Corpus overview


MeSH Disease

Human Phenotype


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    A Framework for SARS-CoV-2 Testing on a Large University Campus: Statistical Considerations

    Authors: Paul J Rathouz; Catherine A Calder

    doi:10.1101/2020.07.23.20160788 Date: 2020-07-24 Source: medRxiv

    We consider testing strategies for active SARS-CoV-2 infection MESHD for a large university community population, which we define. Components of such a strategy include individuals tested because they self-select or are recommended for testing by a health care provider for their own health care; individuals tested because they belong to a high-risk group where testing serves to disrupt transmission TRANS; and, finally, individuals randomly selected for testing from the university community population as part of a proactive community testing, or surveillance, program. The proactive community testing program is predicated on a mobile device application that asks individuals to self-monitor COVID-like symptoms daily. The goals of this report are (i) to provide a framework for estimating prevalence SERO of SARS-CoV-2 infection MESHD in the university community wherein proactive community testing is a major component of the overall strategy, (ii) to address the issue of how many tests should be performed as part of the proactive community testing program, and (iii) to consider how effective proactive community testing will be for purposes of detection of new disease MESHD clusters. We argue that a comprehensive prevalence SERO estimate informed by all testing done of the university community is a good metric to obtain a global picture of campus SARS-CoV-2 infection MESHD rates at a particular point in time and to monitor the dynamics of infection MESHD over time, for example, estimating the population-level reproductive number TRANS, R0 TRANS). Importantly, the prevalence SERO metric can be useful to campus leadership for decision making. One example involves comparing campus prevalence SERO to that in the broader off-campus community. We also show that under some reasonable assumptions, we can obtain valid statements about the comprehensive prevalence SERO by only testing symptomatic persons in the proactive community testing component. The number of tests performed for individual-level and high-risk group-level needs will depend on the disease MESHD dynamics, individual needs, and testing availability. For purposes of this report, we assume that, for these groups of individuals, inferential precision --- that is, the accuracy with which we can estimate the true prevalence SERO from testing a random sample of individuals --- does not drive decisions on the number of tests. On the other hand, for proactive community testing, the desired level of inferential precision {in a fixed period of time can be used to justify the number of tests to perform {in that period. For example, our results show that, if we establish a goal of ruling out with 98\% confidence a background prevalence SERO of 2\% {in a given week, and the actual prevalence SERO is 1\% among those eligible for proactive community testing, we would need to test 835 randomly-selected symptomatics (i.e., those presenting with COVID-like symptoms) per week via the proactive community testing program in a campus of 80k individuals. In addition to justifying decisions about the number of tests to perform, inferential precision can formalize the intuition that testing of symptomatic individuals should be prioritized over testing asymptomatic TRANS individuals in the proactive community testing program.

    Characterizing the Qatar advanced-phase SARS-CoV-2 epidemic

    Authors: Laith J Abu-Raddad; Hiam Chemaitelly; Houssein H Ayoub; Zaina Al Kanaani; Abdullatif Al Khal; Einas Al Kuwari; Adeel A Butt; Peter Coyle; Andrew Jeremijenko; Anvar Hassan Kaleeckal; Ali Nizar Latif; Robert C Owen; Hanan F Abdul Rahim; Samya A Al Abdulla; Mohamed G Al Kuwari; Mujeeb C Kandy; Hatoun Saeb; Shazia Nadeem N. Ahmed; Hamad Eid Al Romaihi; Devendra Bansal; Louise Dalton; Sheikh Mohammad Al Thani; Roberto Bertollini

    doi:10.1101/2020.07.16.20155317 Date: 2020-07-19 Source: medRxiv

    ABSTRACT Background: Qatar has a population of 2.8 million, over half of whom are expatriate craft and manual workers (CMW). We aimed to characterize the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) epidemic in Qatar. Methods: A series of epidemiologic studies were conducted including analysis of the national SARS-CoV-2 PCR testing and hospitalization database, community surveys assessing current infection MESHD, ad-hoc PCR testing campaigns in workplaces and residential areas, serological testing SERO for antibody SERO on blood SERO specimens collected for routine clinical screening/management, national Coronavirus Diseases MESHD 2019 (COVID-19) death MESHD registry, and a mathematical model. Results: By July 10, 397,577 individuals had been PCR tested for SARS-CoV-2, of whom 110,986 were positive, a positivity cumulative rate of 27.9% (95% CI: 27.8-28.1%). PCR positivity of nasopharyngeal swabs in a national community survey (May 6-7) including 1,307 participants was 14.9% (95% CI: 11.5-19.0%); 58.5% of those testing positive were asymptomatic TRANS. Across 448 ad-hoc PCR testing campaigns in workplaces and residential areas including 26,715 individuals, pooled mean PCR positivity was 15.6% (95% CI: 13.7-17.7%). SARS-CoV-2 antibody SERO prevalence SERO was 24.0% (95% CI: 23.3-24.6%) in 32,970 residual clinical blood SERO specimens. Antibody SERO prevalence SERO was only 47.3% (95% CI: 46.2-48.5%) in those who had at least one PCR positive result, but it was 91.3% (95% CI: 89.5-92.9%) among those who were PCR positive >3 weeks before serology testing. There were substantial differences in exposure to infection MESHD by nationality and sex, reflecting risk differentials between the craft/manual workers and urban populations. As of July 5, case severity rate, based on the WHO severity classification, was 3.4% and case fatality rate was 1.4 per 1,000 persons. Model-estimated daily number of infections MESHD and active- infection MESHD prevalence SERO peaked at 22,630 and 5.7%, respectively, on May 21 and May 23. Attack rate TRANS (ever infection MESHD) was estimated at 53.5% on July 12. R0 TRANS ranged between 1.45-1.68 throughout the epidemic. Rt was estimated at 0.70 on June 15, which was hence set as onset date for easing of restrictions. Age TRANS was by far the strongest predictor of severe, critical, or fatal infection MESHD. Conclusions: Qatar has experienced a large SARS-CoV-2 epidemic that is rapidly declining, apparently due to exhaustion of susceptibles. The epidemic demonstrated a classic susceptible-infected-recovered 'SIR' dynamics with a rather stable R0 TRANS of about 1.6. The young demographic structure of the population, in addition to a resourced public health response, yielded a milder disease MESHD burden and lower mortality than elsewhere.

    Community prevalence SERO of SARS-CoV-2 virus in England during May 2020: REACT study

    Authors: Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Benjamin Jeffrey; Caroline E. Walters; Christina J Atchison; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Graham Taylor; Ara Darzi; Paul Elliott

    doi:10.1101/2020.07.10.20150524 Date: 2020-07-11 Source: medRxiv

    Background England has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission TRANS. Methods The REal-time Assessment of Community Transmission TRANS (REACT) study is a nationally representative prevalence SERO survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status. Results We found 159 positives from 120,610 swabs giving an average prevalence SERO of 0.13% (95% CI: 0.11%,0.15%) from 1st May to 1st June 2020. We showed decreasing prevalence SERO with a halving time of 8.6 (6.2, 13.6) days, implying an overall reproduction number TRANS R of 0.57 (0.45, 0.72). Adults TRANS aged TRANS 18 to 24 yrs had the highest swab-positivity rates, while those >64 yrs had the lowest. Of the 126 participants who tested positive with known symptom status in the week prior to their swab, 39 reported symptoms while 87 did not, giving an estimate that 69% (61%,76%) of people were symptom-free for the 7 days prior testing positive in our community sample. Symptoms strongly associated with swab-positivity were: nausea MESHD nausea and/or vomiting HP and/or vomiting MESHD, diarrhoea, blocked nose, loss of smell, loss of taste, headache MESHD headache HP, chills MESHD chills HP and severe fatigue MESHD fatigue HP. Recent contact with a known COVID-19 case was associated with odds of 24 (16, 38) for swab-positivity. Compared with non-key workers, odds of swab-positivity were 7.7 (2.4, 25) among care home (long-term care facilities) workers and 5.2 (2.9, 9.3) among health care workers. However, some of the excess risk associated with key worker status was explained by recent contact with COVID-19 cases. We found no strong evidence for geographical variability in positive swab results. Conclusion Our results provide a reliable baseline against which the impact of subsequent relaxation of lockdown can be assessed to inform future public health efforts to control transmission TRANS.

    Diagnostics and spread of SARS-CoV-2 in Western Africa: An observational laboratory-based study from Benin

    Authors: Anges Yadouleton; Anna-Lena Sander; Andres Moreira-Soto; Carine Tchibozo; Gildas Hounkanrin; Yvette Badou; Carlo Fischer; Nina Krause; Petas Akogbeto; Edmilson F. de Oliveira Filho; Anges Dossou; Sebastian Bruenink; Melchior AIssi; Mamoudou Harouna Djingarey; Benjamin Hounkpatin; Michael Nagel; Jan felix Drexler

    doi:10.1101/2020.06.29.20140749 Date: 2020-07-08 Source: medRxiv

    Information on severe acute respiratory syndrome MESHD coronavirus-2 (SARS-CoV-2) spread in Africa is limited by fragile 2 surveillance systems and insufficient diagnostic capacity. 3 We assessed the coronavirus disease MESHD-19 (COVID-19)-related diagnostic workload in Benin, Western Africa, 4 characterized SARS-CoV-2 genomes from 12 acute cases of COVID-19, used those together with public data to 5 estimate SARS-CoV-2 transmission TRANS dynamics in a Bayesian framework, validated a widely used diagnostic dual target 6 RT-PCR kit donated to African countries, and conducted serological analyses in 68 sera from confirmed COVID-19 7 cases and from febrile patients sampled before the predicted SARS-CoV-2 introduction. 8 We found a 15-fold increase in the monthly laboratory workload due to COVID-19. Genomic surveillance showed 9 introductions of three distinct SARS-CoV-2 lineages. SARS-CoV-2 genome-based analyses yielded an R0 TRANS estimate of 10 4.4 (95% confidence interval: 2.0-7.7), suggesting intense spread of SARS-CoV-2 in Africa. RT-PCR-based tests 11 were highly sensitive but showed variation of internal controls and between diagnostic targets. Commercially available 12 SARS-CoV-2 ELISAs SERO showed up to 25% false-positive results depending on antigen and antibody SERO types, likely due 13 to unspecific antibody SERO responses elicited by acute malaria MESHD according to lack of SARS-CoV-2-specific neutralizing 14 antibody SERO responses and relatively higher parasitemia MESHD in those sera. 15 We confirm an overload of the diagnostic capacity in Benin and provide baseline information on the usability of 16 genome-based surveillance in resource-limited settings. Sero-epidemiological studies SERO Sero-epidemiological studies SERO needed to assess SARS-CoV-2 17 spread may be put at stake by low specificity of tests in tropical settings globally. The increasing diagnostic challenges 18 demand continuous support of national and supranational African stakeholders.

    Reopening universities during the COVID-19 pandemic: A testing strategy to minimize active cases and delay outbreaks

    Authors: Lior Rennert; Corey Andrew Kalbaugh; Lu Shi; Christopher McMahan

    doi:10.1101/2020.07.06.20147272 Date: 2020-07-07 Source: medRxiv

    Background: University campuses present an ideal environment for viral spread and are therefore at extreme risk of serving as a hotbed for a COVID-19 outbreak. While active surveillance throughout the semester such as widespread testing, contact tracing TRANS, and case isolation, may assist in detecting and preventing early outbreaks, these strategies will not be sufficient should a larger outbreak occur. It is therefore necessary to limit the initial number of active cases at the start of the semester. We examine the impact of pre-semester NAT testing on disease MESHD disease spread TRANS spread in a university setting. Methods: We implement simple dynamic transmission TRANS models of SARS-CoV-2 infection MESHD to explore the effects of pre-semester testing strategies on the number of active infections MESHD and occupied isolation beds throughout the semester. We assume an infectious period TRANS of 3 days and vary R0 TRANS to represent the effectiveness of disease MESHD mitigation strategies throughout the semester. We assume the prevalence SERO of active cases at the beginning of the semester is 5%. The sensitivity SERO of the NAT test is set at 90%. Results: If no pre-semester screening is mandated, the peak number of active infections MESHD occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections MESHD when effective mitigation strategies ( R0 TRANS = 1.25) are implemented to over 15,000 active infections MESHD for less effective strategies ( R0 TRANS = 3). When one NAT test is mandated within one week of campus arrival, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak to 40 days and 17 days, respectively, and result in peak size ranging from 1,000 to over 15,000 active infections MESHD. When two NAT tests are mandated, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak through the end of fall HP semester and 20 days, respectively, and result in peak size ranging from less than 1,000 to over 15,000 active infections MESHD. If maximum occupancy of isolation beds is set to 2% of the student population, then isolation beds would only be available for a range of 1 in 2 confirmed cases TRANS ( R0 TRANS = 1.25) to 1 in 40 confirmed cases TRANS ( R0 TRANS = 3) before maximum occupancy is reached. Conclusion: Even with highly effective mitigation strategies throughout the semester, inadequate pre-semester testing will lead to early and large surges of the disease MESHD and result in universities quickly reaching their isolation bed capacity. We therefore recommend NAT testing within one week of campus return. While this strategy is sufficient for delaying the timing of the outbreak, pre-semester testing would need to be implemented in conjunction with effective mitigation strategies to reduce the outbreak size.

    Effective epidemic model for COVID-19 using accumulated deaths MESHD

    Authors: Gilberto Nakamura; Basil Grammaticos; Christophe Deroulers; Mathilde Badoual

    id:2007.02855v1 Date: 2020-07-06 Source: arXiv

    The severe acute respiratory syndrome MESHD COVID-19 has been in the center of the ongoing global health crisis in 2020. The high prevalence SERO of mild cases facilitates sub-notification outside hospital environments and the number of those who are or have been infected remains largely unknown, leading to poor estimates of the crude mortality rate of the disease MESHD. Here we use a simple model to describe the number of accumulated deaths MESHD caused by COVID-19. The close connection between the proposed model and an approximate solution of the SIR model provides a system of equations whose solutions are robust estimates of epidemiological parameters. We find that the crude mortality varies between $10^{-4}$ and $10^{-3}$ depending on the severity of the outbreak which is lower than previous estimates obtained from laboratory confirmed patients. We also estimate quantities of practical interest such as the basic reproduction number TRANS and the expected number of deaths MESHD in the asymptotic TRANS limit with and without social distancing measures and lockdowns, which allow us to measure the efficiency of these interventions.

    The Influence of Time-Limited Immunity on a COVID-19 Epidemic: A Simulation Study

    Authors: Robert Joseph Kosinski

    doi:10.1101/2020.06.28.20142141 Date: 2020-06-29 Source: medRxiv

    A series of spreadsheet simulations using SEIS, SEIR, and SEIRS models showed that different durations of effective immunity could have important consequences for the prevalence SERO of an epidemic disease MESHD with COVID-19 characteristics. Immunity that lasted four weeks, twelve weeks, six months, one year, and two years was tested with pathogen R0 TRANS values of 1.5, 2.3, and 3.0. Shorter durations of immunity resulted in oscillations in disease MESHD prevalence SERO. Immunity that lasted from three months to two years produced recurrent disease MESHD outbreaks triggered by the expiration of immunity. If immunity faded out gradually instead of persisting at full effectiveness to the end of the immune period, the recurrent outbreaks became more frequent. The duration of effective immunity is an important consideration in the epidemiology of a disease MESHD like COVID-19.

    Evaluating COVID-19 screening strategies based on serological tests SERO

    Authors: Michela Baccini; Alessandra Mattei; Emilia Rocco; Giulia Vannucci; Fabrizia Mealli

    doi:10.1101/2020.06.12.20129403 Date: 2020-06-14 Source: medRxiv

    Background. Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. Although RT-PCR is the most reliable technique to detect ongoing infections MESHD, serological tests SERO are frequently proposed as tools in heterogeneous screening strategies. We analyze the performance SERO of a screening strategy proposed in Tuscany (Italy), which first uses qualitative rapid tests SERO for antibody SERO detection, and then RT-PCR tests on the positive subjects. Methods. We simulate the number of RT-PCR tests required by the screening strategy and the undetected ongoing infections MESHD in a pseudo-population of 500000 subjects, under different prevalence SERO scenarios and assuming a sensitivity SERO of the serological test SERO ranging from 0.50 to 0.80 (specificity=0.98). A compartmental model is used to predict the number of new infections MESHD generated by the false negatives two months after the screening, under different values of the infection MESHD reproduction number TRANS. Results. Assuming a sensitivity SERO equal to 0.80 and a prevalence SERO of 0.3%, the screening procedure would require on average 11167.6 RT-PCR tests and would produce 300 false negatives, responsible after two months of a number of contagions ranging from 526 to 1132, under the optimistic scenario of a reproduction number TRANS between 0.5 to 1. Costs and false negatives increase with the prevalence SERO. Conclusions. The analyzed screening procedure should be avoided unless the prevalence SERO and the rate of contagion are very low. The cost and effectiveness of the screening strategies should be evaluated in the actual context of the epidemic, accounting for the fact that it may change over time.

    Spread of COVID-19 in Odisha (India) due to Influx of Migrants and Stability Analysis using Mathematical Modelling

    Authors: ASWIN KUMAR RAUTA; YERRA SHANKAR RAO; Jangyadatta Behera

    doi:10.21203/ Date: 2020-06-07 Source: ResearchSquare

    This paper deals with the investigation on spread of COVID-19 and its stability analysis (both local and global stability) in Odisha, India. Being the second most populous country in the world, It is urgent need to investigate the spread and control of disease MESHD in India .However, due to diversity of vast population, uncertainty of infection MESHD, varying rate of recovery, state wise different COVID-19 induced death MESHD rate and non uniform quarantine policy of the states, it is strenuous to predict the spread and control of disease MESHD accurately in the country. So, it is crucial to study the aspects of disease MESHD in each state for the better prediction. We have considered the state Odisha (India) having population nearly equal to the population of Spain because the entry of huge migrants to the state suddenly enhanced the number of COVID-19 patients from below two hundred to more than eight hundred within one week even after forty days of lockdown period. We have developed SIAQR epidemic model fabricated with influx of out-migrants diagnosed at compartment (A) , then sent to the compartment (I) for treatment those have confirmed the disease MESHD and the remaining healthy individuals are sent to quarantine compartment (Q) for a period of twenty one days under surveillance and observation. The set of ordinary (nonlinear) differential equations are formulated and they are solved using Runge -Kutta fourth order method. The simulation of numerical data is performed using computer software MATLAB. As there is no specific treatment, vaccine or medicine available for the disease MESHD till the date, so the only intervention procedure called quarantine process is devised in this model to check the stability behaviour of the disease MESHD. The numerical and analytical results of the study show that the disease MESHD free equilibrium is locally stable when basic reproduction number TRANS is less than unity and unstable when it is more than unity. Further the study shows that it persists to endemic equilibrium for global stability when basic reproduction number TRANS greater than unity. As per the current trends ,this study shows that the prevalence SERO of COVID -19 would remain nearly 250 to 300 days in Odisha as for as the infected migrants would have been entering to the state. This mathematical modelling embedded with important risk factor like migration could be adopted for each state that will be helpful for better prediction of the entire country and world.

    Variation in Covid-19 Cases Across New York City

    Authors: Awi Federgruen; Sherin R Naha

    doi:10.1101/2020.05.25.20112797 Date: 2020-05-29 Source: medRxiv

    The number of confirmed COVID-19 cases, relative to population size, has varied greatly throughout the United States and even within the same city. In different zip codes in New York City, the epicentre of the epidemic, the number of cases per 100,000 residents has ranged from 437 to 4227, a 1:10 ratio. To guide policy decisions regarding containment and reopening of the economy, schools, and other institutions, it is vital to identify the factors that drive this large variation. This paper reports on a statistical study of incidence variation by zip code across New York City. Among many socio-economic and demographic measures considered, the average household size emerges as the single most important explanatory variable: an increase in average household size by one member increases the zip code incidence rate, in our final model specification, by at least 876 cases, 23% of the range of incidence rates, at a 95% confidence level. The percentage of the population above the age TRANS of 65, the percentage below the poverty line, and their interaction term are also strongly positively associated with zip code incidence rates, In terms of ethnic/racial characteristics, the percentages of African Americans, Hispanics, and Asians within the population, are significantly associated, but the magnitude of the impact is considerably smaller. (The proportion of Asians within a zip code has a negative association.) These significant associations may be explained by comorbidities, known to be more (less) prevalent among the black and Hispanic (Asian) population segments. In turn, the increased prevalence SERO of these comorbidities among the black and Hispanic population, is, in large part, the result of poorer dietary habits and more limited access to healthcare, themselves driven by lower incomes Contrary to popular belief, population density, per se, does not have a significantly positive impact. Indeed, population density and zip code incidence rates are negatively correlated, with a -33% correlation coefficient. Our model specification is based on a well-established epidemiologic model that explains the effects of household sizes on R0 TRANS, the basic reproductive number TRANS of an epidemic. Our findings support implemented and proposed policies to quarantine pre-acute and post-acute patients, as well as nursing home admission policies.

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MeSH Disease
Human Phenotype

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