8.38%) in public transport and similar effects in other mobility indicators. Ten days after implementation, the small-area lockdown produced a reduction of the effective reproductive number TRANS (Re) of 0.86 (95%CI -1.70 to -0.02). School and university closures, implemented earlier, led to a 40% reduction in urban mobility. Closure of educational institutions resulted in an even greater Re reduction compared with small-area lockdowns. Conclusions Small-area lockdowns produced a reduction in mobility and viral transmission TRANS, but the effects were smaller than the early closures of schools and universities. Small-area lockdowns may have a relevant supporting role in reducing SARS-CoV-2 transmission TRANS and could be useful for countries considering scaling-down stricter social distancing interventions.

    Using viral genomics to estimate undetected infections MESHD and extent of superspreading events for COVID-19

    Authors: Lucy M Li; Patrick Ayscue

    doi:10.1101/2020.05.05.20092098 Date: 2020-05-09 Source: medRxiv

    Asymptomatic infections MESHD Asymptomatic TRANS and limited testing capacity have led to under-reporting of SARS-CoV-2 cases. This has hampered the ability to ascertain true infection MESHD numbers, evaluate the effectiveness of surveillance strategies, determine transmission TRANS dynamics, and estimate reproductive numbers TRANS. Leveraging both viral genomic and time series case data offers methods to estimate these parameters. Using a Bayesian inference framework to fit a branching process model to viral phylogeny and time series case data, we estimated time-varying reproductive numbers TRANS and their variance, the total numbers of infected individuals, the probability of case detection over time, and the estimated time to detection of an outbreak for 12 locations in Europe, China, and the United States. The median percentage of undetected infections MESHD ranged from 13% in New York to 92% in Shanghai, China, with the length of local transmission TRANS prior to two cases being detected ranging from 11 days (95% CI: 4-21) in California to 37 days (9-100) in Minnesota. The probability of detection was as low as 1% at the start of local epidemics, increasing as the number of reported cases increased exponentially. The precision of estimates increased with the number of full-length viral genomes in a location. The viral phylogeny was informative of the variance in the reproductive number TRANS with the 32% most infectious individuals contributing 80% of total transmission TRANS events. This is the first study that incorporates both the viral genomes and time series case data in the estimation of undetected COVID-19 infections MESHD. Our findings suggest the presence of undetected infections MESHD broadly and that superspreading events are contributing less to observed dynamics than during the SARS epidemic in 2003. This genomics-informed modeling approach could estimate in near real-time critical surveillance metrics to inform ongoing COVID-19 response efforts.

    Elevated ACE2 expression in the olfactory neuroepithelium: implications for anosmia HP and upper respiratory SARS-CoV-2 entry and replication

    Authors: Mengfei Chen; Wenjuan Shen; Nicholas Rowan; Heather Kulaga; Alexander Hillel; Murugappan Ramanathan; Andrew P Lane

    doi:10.1101/2020.05.08.084996 Date: 2020-05-09 Source: bioRxiv

    The site of SARS-CoV-2 entry and replication critically impacts strategies for COVID-19 diagnosis, transmission TRANS mitigation, and treatment. We determined the cellular location of the SARS-CoV-2 target receptor protein, ACE2, in the human upper airway, finding striking enrichment (200-700 folds) in the olfactory neuroepithelium relative to nasal respiratory or tracheal epithelial cells. This cellular tropism of SARS-CoV-2 may underlie its high transmissibility TRANS and association with olfactory dysfunction, while suggesting a viral reservoir potentially amenable to intranasal therapy.

    Knowledge, attitude and practice of secondary school students toward COVID-19 epidemic in Italy: a cross selectional study

    Authors: Maddalena Dilucca; Dafni Souli

    doi:10.1101/2020.05.08.084236 Date: 2020-05-09 Source: bioRxiv

    The coronavirus disease MESHD (COVID-19) is a highly transmittable and pathogenic viral infection MESHD caused by Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2), which emerges in December 2019 in Wuhan, China and spreads around the world at the beginning of 2020. The World Health Organization declares the outbreak a Public Health Emergency MESHD of International Concern on the 30th of January, and a pandemic on the 11th of March. On the 4th of March, the Italian government orders the full closure of all schools and universities nationwide.The aim of this study is to investigate the knowledge, practice and attitudes (KAP) of secondary school at the time of COVID-19 pandemic in Italy. In this cross-sectional, web-based survey, conducted among the high school student population with age TRANS ranging from 14 to 19 years old, a questionnaire with 19 items regarding the KAP toward COVID-19 is asked. Study participants are recruited from several secondary schools of different areas. Frequencies and histograms are computed for descriptive purposes. Statistical analysis is computed with Chi square test, utilized to depict relevant difference between geender. Among a total of 2380 students who answers the questionnaire, 40.7% are male TRANS and 59.3% are female TRANS.Level of knowledge about generical characteristics of COVID-19 is quite similar among gender TRANS. Students present a good level of knowledge about the clinical presentation of the disease MESHD, the basic hygiene principles, the modes of transmission TRANS and the method of protection against virus transmission TRANS. The knowledge about number of this pandemia and easy scientific correlation with COVID-19 is quite confused. The most frequently reported source of knowledge about COVID-19 is television, whereas the less is the school. Our findings suggest that student population shows appropriate practice, and positive attitude towards COVID-19 at the time of its outbreak.More emphasis should be placed on education of the student partecipants about biological meaning of this infection MESHD and relative preventive or future measures.Competing Interest StatementThe authors have declared no competing interest.View Full Text

    Prevalence SERO and Acceptance of Face Mask Practice among Individuals Visiting Hospital during COVID-19 Pandemic: An Observational Study

    Authors: Gobi Hariyanayagam Gunasekaran; Sera Selvanthan Sundram Gunasekaran; Shargunan Selvanthan Gunasekaran; Fouzia Hanim Binti Abdul Halim

    id:10.20944/preprints202005.0152.v1 Date: 2020-05-09 Source:

    Background: The COVID-19 transmission TRANS has been established to occur through respiratory droplets from coughing MESHD coughing HP and sneezing MESHD sneezing HP. Health agencies have strongly recommended the use of facemask as a precaution from cross- transmission TRANS. Objective: This study investigated the prevalence SERO of facemask use among visitors to the hospital. This study also investigated the demographic factors contributing to unacceptable facemask practice. Setting: This prospective observational study was done among hospital visitors to a district specialist hospital during COVID-19 pandemic outbreak. Methods: Individuals entering through dedicated entry point were observed for the type, category and practice of wearing personal protective equipment. Inclusion criteria for this study were any individual's ≥ 2 years old entering the treatment facility from selected entry points. Patients were categorized into two groups of acceptable and unacceptable facemask practice. The Pearson chi-square was used to test for differences in investigated variables in the univariate setting and Binary Logistic regression model was used in the multivariate setting. Main Outcome Measure: Prevalence SERO, acceptance practice and odds ratio of unacceptance of facemask use. Results: Among 1652 individuals included in the final analysis, 1574 (96.9%) was observed wearing facemask with 1269 (72.0%) of individuals worn medical-grade facemask. However, among them, only 1397 (88.8%) individuals' facemask practice was acceptable while the reaming 177 (11.2) individuals were perceived with unacceptable facemask practice. Male TRANS individuals, Malay ethnic and high risk age group TRANS are 1.47 times (Odds Ratio: OR=1.47; 95% CI, 1.06-2.06; p=.023), 2.18 times (OR=2.18; 95% CI, 1.55-3.08; p<.001) and 1.99 times (OR=2.18; 95% CI, 1.42 - 2.77; p<.001) more likely to exhibit unacceptable facemask practice respectively. Conclusion: Extensive use of facemasks coupled with environmental hygiene measures is a public health strategy which can help to mitigate the COVID-19 epidemic impact. However, a targeted comprehensive strategy to improve compliance to proper facemask practice among the high-risk population is needed to achieve maximal protective benefit.

    Public knowledge of novel coronavirus diseases MESHD 2019: a web-based national survey

    Authors: Yu Liu; Dan Wang; Hao Xu; Ying Xiao; Cui Chen; Ru-Nan Chen; Liang-Hao Hu; Zhao-Shen Li

    doi:10.21203/ Date: 2020-05-09 Source: ResearchSquare

    Background Although the existing cases of COVID-19 in China have been reducing since late February 2020, the confirmed cases TRANS are surging abroad. Improving public knowledge regarding COVID-19 is critical to control the epidemic. The study aimed to determine the China’s public knowledge of COVID-19 and attitude towards the control measures.Methods A cross-sectional study was conducted in 48 hours, from 29 February 2020, 22:30 to 2 March 2020, 22:30, based on a self-administered web-based questionnaire. The survey was conducted on the WeChat network. Exponential non-discriminative snowball sampling were applied. The questionnaire was voluntarily submitted by WeChat users. The questionnaire covered the basic demographic information, public knowledge about epidemiological and clinical characteristics of COVID-19, psychological state, and attitude towards overall control measures. The primary outcome was the Chinese public knowledge regarding COVID-19 and the attitude towards the control measures and secondary outcome was psychological state of the public during this epidemic.Results The study included 10,905 participants and 10,399 valid questionnaires were included for analysis. Participants with tertiary education, younger age TRANS and healthcare workers had better overall knowledge compared with other participants (all P<0.05). About 91.9% of the participants believed in person-to-person transmission TRANS and 39.1% believed in animal-to-person transmission TRANS. No significant correlation between anxiety HP and regional number of existing cases was found, while participants in Hubei were more anxious than those in other regions. In general, 74.1% of participants acknowledged the effectiveness of overall control measures and it was negatively correlated with regional number of existing cases (r=-0.492, P=0.007).Conclusions In conclusion, the survey revealed that Chinese public had overall good knowledge regarding COVID-19 except for those indeterminate knowledge. With the dynamic change of global epidemic situation and more researches, further study would be conducted to explore the change of public knowledge and attitude about COVID-19 in the future.

    County-level factors influence the trajectory of Covid-19 incidence

    Authors: Ashley Wendell Kranjac; Dinko Kranjac

    doi:10.1101/2020.05.05.20092254 Date: 2020-05-09 Source: medRxiv

    With new cases of Covid-19 surging in the United States, we need to better understand how the spread of novel coronavirus varies across all segments of the population. We use hierarchical exponential growth curve modeling techniques to examine whether community social and economic characteristics uniquely influence the incidence of Covid-19 cases in the urban built environment. We show that, as of May 3, 2020, confirmed coronavirus infections MESHD are concentrated along demographic and socioeconomic lines in New York City and surrounding areas, the epicenter of the Covid-19 pandemic in the United States. Furthermore, we see evidence that, after the onset of the pandemic, timely enactment of physical distancing measures such as school closures is imperative in order to limit the extent of the coronavirus spread in the population. Public health authorities must impose nonpharmaceutical measures early on in the pandemic and consider community-level factors that associate with a greater risk of viral transmission TRANS.

    Intra-genome variability in the dinucleotide composition of SARS-CoV-2

    Authors: Paul Digard; Hui-Min Lee; Colin Sharp; Finn Grey; Eleanor R Gaunt

    doi:10.1101/2020.05.08.083816 Date: 2020-05-09 Source: bioRxiv

    CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development, and if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the newly emerged SARS-CoV-2 genome was characterised in the context of other coronaviruses. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission TRANS. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. While ORF10 is only present in the genomes of a subset of coronaviruses, E is essential for virus replication. Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. Phylogeny indicates that this is an ancestrally-derived trait reflecting their origin in bats, rather than something selected for after zoonotic transfer. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from and is updated on a daily basis (7am CET/CEST).



MeSH Disease
Human Phenotype

Export subcorpus as Endnote

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.