Corpus overview


Overview

MeSH Disease

Human Phenotype

Fever (63)

Cough (51)

Pneumonia (43)

Hypertension (22)

Fatigue (18)


Transmission

Seroprevalence
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    The potential health and economic value of SARS-CoV-2 vaccination alongside physical distancing in the UK: transmission TRANS model-based future scenario analysis and economic evaluation

    Authors: Frank Sandmann; Nicholas Davies; - Centre for the Mathematical Modelling of Infectious Diseases COVID-19 working group; Anna Vassall; W John Edmunds; Mark Jit; Jun Liu; Di Zhao; Rosy Reynolds; Lucy Yardley; Matthew Hickman; Isabel Oliver; Helen Lambert

    doi:10.1101/2020.09.24.20200857 Date: 2020-09-25 Source: medRxiv

    Background In response to the coronavirus disease MESHD 2019 (COVID-19), the UK adopted mandatory physical distancing measures in March 2020. Vaccines against the newly emerged severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) may become available as early as late 2020. We explored the health and economic value of introducing SARS-CoV-2 immunisation alongside physical distancing scenarios in the UK. Methods We used an age TRANS-structured dynamic- transmission TRANS and economic model to explore different scenarios of immunisation programmes over ten years. Assuming vaccines are effective in 5-64 year olds, we compared vaccinating 90% of individuals in this age group TRANS to no vaccination. We assumed either vaccine effectiveness of 25% and 1-year protection and 90% re-vaccinated annually, or 75% vaccine effectiveness and 10-year protection and 10% re-vaccinated annually. Natural immunity was assumed to last 45 weeks in the base case. We also explored the additional impact of physical distancing. We considered benefits from disease prevented in terms of quality-adjusted life-years (QALYs), and costs to the healthcare payer versus the national economy. We discounted at 3.5% annually and monetised health impact at 20,000 per QALY to obtain the net monetary value, which we explored in sensitivity SERO analyses. Findings Without vaccination and physical distancing, we estimated 147.9 million COVID-19 cases (95% uncertainty interval: 48.5 million, 198.7 million) and 2.8 million (770,000, 4.2 million) deaths in the UK over ten years. Vaccination with 75% vaccine effectiveness and 10-year protection may stop community transmission TRANS entirely for several years, whereas SARS-CoV-2 becomes endemic without highly effective vaccines. Introducing vaccination compared to no vaccination leads to economic gains (positive net monetary value) of 0.37 billion to +1.33 billion across all physical distancing and vaccine effectiveness scenarios from the healthcare perspective, but net monetary values of physical distancing scenarios may be negative from societal perspective if the daily national economy losses are persistent and large. Interpretation Our model findings highlight the substantial health and economic value of introducing SARS-CoV-2 vaccination. Given uncertainty around both characteristics of the eventually licensed vaccines and long-term COVID-19 epidemiology, our study provides early insights about possible future scenarios in a post-vaccination era from an economic and epidemiological perspective.

    CHARACTERISTICS, MANAGEMENT AND OUTCOMES OF CRITICALLY ILL COVID-19 PATIENTS ADMITTED TO ICU IN HOSPITALS IN MESHD BANGLADESH: A RETROSPECTIVE STUDY

    Authors: Ayan Saha; Mohammad Moinul Ahsan; Tarek-Ul Quader; Mohammad Umer Sharif Shohan; Sabekun Naher; Preya Dutta; Al-Shahriar Akash; H M Hamidullah Mehedi; A S M Arman Ullah Chowdhury; Hasanul Karim; Tazrina Rahman; Ayesha Parvin; Dilcia Sambrano; Yamitzel Zaldivar; Danilo Franco; Sandra Lopez Verges; Dexi Zhang; Fanjing Fan; Baojun Wang; Xavier Saez Llorens; Rodrigo DeAntonio; Ivonne Torres-Atencio; Eduardo Ortega-Barria; Rao Kosagisharaf; Ricardo Lleonart; Li Chong; Amador Goodridge; - COVID-19 SEROLOGY COLLABORATOR GROUP

    doi:10.1101/2020.09.24.20201285 Date: 2020-09-25 Source: medRxiv

    Objectives: This study aimed to analyse the epidemiological and clinical characteristics of critical COVID-19 cases and investigate risk factors including comorbidities and age TRANS in relation with the clinical aftermath of COVID-19 in critical cases in Bangladesh. Methods: In this retrospective study, epidemiological and clinical characteristics, complications, laboratory results, and clinical management of the patients were studied from data obtained from 168 individuals diagnosed with an advanced prognosis of COVID-19 admitted in two hospitals in Bangladesh. Results: Individuals in the study sample contracted COVID-19 through community transmission TRANS. 56.5% (n = 95) cases died in intensive care units (ICU) during the study period. The median age TRANS was 56 years and 79.2% (n=134) were male TRANS. Typical clinical manifestation included Acute respiratory distress HP respiratory distress MESHD syndrome ( ARDS MESHD) related complications (79.2%), fever HP fever MESHD (54.2%) and cough HP (25.6%) while diabetes mellitus HP diabetes mellitus MESHD (52.4%), hypertension HP hypertension MESHD (41.1%) and heart diseases MESHD (16.7%) were the conventional comorbidities. Clinical outcomes were detrimental due to comorbidities rather than age TRANS and comorbid individuals over 50 were at more risk. In the sample, oxygen saturation was low (< 95% SpO2) in 135 patients (80.4%) and 158 (93.4%) patients received supplemental oxygen. Identical biochemical parameters were found in both deceased and surviving cases. Administration of antiviral drug Remdesivir and the glucocorticoid, Dexamethasone increased the proportion of surviving patients slightly. Conclusions: Susceptibility to developing critical illness MESHD due to COVID-19 was found more in comorbid males TRANS. These atypical patients require more clinical attention from the prospect of controlling mortality rate in Bangladesh.

    Evidence for and level of herd immunity against SARS-CoV-2 infection MESHD: the ten-community study

    Authors: Andrew Jeremijenko; Hiam Chemaitelly; Houssein H. Ayoub; Moza Abdellatif Hassan Abdulla; Abdul Badi Abou-Samra; Jameela Ali A.A. Al Ajmi; Nasser Ali Asad Al-Ansari; Zaina Al Kanaani; Abdullatif Al Khal; Einas Al Kuwari; Ahmed Al-Mohammed; Naema Hassan Abdulla Al Molawi; Huda Mohamad Al Naomi; Adeel A Butt; Peter Coyle; Reham Awni El Kahlout; Imtiaz Gillani; Anvar Hassan Kaleeckal; Naseer Ahmad Masoodi; Anil George Thomas; Hanaa Nafady Hego; Ali Nizar Latif; Riyazuddin Mohammad Shaik; Nourah B M Younes; Hanan F. Abdul Rahim; Hadi M. Yassine; Mohamed G. Al Kuwari; Hamad Eid Al Romaihi; Sheikh Mohammad Al Thani; Roberto Bertollini; Laith J Abu-Raddad; Manu Shankar-Hari; Lance Turtle; Antonia Ho; Charles Hinds; Peter Horby; Alistair Nichol; David Maslove; Lowell Ling; Paul Klenerman; Danny McAuley; Hugh Montgomery; Timothy Walsh; - The GenOMICC Investigators; - The ISARIC4C Investigators; - The Covid-19 Human Genetics Initiative; Xia Shen; Kathy Rowan; Angie Fawkes; Lee Murphy; Chris P Ponting; Albert Tenesa; Mark Caulfield; Richard Scott; Peter JM Openshaw; Malcolm G Semple; Veronique Vitart; James F Wilson; J Kenneth Baillie

    doi:10.1101/2020.09.24.20200543 Date: 2020-09-25 Source: medRxiv

    Background: Qatar experienced a large severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) epidemic that disproportionately affected the craft and manual workers (CMWs) who constitute 60% of the population. This study aimed to investigate level of immunity in communities within this population as well as infection exposure required to achieve herd immunity. Methods: Anti-SARS-CoV-2 seropositivity was assessed in ten CMW communities between June 21 and September 9, 2020. PCR positivity, infection MESHD positivity ( antibody SERO and/or PCR positive), and infection MESHD severity rate were also estimated. Associations with anti-SARS-CoV-2 positivity were investigated using regression analyses. Results: Study included 4,970 CMWs who were mostly men (95.0%) and <40 years of age TRANS (71.5%). Seropositivity ranged from 54.9% (95% CI: 50.2-59.4%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean seropositivity across all communities was 66.1% (95% CI: 61.5-70.6%). PCR positivity ranged from 0.0% to 10.5% (95% CI: 7.4-14.8%) in the different CMW communities. Pooled mean PCR positivity was 3.9% (95% CI: 1.6-6.9%). Median cycle threshold (Ct) value was 34.0 (range: 15.8-37.4). The majority (79.5%) of PCR-positive individuals had Ct value >30 indicative of earlier rather than recent infection. Infection positivity ( antibody SERO and/or PCR positive) ranged from 62.5% (95% CI: 58.3-66.7%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean infection positivity was 69.5% (95% CI: 62.8-75.9%). Only five infections MESHD were ever severe and one was ever critical, an infection MESHD severity rate of 0.2% (95% CI: 0.1-0.4%). Conclusions: Based on an extended range of epidemiological measures, active infection is rare in these communities with limited if any sustainable infection transmission TRANS for clusters to occur. At least some CMW communities in Qatar have reached or nearly reached herd immunity for SARS-CoV-2 infection MESHD at a proportion of ever infection of 65-70%.

    Predictors of Incident Viral Symptoms Ascertained in the Era of Covid-19

    Authors: Gregory Marcus; Jeffrey E Olgin; Noah Peyser; Eric Vittinghoff; Vivian Yang; Sean Joyce; Robert Avram; Geoffrey Tison; David Wen; Xochitl Butcher; Helena Eitel; Mark Pletcher; Dilcia Sambrano; Yamitzel Zaldivar; Danilo Franco; Sandra Lopez Verges; Dexi Zhang; Fanjing Fan; Baojun Wang; Xavier Saez Llorens; Rodrigo DeAntonio; Ivonne Torres-Atencio; Eduardo Ortega-Barria; Rao Kosagisharaf; Ricardo Lleonart; Li Chong; Amador Goodridge; - COVID-19 SEROLOGY COLLABORATOR GROUP

    doi:10.1101/2020.09.24.20197632 Date: 2020-09-25 Source: medRxiv

    Background: In the absence of universal testing, effective therapies, or vaccines, identifying risk factors for viral infection MESHD, particularly readily modifiable exposures and behaviors, is required to identify effective strategies against viral infection MESHD and transmission TRANS. Methods: We conducted a world-wide mobile application-based prospective cohort study available to English speaking adults TRANS with a smartphone. We collected self-reported characteristics, exposures, and behaviors, as well as smartphone-based geolocation data. Our main outcome was incident symptoms of viral infection MESHD, defined as fevers HP and chills HP plus one other symptom previously shown to occur with SARS-CoV-2 infection MESHD, determined by daily surveys. Findings: Among 14, 335 participants residing in all 50 US states and 93 different countries followed for a median 21 days (IQR 10-26 days), 424 (3%) developed incident viral symptoms. In pooled multivariable logistic regression models, female TRANS biological sex (odds ration [OR] 1.75, 95% CI 1.39-2.20, p<0.001), anemia HP anemia MESHD (OR 1.45, 95% CI 1.16-1.81, p=0.001), hypertension HP hypertension MESHD (OR 1.35, 95% CI 1.08-1.68, p=0.007), cigarette smoking in the last 30 days (OR 1.86, 95% CI 1.35-2.55, p<0.001), any viral symptoms among household members 6-12 days prior (OR 2.06, 95% CI 1.67-2.55, p<0.001), and the maximum number of individuals the participant interacted with within 6 feet in the past 6-12 days (OR 1.15, 95% CI 1.06-1.25, p<0.001) were each associated with a higher risk of developing viral symptoms. Conversely, a higher subjective social status (OR 0.87, 95% CI 0.83-0.93, p<0.001), at least weekly exercise (OR 0.57, 95% CI 0.47-0.70, p<0.001), and sanitizing one's phone (OR 0.79, 95% CI 0.63-0.99, p=0.037) were each associated with a lower risk of developing viral symptoms. Interpretation: While several immutable characteristics were associated with the risk of developing viral symptoms, multiple immediately modifiable exposures and habits that influence risk were also observed, potentially identifying readily accessible strategies to mitigate risk in the Covid-19 era.

    Modelling optimal vaccination strategy for SARS-CoV-2.

    Authors: Sam Moore; Edward M Hill; Louise Dyson; Michael Tildesley; Matt J Keeling; Itse Yusuf Nyam; Bamidele Iwalokun; Chika Onwuamah; Mabel Uwandu; Babatunde Lawal Salako; Akinola Abayomi; Akin Osibogun; Abimbola Bowale; Bodunrin Osikomaiya; Babafemi Thomas; Bamidele Mutiu; Nkiruka Nnonyelum Odunukwe

    doi:10.1101/2020.09.22.20194183 Date: 2020-09-24 Source: medRxiv

    The COVID-19 outbreak has highlighted our vulnerability to novel infections. Faced with this threat and no effective treatment, most countries adopted some form of enforced social distancing (lockdown) to reduce transmission TRANS - in most cases successfully reducing the reproductive number,R TRANS, below one. However, given the large pool of susceptible individuals that remain, complete relaxation of controls is likely to generate a substantial second wave. Vaccination remains the only foreseeable means of both containing the infection MESHD and returning to normal interactions and behaviour. Here, we consider the optimal targeting of vaccination with the aim of minimising future deaths MESHD or quality adjusted life year (QALY) losses. We show that, for a range of assumptions on the action and efficacy of the vaccine, targeting older age groups TRANS first is optimal and can avoid a second wave if the vaccine prevents transmission TRANS as well as disease.

    Optimal Dynamic Prioritization of Scarce COVID-19 Vaccines

    Authors: Jack Hoyt Buckner; Gerardo Hoyt Chowell; Michael R Springborn; Jan-Niklas Salewski; Frederike Winter; Simone Buchtler; Maximilian V Malfertheiner; Matthias Lubnow; Dirk Lunz; Bernhard Graf; Florian Hitzenbichler; Frank Hanses; Hendrik Poeck; Marina Kreutz; Evelyn Orso; Ralph Burkhardt; Tanja Niedermair; Christoph Brochhausen; Andre Gessner; Bernd Salzberger; Matthias Mack; Christine Goffinet; Florian Kurth; Martin Witzenrath; Maria Theresa Völker; Sarah Dorothea Müller; Uwe Gerd Liebert; Naveed Ishaque; Lars Kaderali; Leif Erik Sander; Sven Laudi; Christian Drosten; Roland Eils; Christian Conrad; Ulf Landmesser; Irina Lehmann

    doi:10.1101/2020.09.22.20199174 Date: 2020-09-23 Source: medRxiv

    Multiple promising COVID-19 vaccines are under rapid development, with deployment of the initial supply expected by 2021. Careful design of a vaccine prioritization strategy across socio-demographic groups is an imminent and crucial public policy challenge given that (1) the eventual vaccine supply will be highly constrained for at least the first several months of the vaccination campaign, and (2) there are stark differences in transmission TRANS and severity of impacts from SARS-CoV-2 across groups. Previous experience with vaccine development mid-pandemic offers limited insights for SARS-CoV-2 prioritization: SARS and Zika vaccine development was incomplete when those outbreaks ended and the epidemiology of endemic human influenza viruses differ substantially from that of SARS-CoV-2. We assess the optimal allocation of a limited and dynamic COVID-19 vaccine supply in the U.S. across socio-demographic groups differentiated by age TRANS and essential worker status. The transmission TRANS dynamics are modeled using a compartmental (SEIR) model parameterized to capture our current understanding of the transmission TRANS and epidemiological characteristics of COVID-19, including key sources of group heterogeneity (susceptibility, severity, and contact rates). We investigate tradeoffs between three alternative policy objectives: minimizing infections, years of life lost, or deaths. Moreover, we model dynamic vaccine prioritization policies that respond to changes in the epidemiological status of the population as SARS-CoV-2 continues its march. Because contacts tend to be concentrated within age groups TRANS, there is diminishing marginal returns as vaccination coverage increases in a given group, increasing the group's protective immunity against infection MESHD and mortality. We find that optimal prioritization consistently targets older essential workers. However, depending on the policy objective, younger essential workers are prioritized to minimize infections MESHD or seniors in order to minimize mortality. Optimal prioritization outperforms non-targeted vaccination strategies by up to 18% depending on the outcome optimized. For example, in our baseline model, cumulative mortality decreased on average by 17% (25,000 deaths in the U.S. population) over the course of the outbreak.

    Age groups TRANS that sustain resurging COVID-19 epidemics in the United States

    Authors: Mélodie Monod; Alexandra Blenkinsop; Xiaoyue Xi; Daniel Hebert; Sivan Bershan; Valerie C Bradley; Yu Chen; Helen Coupland; Sarah Filippi; Jonathan Ish-Horowicz; Martin McManus; Thomas A Mellan; Axel Gandy; Michael Hutchinson; H Juliette T Unwin; Michaela A. C. Vollmer; Sebastian Weber; Harrison Zhu; Anne Bezancon; Simon Tietze; Neil M Ferguson; Swapnil Mishra; Seth Flaxman; Samir Bhatt; Oliver Ratmann; - Imperial College London COVID-19 Response Team

    doi:10.1101/2020.09.18.20197376 Date: 2020-09-22 Source: medRxiv

    Following initial declines MESHD, in mid 2020, a resurgence in transmission TRANS of novel coronavirus disease MESHD (COVID-19) has occurred in the United States and parts of Europe. Despite the wide implementation of non-pharmaceutical interventions, it is still not known how they are impacted by changing contact patterns, age TRANS and other demographics. As COVID-19 disease control becomes more localised, understanding the age TRANS demographics driving transmission TRANS and how these impacts the loosening of interventions such as school reopening is crucial. Considering dynamics for the United States, we analyse aggregated, age TRANS-specific mobility trends from more than 10 million individuals and link these mechanistically to age TRANS-specific COVID-19 mortality data. In contrast to previous approaches, we link mobility to mortality via age TRANS-specific contact patterns and use this rich relationship to reconstruct accurate transmission TRANS dynamics. Contrary to anecdotal evidence, we find little support for age TRANS-shifts in contact and transmission TRANS dynamics over time. We estimate that, until August, 63.4% [60.9%-65.5%] of SARS-CoV-2 infections MESHD in the United States originated from adults TRANS aged TRANS 20-49, while 1.2% [0.8%-1.8%] originated from children TRANS aged TRANS 0- 9. In areas with continued, community-wide transmission TRANS, our transmission TRANS model predicts that re-opening kindergartens and elementary schools could facilitate spread and lead to additional COVID-19 attributable deaths over a 90-day period. These findings indicate that targeting interventions to adults TRANS aged TRANS 20-49 are an important consideration in halting resurgent epidemics and preventing COVID-19-attributable deaths when kindergartens and elementary schools reopen.

    Who should be Prioritized for COVID-19 Vaccination in China? A Descriptive Study

    Authors: Juan Yang; Wen Zheng; Huilin Shi; Xuemei Yan; Kaige Dong; Qian You; Guangjie Zhong; Hui Gong; Zhiyuan Chen; Mark Jit; Cecile Viboud; Marco Ajelli; Hongjie Yu

    id:202009.0446/v1 Date: 2020-09-19 Source: Preprints.org

    All countries are facing decisions about which groups to prioritise for COVID-19 vaccination after the first vaccine product has been licensed, at which time supply shortages are inevitable. Here we define the key target populations and their size in China for a phased introduction of COVID-19 vaccination with evolving goals, accounting for the risk of illness and transmission TRANS. Essential workers (47.2 million) like healthcare workers could be prioritized for vaccination to maintain essential services. Subsequently, older adults TRANS, individuals with underlying health conditions and pregnant women (616.0 million) could be targeted to reduce severe COVID-19 outcomes. Then it could be further extended to target adults TRANS without underlying health conditions and children TRANS (738.7 million) to reduce symptomatic infections and/or to stop virus transmission TRANS. The proposed framework could assist Chinese policy-makers in the design of a vaccination program, and could be generalized to inform other national and regional COVID-19 vaccination strategies.

    Who should be Prioritized for COVID-19 Vaccination in China? A Descriptive Study

    Authors: Juan Yang; Wen Zheng; Huilin Shi; Xuemei Yan; Kaige Dong; Qian You; Guangjie Zhong; Hui Gong; Zhiyuan Chen; Mark Jit; Cecile Viboud; Marco Ajelli; Hongjie Yu

    id:10.20944/preprints202009.0446.v1 Date: 2020-09-19 Source: Preprints.org

    All countries are facing decisions about which groups to prioritise for COVID-19 vaccination after the first vaccine product has been licensed, at which time supply shortages are inevitable. Here we define the key target populations and their size in China for a phased introduction of COVID-19 vaccination with evolving goals, accounting for the risk of illness and transmission TRANS. Essential workers (47.2 million) like healthcare workers could be prioritized for vaccination to maintain essential services. Subsequently, older adults TRANS, individuals with underlying health conditions and pregnant women (616.0 million) could be targeted to reduce severe COVID-19 outcomes. Then it could be further extended to target adults TRANS without underlying health conditions and children TRANS (738.7 million) to reduce symptomatic infections and/or to stop virus transmission TRANS. The proposed framework could assist Chinese policy-makers in the design of a vaccination program, and could be generalized to inform other national and regional COVID-19 vaccination strategies.

    Epidemic Response and Transmission TRANS Dynamics of Coronavirus Disease MESHD (COVID-19) in Khartoum State- Sudan 2020: Study Protocol

    Authors: Mustafa Khidir Mustafa Elnimeiri; Mohanad Kamaleldin Mahmoud Ibrahim; Shahenaz Seifaldeen Mustafa Satti

    doi:10.21203/rs.3.rs-80602/v1 Date: 2020-09-19 Source: ResearchSquare

    Background: A novel Coronavirus was identified as severe acute respiratory syndrome Coronavirus 2 MESHD (SARS-CoV-2), and the syndrome of clinical manifestation was named (COVID-19). Consequently, on Jan 30, 2020, the World Health Organization (WHO) declared the outbreak as a pandemic and a public health emergency of international concern. The objectives of this research are to investigate the response of the health system at different levels towards the control of the COVID-19 epidemic and to explore the COVID-19 transmission TRANS dynamics among Sudanese community. Methods: A community and institutional-based cross sectional based study will be conducted in Khartoum State include all the seven localities. The sample size of participant is estimated at 920 using the population formula (n=N/1+ (n*d2)) and considering the response rate. The sample will be drawn using multistage cluster sampling. Data will be collected using interview with key informant and concerned bodies/institutes involved in the response at both the federal and Khartoum State levels. Administered pre-coded, pretested closed ended questionnaire will be developed to collect data from community participants. Data will be managed and analyzed using Statistical Package for Social Sciences version 21. Analysis is mostly univariate descriptive and bi-variate with Chi Square & Fischer Exact tests analysis to find associations between variables of interest.Discussion: This study is expected to evaluate the extent and magnitude of the epidemic response at different levels in addition to the adequacy of the epidemic response. The study participants will be screened to estimate proportion of individuals per age TRANS strata who show sero-positivity for virus infection MESHD, thus it will estimate the percentages of individuals reporting symptoms/signs of infection MESHD and asymptomatic TRANS fraction. The results of this study will strengthen the current interventional approaches of COVID-19 epidemic control and will provide set of database for better planning and implementation of COVID-19 control across the country. It will contribute to in-depth understanding of the COVID-19 transmission TRANS dynamics among Sudanese community and will improve the community awareness about COVID-19.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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