Corpus overview


MeSH Disease

Human Phenotype


    displaying 1 - 10 records in total 375
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    How Efficient is Contact Tracing TRANS in Mitigating the Spread of Covid-19? A Mathematical Modeling Approach

    Authors: T. A. Biala; Y. O. Afolabi; A. Q. M. Khaliq

    id:2008.03859v1 Date: 2020-08-10 Source: arXiv

    Contact Tracing TRANS (CT) is one of the measures taken by government and health officials to mitigate the spread of the novel coronavirus. In this paper, we investigate its efficacy by developing a compartmental model for assessing its impact on mitigating the spread of the virus. We describe the impact on the reproduction number TRANS $\mathcal{R}_c$ of Covid-19. In particular, we discuss the importance and relevance of parameters of the model such as the number of reported cases, effectiveness of tracking and monitoring policy, and the transmission TRANS rates to contact tracing TRANS. We describe the terms ``perfect tracking'', ``perfect monitoring'' and ``perfect reporting'' to indicate that traced contacts TRANS will be tracked while incubating, tracked contacts are efficiently monitored so that they do not cause secondary infections MESHD, and all infected persons are reported, respectively. We consider three special scenarios: (1) perfect monitoring and perfect tracking of contacts of a reported case, (2) perfect reporting of cases and perfect monitoring of tracked reported cases and (3) perfect reporting and perfect tracking of contacts of reported cases. Furthermore, we gave a lower bound on the proportion of contacts to be traced TRANS to ensure that the effective reproduction, $\mathcal{R}_c$, is below one and describe $\mathcal{R}_c$ in terms of observable quantities such as the proportion of reported and traced TRANS cases. Model simulations using the Covid-19 data obtained from John Hopkins University for some selected states in the US suggest that even late intervention of CT may reasonably reduce the transmission TRANS of Covid-19 and reduce peak hospitalizations and deaths MESHD. In particular, our findings suggest that effective monitoring policy of tracked cases and tracking of traced contacts TRANS while incubating are more crucial than tracing TRANS more contacts.

    Data-driven Inferences of Agency-level Risk and Response Communication on COVID-19 through Social Media based Interactions

    Authors: Md Ashraf Ahmed; Arif Mohaimin Sadri; M. Hadi Amini

    id:2008.03866v1 Date: 2020-08-10 Source: arXiv

    Risk and response communication of public agencies through social media played a significant role in the emergence and spread of novel Coronavirus (COVID-19) and such interactions were echoed in other information outlets. This study collected time-sensitive online social media data and analyzed such communication patterns from public health (WHO, CDC), emergency MESHD (FEMA), and transportation (FDOT) agencies using data-driven methods. The scope of the work includes a detailed understanding of how agencies communicate risk information through social media during a pandemic and influence community response (i.e. timing of lockdown, timing of reopening) and disease MESHD outbreak indicators (i.e. number of confirmed cases TRANS, number of deaths MESHD). The data includes Twitter interactions from different agencies (2.15K tweets per agency on average) and crowdsourced data (i.e. Worldometer) on COVID-19 cases and deaths MESHD were observed between February 21, 2020 and June 06, 2020. Several machine learning techniques such as (i.e. topic mining and sentiment ratings over time) are applied here to identify the dynamics of emergent topics during this unprecedented time. Temporal infographics of the results captured the agency-levels variations over time in circulating information about the importance of face covering, home quarantine, social distancing and contact tracing TRANS. In addition, agencies showed differences in their discussions about community transmission TRANS, lack of personal protective equipment, testing and medical supplies, use of tobacco, vaccine, mental health issues, hospitalization, hurricane season, airports, construction work among others. Findings could support more efficient transfer of risk and response information as communities shift to new normal as well as in future pandemics.

    The effect of school closures and reopening strategies on COVID-19 infection MESHD dynamics in the San Francisco Bay Area: a cross-sectional survey and modeling analysis

    Authors: Jennifer R Head; Kristin Andrejko; Qu Cheng; Philip A Collender; Sophie Phillips; Anna Boser; Alexandra K Heaney; Christopher M Hoover; Sean L Wu; Graham R Northrup; Karen Click; Robert Harrison; Joseph A Lewnard; Justin V Remais

    doi:10.1101/2020.08.06.20169797 Date: 2020-08-07 Source: medRxiv

    Background Large-scale school closures have been implemented worldwide to curb the spread of COVID-19. However, the impact of school closures and re-opening on epidemic dynamics remains unclear. Methods We simulated COVID-19 transmission TRANS dynamics using an individual-based stochastic model, incorporating social- contact data TRANS of school- aged TRANS children TRANS during shelter-in-place orders derived from Bay Area (California) household surveys. We simulated transmission TRANS under observed conditions and counterfactual intervention scenarios between March 17-June 1, and evaluated various fall HP 2020 K-12 reopening strategies. Findings Between March 17-June 1, assuming children TRANS <10 were half as susceptible to infection MESHD as older children TRANS and adults TRANS, we estimated school closures averted a similar number of infections MESHD (13,842 cases; 95% CI: 6,290, 23,040) as workplace closures (15,813; 95% CI: 9,963, 22,617) and social distancing measures (7,030; 95% CI: 3,118, 11,676). School closure effects were driven by high school and middle school closures. Under assumptions of moderate community transmission TRANS, we estimate that fall HP 2020 school reopenings will increase symptomatic illness among high school teachers (an additional 40.7% expected to experience symptomatic infection MESHD, 95% CI: 1.9, 61.1), middle school teachers (37.2%, 95% CI: 4.6, 58.1), and elementary school teachers (4.1%, 95% CI: -1.7, 12.0). Results are highly dependent on uncertain parameters, notably the relative susceptibility and infectiousness of children TRANS, and extent of community transmission TRANS amid re-opening. The school-based interventions needed to reduce the risk to fewer than an additional 1% of teachers infected varies by grade level. A hybrid-learning approach with halved class sizes of 10 students may be needed in high schools, while maintaining small cohorts of 20 students may be needed for elementary schools. Interpretation Multiple in-school intervention strategies and community transmission TRANS reductions, beyond the extent achieved to date, will be necessary to avoid undue excess risk associated with school reopening. Policymakers must urgently enact policies that curb community transmission TRANS and implement within-school control measures to simultaneously address the tandem health crises posed by COVID-19 and adverse child TRANS health and development consequences of long-term school closures.

    Social Behaviors Associated with a Positive COVID-19 Test Result

    Authors: Sidra Speaker; Christine Marie Doherty; Elizabeth R Pfoh; Aaron Dunn; Bryan Hair; Victoria Shaker; Lynn Daboul; Michael B Rothberg

    doi:10.1101/2020.08.04.20168450 Date: 2020-08-06 Source: medRxiv

    Objective: To compare behaviors of individuals who tested positive for COVID-19 relative to non-infected individuals. Methods: We sent COVID positive cases and age TRANS/ gender TRANS matched controls a survey regarding their social behaviors via MyChart (online patient portal). We called cases if they did not complete the electronic survey within two days. Data was collected from May-June 2020. Survey responses for cases without a close contact TRANS and controls were compared using Pearson chi-square or Fishers Exact tests as appropriate. Results: A total of 339 participants completed the survey (113 cases, 226 controls); 45 (40%) cases had known contact with COVID-19. Cases were more likely to have recently traveled TRANS (4% vs. 0%, p=0.01) or to work outside the home (40% vs. 25%, p=0.02). There was no difference in the rates of attending private or public gatherings, mask/glove use, hand-washing, cleaning surfaces and cleaning mail/groceries between cases and controls. Conclusions: Sixty percent of cases had no known contact with COVID-19, indicating ongoing community transmission TRANS and underlining the importance of contact tracing TRANS. The greater percentage of cases who work outside the home provides further evidence for social distancing.

    An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic

    Authors: Alfonso Landeros; Xiang Ji; Kenneth L. Lange; Timothy C. Stutz; Jason Xu; Mary E. Sehl; Janet S. Sinsheimer

    doi:10.1101/2020.08.05.20169086 Date: 2020-08-06 Source: medRxiv

    The SARS-CoV-2 pandemic led to the closure of nearly all K-12 schools in the United States of America in March 2020. Although reopening K-12 schools for in-person schooling is desirable for many reasons, officials also understand that risk reduction strategies and detection of cases must be in place to allow children TRANS to safely return to school. Furthermore, the consequences of reclosing recently reopened schools are substantial and impact teachers, parents TRANS, and ultimately the educational experience in children TRANS. Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission TRANS mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence SERO. Our model predicts that a combination of all three approaches will substantially reduce SARS-CoV-2 prevalence SERO. The model also shows that reduction of class density and the implementation of rapid viral testing, even with imperfect detection, have greater impact than moderate measures for transmission TRANS mitigation.

    Identification of SARS-CoV-2 recombinant genomes

    Authors: David VanInsberghe; Andrew S Neish; Anice C Lowen; Katia Koelle

    doi:10.1101/2020.08.05.238386 Date: 2020-08-05 Source: bioRxiv

    Viral recombination has the potential to bring about viral genotypes with modified phenotypic characteristics, including transmissibility TRANS and virulence. Although the capacity for recombination among Betacoronaviruses is well documented, SARS-CoV-2 has only been circulating in humans for approximately 8 months and thus has had a relatively short window of opportunity for the occurrence of recombination. The ability to detect recombination has further been limited by the relatively low levels of genetic diversity in SARS-CoV-2. Despite this, two studies have reported recombinants among SARS-CoV-2 strains. Here we first revisit these findings with a new analysis approach, arguing that neither presents a clear case of within-SARS-CoV-2 recombination. Applying this same approach to available SARS-CoV-2 sequences, we then identify five recombinant genomes. Each of these genomes contain phylogenetic markers of two distinct SARS-CoV-2 clades. Further, the predicted parent TRANS clades of these recombinant genomes were, with one exception, documented to be co-circulating in the country of infection MESHD in the two weeks prior to the sample being collected. Our results indicate that recombination among SARS-CoV-2 strains is occurring, but is either not widespread or often remains undetectable given current levels of viral genetic diversity. Efforts to monitor the emergence of new recombinant genomes should therefore be sustained.

    Implication of backward contact tracing TRANS in the presence of overdispersed transmission TRANS in COVID-19 outbreak

    Authors: Akira Endo; - Centre for the Mathematical Modelling of Infectious Diseases (CMMID) COVID-19 Working Group; Quentin J Leclerc; Gwenan M Knight; Graham F Medley; Katherine E Atkins; Sebastian Funk; Adam J Kucharski

    doi:10.1101/2020.08.01.20166595 Date: 2020-08-04 Source: medRxiv

    Unlike forward contact tracing TRANS, backward contact tracing TRANS identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions TRANS. By using a simple branching process model, we explored the potential of combining backward contact tracing TRANS with more conventional forward contact tracing TRANS for control of COVID-19.

    Early transmission TRANS dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama.

    Authors: Danilo Franco; Claudia Gonzalez; Leyda E Abrego; Jean P Carrera; Yamilka Diaz; Yaset Caisedo; Ambar Moreno; Oris Chavarria; Jessica Gondola; Marlene Castillo; Elimelec Valdespino; Melissa Gaitan; Jose Martinez-Mandiche; Lizbeth Hayer; Pablo Gonzalez; Carmen Lange; Yadira Molto; Dalis Mojica; Ruben Ramos; Maria Mastelari; Lizbeth Cerezo; Lourdes Moreno; Christl A Donnelly; Nuno R. Faria; Juan M Pascale; Sandra Lopez-Verges; Alexander A Martinez

    doi:10.1101/2020.07.31.20160929 Date: 2020-08-04 Source: medRxiv

    Background With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease MESHD control strategies. We investigated the early transmission TRANS patterns of the virus and the outcomes of mitigation measures in the country. Methods We collected information from epidemiological surveillance, including contact tracing TRANS, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number TRANS (Rt) using date of symptom onset TRANS in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission TRANS of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission TRANS dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission TRANS clusters is crucial to interrupt local transmission TRANS of SARS-CoV-2 in a region.

    Stepwise School Opening Online and Off-line and an Impact on the Epidemiology of COVID-19 in the Pediatric Population

    Authors: Yoonsun Yoon; Kyung-Ran Kim; Hwanhee Park; So young Kim; Yae-Jean Kim

    doi:10.1101/2020.08.03.20165589 Date: 2020-08-04 Source: medRxiv

    Background Data on SARS-CoV-2 transmission TRANS from a pediatric index patient to others at the school setting are limited. Epidemiologic data on pediatric COVID-19 cases after school opening is warranted. Methods We analyzed data of the pediatric patients with COVID-19 collected from the press release of the Korea Centers for Disease MESHD Control and Prevention. Information on the school opening delay and re-opening policies were achieved from the press release from Korean Ministry of Education. Findings The school openings were delayed three times in March 2020. Online classes started from April 9, and off-line classes started from May 20 to June 8 at four steps in different grades of students. There was no sudden increase in pediatric cases after the school opening, and the proportion of pediatric cases remained around 7.0% to 7.1%. As of July 11, 45 children TRANS from 40 schools and kindergartens were diagnosed with COVID-19 after off-line classes started. More than 11,000 students and staff were tested; only one additional student was found to be infected in the same classroom TRANS. Among those 45, 32 (71.1%) patients had available information for the source of infection MESHD. Twenty-five (25/45, 55.6%) were infected by the family members TRANS. The proportions of pediatric patients without information on infection MESHD sources were higher in older age group TRANS (middle and high school students) than in younger age group TRANS (kindergarten and elementary school students) (47.6% vs 12.5%, p=0.010). In the younger age group TRANS, 79.1% of children TRANS were infected by family members TRANS, while only 28.6% of adolescents in the older age group TRANS were infected by family members TRANS (p<0.001). Interpretation Korea had a successful transition from school closure to re-opening with online and off-line classes. Although partial, off-line school opening did not cause significant school-related outbreak among pediatric population although young children TRANS and adolescents may have different epidemiologic features.

    Risk stratification as a tool to rationalize quarantine among health care workers exposed to COVID-19 cases - Evidence from a tertiary healthcare centre in India

    Authors: Ravneet Kaur; Shashi Kant; Mohan Bairwa; Arvind Kumar; Shivram Dhakad; Vignesh Dwarakanathan; Aftab Ahmad; Pooja Pandey; Arti Kapil; Rakesh Lodha; Naveet Wig

    doi:10.1101/2020.07.31.20166264 Date: 2020-08-04 Source: medRxiv

    Background: Quarantine of healthcare workers (HCWs) exposed to COVID 19 confirmed cases TRANS is a well known strategy for limiting the transmission TRANS of infection MESHD. However, there is a need for evidence-based guidelines for the quarantine of HCWs in COVID 19. Methods: We describe our experience of contact tracing TRANS and risk stratification of 3853 HCWs who were exposed to confirmed COVID-19 cases in a tertiary health care institution in India. We developed an algorithm, on the basis of risk stratification, to rationalize quarantine among HCWs. Risk stratification was based on the duration of exposure, distance from the patient, and appropriateness of personal protection equipment (PPE) usage. Only high-risk contacts were quarantined for 14 days. They underwent testing for COVID 19 after five days of exposure, while low risk contacts continued their work with adherence to physical distancing, hand hygiene, and appropriate use of PPE. The low-risk contacts were encouraged to monitor for symptoms and report for COVID 19 screening if fever MESHD fever HP, cough MESHD cough HP, or shortness of breath occurred. We followed up all contacts for 14 days from the last exposure and observed for symptoms of COVID 19 and test positivity. Results and interpretation: Out of total 3853 contacts, 560 (14.5%) were categorized as high-risk contacts, and 40 of them were detected positive for COVID 19, with a test positivity rate of 7.1% (95% CI = 5.2, 9.6). Overall, 118 (3.1%) of all contacts tested positive. Our strategy prevented 3215 HCWs from being quarantined and saved 45,010 person-days of health workforce until June 8, 2020, in the institution. We conclude that exposure-based risk stratification and quarantine of HCWs is a viable strategy to prevent unnecessary quarantine, in a healthcare institution.

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MeSH Disease
Human Phenotype

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